2021 Citations

Authors & Works cited in this section (citations below):                 Up

Allen, TFH. & Starr. Hierarchy: Perspectives for Ecological Complexity, Second Edition.
Allen, Timothy & Thomas Hoekstra. Toward a Unified Ecology, Second Edition.
Archibald, S. et al. “Biological and geophysical feedbacks with fire in the Earth system
Arndt, Markus, Juffmann & Vedral. “Quantum physics meets biology
Arnellos, Argyris. From Organizations of Processes to Organisms and Other Biological
Arnellos, Argyris & Moreno. How functional differentiation originated in prebiotic evolution
Atkins, Peter. 2010. The Laws of Thermodynamics: A Very Short Introduction.
Austin, Christopher. “Organisms, activity, and being: on the substance of process ontology.
Austin, Christopher. “Aristotelian Essentialism: Essence in the Age of Evolution.
Axtell, Robert et al. Challenges of Integrating Complexity and Evolution into Economics
Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization.
Ayres, Robert. “Gaps in Mainstream Economics: Energy, Growth, and Sustainability
Baedke, Jan. “O Organism, Where Are Thou? Old and New Challenges for Organism-Centered
Baetu, Tudor. 2019. Mechanisms in Molecular Biology.
Bandini, Elisa et al. Naive orangutans … individually acquire nut-cracking using hammer tools
Bartlett, Stuart & Beckett. Probing complexity: thermodynamics and computational mechanics
Bartlett, Stuart & Wong. Defining Lyfe in the Universe: From Three Privileged Functions to
Bauwens, Michel & Ramos. Re-imagining the left through an ecology of the commons: towards
Bellwood, David et al. The meaning of the term ‘function’ in ecology: A coral reef perspective
Black, Andrew et al. “Ecological scaffolding and the evolution of individuality
Bonta, Mark et al. “Intentional fire-spreading by ‘firehawk’ raptors in Northern Australia
Bouchard, Frederic. Ecosystem Evolution is About Variation and Persistence, not Populations
Bouchard, Frederic. Symbiosis, Transient Biological Individuality, and Evolutionary Processes
Bourrat, Pierrick & Paul Griffiths. 2018. “Multispecies individuals.
Braakman, Rogier et al. “Metabolic evolution and the self-organization of ecosystems.
Braakman, Rogier. “Evolution of cellular metabolism and the rise of a globally productive
Branscomb, Elbert & Russell. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible
Bray, Dennis. 1995. “Protein molecules as computational elements in living cells
Brunk, Clifford & Marshall. ‘Whole Organism’, Systems Biology, and Top-Down Criteria for
Buescher, Bram & Fletcher. The Conservation Revolution: Radical Ideas for Saving Nature
Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology.
Call, Josep. Contrasting the Social Cognition of Humans and Nonhuman Apes: The Shared
Canguilhem, Georges. 2008[1965]. Knowledge of Life.
Cassirer, Ernst. The Problem of Knowledge: Philosophy, Science, and History Since Hegel.
Chapman, Eric et al. How the Second Law of Thermodynamics Has Informed Ecosystem
Claidiere, Nicolas, Scott-Phillips & Sperber. “How Darwinian is cultural evolution?”
Cleland, Carol. The Quest for a Universal Theory of Life: Searching for Life As We
Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition.
Corning, P. & Szathmary. ‘Synergistic selection’: A Darwinian frame for the evolution of
Cornish-Bowden & Cardenas. Contrasting Theories of Life: Historical Context, Current
Cornish-Bowden, A. & Cardenas. The essence of life revisited: how theories can shed light on it
D’Souza, G. et al. Ecology and evolution of metabolic cross-feeding interactions in bacteria
Davis, Jason, et al. Toward a Universal Theoretical Framework to Understand Robustness and
De la Fuente, Ildefonso et al. “Attractor Metabolic Networks.
Decaens, Thibaud et al. 2008. “Priorities for conservation of soil animals
DeDeo, Simon. 2017. “Major Transitions in Political Order.”
Depew, David Organisms, Development, and Evolution: Invitation to a New Understanding.
Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?
Doolittle, W.F. & Inkpen. Processes and patterns of interaction as units of selection… ITSNTS
Drake, James A. et al. 2006. “Emergence in ecological systems
Dumont, Sophie & M. Prakash. “Emergent mechanics of biological structures
Dunne, Jennifer A. et al. “Compilation and Network Analyses of Cambrian Food Webs
Dupre, John. It Is Not Possible to Reduce Biological Explanations to Explanations in Chemistry
Dupré, John. 2021. The Metaphysics of Biology.
Ellis, George. “Top-down causation and emergence: some comments on mechanisms
England, Jeremy. Every Life is on Fire: How Thermodynamics Explains the Origins of Living
Enserink, Martin. Newsmaker Interview: Luc Montagnier: French Nobelist Escapes ‘Intellectual
Ereshefsky, Marc & Makmiller Pedroso. 2015. “Rethinking evolutionary individuality
Falkowski, Paul. Life’s Engines: How Microbes Made Earth Habitable.
Falkowski, Paul et al. The Microbial Engines That Drive earth’s Biogeochemical Cycles
Farnsworth, Keith et al. Unifying concepts of biological function from molecules to ecosystems
Farnsworth, Keith et al. Living through Downward Causation: From Molecules to Ecosystems
Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability
Fath, Brian, Patten & Choi. “Complementarity of Ecological Goal Functions
Fox Keller, Evelyn. 2007. “The disappearance of function from ‘self-organizing systems
Free, Andrew & Nicholas Barton. “Do evolution and ecology need the Gaia hypothesis?
Gatherer, Derek. Modelling versus Realisation: Rival Philosophies of Computational Theory in
Giampietro, Mario. On the Circular Bioeconomy and Decoupling: Implications for Sustainable
Goldenfeld, Nigel & Woese. Life is physics: evolution as a collective phenomenon far from
Goldfarb, Ben. Eager: The Surprising Secret Life of Beavers and Why They Matter.
Goldford, Joshua & Daniel Segré. “Modern views of ancient metabolic networks
Goldford, Joshua E. & Daniel Segre. “Modern views of ancient metabolic networks
Graeber, David & Wengrow. The Dawn of Everything: A New History of Humanity.
Grene, Marjorie & D. Depew. The Philosophy of Biology: An Episodic History.
Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?”
Guimaraes, Paulo et al. “Evolution and coevolution in mutualistic networks
Gunton, Richard & Gilbert. The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense
Haas, Robert et al. “Designing and interpreting ‘multi-omic’ experiments that may change
Harding, Stephan. 2009. Animate Earth: Science, Intuition and Gaia.
Harmon, Luke et al. 2019. Detecting the macroevolutionary signal of species interactions
Harvey, Graham. Animism: Respecting the Living World.
Hauert, Christoph et al. “Synergy and discounting of cooperation n social dilemmas
Henry, Richard Conn. 2005. “The mental Universe.”
Hoelzer, G.A. et al. “On the logical relationship between natural selection and self-organization
Holling, C.S. The resilience of terrestrial ecosystems: local surprise and global change
Holling, Crawford S., Peterson & Allen. 2008. “Panarchies and Discontinuities.
Horowitz, Jordan & England. “Spontaneous fine-tuning to environment in many-species
Jacob, Eshel Ben et al. “Bacterial linguistic communication and social intelligence.
Jaeger, Luc & Calkins. “Downward causation by information control in micro-organisms
Jasanoff, Sheila. 2019. Can Science Make Sense of Life?
Jinich, Adrian et al. A thermodynamic atlas of carbon redox chemical space.
Jorgensen, Sven, Nielsen & Fath. 2015. “Recent progress in systems ecology
Justus, James. 2021. The Philosophy of Ecology: An Introduction.
Kampourakis, Kostas. Why Does It Matter That Many Biology Concepts Are Metaphors?
Keller, Evelyn Fox. It Is Possible to Reduce Biological Explanations to Explanations in
Kelly, Sean. 2021. Becoming Gaia: On the Threshold of Planetary Initiation.
Kim, Hyunju et al. “Universal scaling across biochemical networks on Earth
Kimmerer, Robin. Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the
Klinger, Lee & Erickson. “Geophysiological coupling of marine and terrestrial ecosystems
Koenig, Harold. Religion, Spirituality, and Health: The Research and Clinical Implications
Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe.
Krakauer, David et al. 2020. “The information theory of individuality
Krakauer, David. 2017. “Cryptographic Nature.”
Kurakin, Alexei. Scale-free flow of life: on the biology, economics, and physics of the cell
Kurakin, Alexei. Scale-free flow of life: on the biology, economics, and physics of the cell
Latour, Bruno. Facing Gaia; Eight Lectures on the New Climatic Regime.
Lenton, Timothy & Latour. “Gaia 2.0: Could humans add some level of self-awareness to Earth’s
Lenton, Tim. 2016. Earth System Science: A Very Short Introduction.
Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot
Levchenko, Vladimir et al. “Early Biosphere: Origin and Evolution.”
Levin, Simon. Self-organization and the Emergence of Complexity in Ecological Systems
Leyser, Ottoline & Wiseman. “Integrative Biology: Parts, Wholes, Levels and Systems
Loreau, Michel. Linking biodiversity and ecosystems: towards a unifying ecological theory
Louca, Stilianos et al. “Function and functional redundancy in microbial systems
Marshall, William et al. How causal analysis can reveal autonomy in models of biological
Mayr, Ernst. 2004. What Makes Biology Unique.
Montevil, Mael & Mossio. The Identify of Organisms in Scientific Practice: Integrating
Morowitz, Harold & Eric Smith. “Energy Flow and the Organization of Life
Morowitz, Harold et al. “The Swiss Army Knife of Biological Catalysis
Morowitz, Harold J. 1992. Beginnings of Cellular Life.
Morris, J. Jeffrey et al. The Black Queen Hypothesis: Evolution of Dependencies through
Motes-Rodrigo & Tennie. “Captive great apes tend to innovate simple tool behaviors quickly
Mukherjee, Indrani et al. The Boring Billion, a slingshot for Complex Life on Earth
Noble, Denis. 2012. “A theory of biological relativity: no privileged level of causation
Nurse, Paul. 2020. What is Life?
O’Connor, Mary et al. Principles of Ecology Revisited: Integrating Information and Ecological
Parker, Christopher et al. “The Pyrophilic Primate Hypothesis
Pascal, Robert et al. Towards an evolutionary theory of the origin of life based on kinetics …
Peterson, Garry. 2008. “Self-Organization and Discontinuities in Ecosystems
Phillips, Rob & Ron Milo. 2009. “A feeling for the numbers in biology.”
Polanyi, Michael. 1968. “Life’s Irreducible Structure
Polkinghorne, John. 2002. Quantum Theory: A Very Short Introduction.
Pradeu, Thomas. 2016. “The many faces of biological individuality
Prechtel, Martin. Rescuing the Light: Quotes from the Oral Teachings of Martin Prechtel.
Preiner, Martina et al. 2020. The Future of Origin of Life Research: Bridging Decades-Old
Preutz, Jill & Herzog. “Savanna Chimpanzees at Fongoli, Senegal, Navigate a Fire Landscape.
Reid, Jasper. The Metaphysics of Henry More.
Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy.
Rickaby, R.E.M. Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life
Rogers, Deborah & Paul Ehrlich. “Natural selection and cultural rates of change
Rosati, Alexandra. Foraging Cognition: Reviving the Ecological Intelligence Hypothesis
Rosenberg, Alex. 2020. Reduction and Mechanism.
Rubenstein, Mary-Jane. Pantheologies: Gods, Worlds, Monsters.
Ruby, Edward et al. We Get By with a Little Help from Our (Little) Friends
Rull, Valenti. 2010. “Ecology and Palaeoecology: Two Approaches, One Objective
Russell, Michael & Nitschke. “Methane: Fuel or Exhaust at the Emergence of Life?
Sandgathe, Dennis “Identifying and Describing Pattern and Process in the Evolution of Hominin
Scharf, Caleb et al. 2015. “A Strategy for Origins of Life Research
Seibt, Johanna. Ontological Tools for the Process Turn in Biology: Some Basic Notions
Shugart. H.H. How the Earthquake Bird Got Its Name and Other Tales of an Unbalanced
Simon, Herbert. 1962. “The Architecture of Complexity.
Smith, Hillary H. et al. 2021. “The Grayness of the Origin of Life
Smith, Eric & Harold J. Morowitz. 2004. “Universality in intermediary metabolism
Smith, Eric. Emergent order in processes: the interplay of complexity, robustness, correlation
Smith, Eric & Morowitz. The Origin and Nature of Life on Earth: The Emergence of the Fourth
Smith, Eric. “Thermodynamics of natural selection I: Energy flow and the limits on organization
Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life.
Sorensen, Andrew “The Uncertain Origins of Fire-Making by Humans: The State of the Art
Stotz, Karola & Griffiths. “Biological Information, Causality, and Specificity.
Stueken, E.E. et al. “Did life originate from a global chemical reactor?
Sundstrom, Shana & C.R. Allen. 2019. “The adaptive cycle: More than a metaphor
Swilling, Mark. The Age of Sustainability: Just Transitions in a Complex World.
Taborsky, Michael et al. 2021. The Evolution of Social Behaviour.
Tainter, Joseph et al. “Energy transformations and post-normal science
Taylor, Bron. 2010. Dark Green Religion: Nature Spirituality and the Planetary Future.
Tomasello, M. & Herrmann. “Ape and Human Cognition: What’s the Difference?
Tomasello, M. et al. Understanding and sharing intentions: The origins of cultural cognition
Tyrrell, Toby. On Gaia: A Critical Investigation of the Relationship Between Life and Earth.
Ulanowicz, Robert E. 2014. “Reckoning the nonexistent: Putting the science right
Ulanowicz, Robert E. 2018. “Dimensions Missing from Ecology”
Ulanowicz, Robert E. 2009. “The dual nature of ecosystem dynamics
Ulanowicz, Robert E. 2016. “Process Ecology: Philosophy Passes into Praxis.
Van Cleve & Akcay. “Pathways to social evolution: reciprocity, relatedness, and synergy
Vogel, Hans-Joerg et al. 2018. “A systemic approach for modeling soil functions
Walker, Sara Imari et al. “Evolutionary Transitions and Top-Down Causation
Walker, Sara I. & Davies. 2017. “The ‘Hard Problem’ of Life.”
Walker, Sara. Top-Down Causation and the Rise of Information in the Emergence of Life
Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.
Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.”
Washington, Haydn. A Sense of Wonder Towards Nature: Healing the Planet through.
Weiss, Madeline et al. The last universal common ancestor between ancient Earth chemistry and
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Williams, R.J.P. & Frausto da Silva. The Chemistry of Evolution: The Development of our.
Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual
Wohlleben, Peter. The Hidden Life of Trees: What They Feel, How They Communicate:
Wolff, Robert. Original Wisdom: Stories of an Ancient Way of Knowing.
Xavier, Joana et al. The metabolic network of the last bacterial common ancestor
Xavier, Joana et al. Autocatalytic chemical networks at the origin of metabolism
Zerkle, Aubrey. Biogeodynamics: bridging the gap between surface and deep Earth processes

Citations collected in 2021 (works listed above):

“Setting the Cartesian enterprise within its Scholastic context, we see it reducing to local motion the four Aristotelian kinds of change: substantial, quantitative, qualitative, and local. Apart from God and mind, there is just spread-outness, and those things that look in some ways a little like us are only bits of matter ingeniously engineered by their creator. In effect, the notorious doctrine of the beast-machine does away with life.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. xvii.

“For Aristotle, on the contrary, what we recognize as biology was part, indeed a central part, of the science of natural philosophy or physics….

“For Aristotle, physics, which in Greek means ‘things that grow or develop,’ is the study of any and all beings that have within themselves a non-incidental source of motion and of rest.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 5.

“To understand more precisely what Aristotle means by ‘nature,’ it helps to see that what happens naturally is contrasted in various places in his works with three other sorts of things:

“1. Natural philosophy (physics) is contrasted in the first instance with the study of substances that do not move at all, even if they move other things. What Aristotle has in mind here is the outermost sphere of the kosmos, which for him is also the divine self-understanding of the eternal world-order itself, to which finite things are both oriented and subordinated. This substance is the ultimate subject of ‘first philosophy,’ or what Aristotle calls ‘theology’ (of a highly rationalized sort by typical Greek standards). The sphere of physics, by contrast, is ‘second philosophy.’

“2. what happens by nature is also contrasted with what happens by art or craft (techne)…. In artefacts, matter and the form (the kind of thing it is) do not fully fuse. In natural entities, matter and form are not so separate.

“Granted, there is an important analogy for Aristotle between what comes to be by art and what comes to be by nature. In both processes, as in both kinds of entities, Aristotle distinguishes four ‘causes’ – one might say four reasons why a thing is as it is. Its matter and form are two of these, which are always distinguishable when we look at a substance (or an artefact) in cross-section, so to speak, at a given period of its existence. When we consider its life-history over time, however, we find two more correlative explanatory factors: the efficient or moving cause, which names the agency by which a thing comes into existence, and the final cause, which refers to the end for which it comes into existence or its terminal point of development. In the case of natural substances, as we will see, form, end, and efficient cause are often identified. Matter, which for Aristotle is the potentiality for assuming form, is decidedly subordinate to the other three….

“3. Finally, what changes by a natural internal impulse is also contrasted with what happens spontaneously by chance or coincidence, and by force. Aristotle thinks that just because natural substances have an internal principle of change and rest, their behavior is, to one degree or another, predictable and regular. What happens spontaneously or by coincidence does not conform to this pattern…. For Aristotle, what is spontaneous, chancy, or forced cannot be scientifically known.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 6-7.

“For Aristotle, soul means primarily ‘organizing principle.’ It is not a separate substance that ingresses into the body, as it is for Descartes and various Christian theologians. Soul is instead a principle of life. It integrates beings composed of differentiated parts, or organs, into substantial unities – that is, organisms.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 8.

“Aristotle’s conviction that biological form can come for the most part only from entities that have already actualized such forms, thereby constituting an endless chain that runs from parents to offspring, rests on his conviction that in most cases it cannot come from anywhere else. It cannot ‘always or for the most part’ come from material processes below, as his argument with Empedocles and Democritus shows. But neither can it come from Platonic forms above. Aristotle’s quarrel with Plato turns, in fact, on the same considerations as his quarrel with the materialists. The same arguments that call into question whether an organism could ever be a unitary substance if it had been assembled haphazardly from a series of chance events are also arguments against the possibility that Platonic forms, when pressed into physical materials, could ever produce anything of more substantial integrity than a mere artefact like a bed. In Plato’s theory, organisms can at most be matter-form compounds that are too weakly unified to count as substances. Aristotle’s conception of form, accordingly, is more dynamic than Plato’s.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 30-1.

“This delicate balance [of Aristotle’s philosophy of biology] was disrupted when Alexandrian physicians discovered the nervous system, which disrupted Aristotle’s image of a qualitative body centered in the heart…. The effect of these discoveries was the emergence of the image of the body that we still recognize. This new image shifted the center of life, awareness, and emotion away from the heart – the traditional Greek folk-biological locus, which Aristotle still shared – toward the brain, which Aristotle had regarded merely as a sort of radiator or cooling device. The discovery of the nervous system also unsettled Aristotle’s rather ambiguous concept of pneuma as the motor of life, replacing it with a system of pulls and pushes. In short, the discoveries of Alexandrian physicians led to a more mechanistic biology. Nor is this surprising, given that Herophilus and Erasistratus lived and worked in a city that was as technologically oriented as it was devoted to pure inquiry, a city in which automata such as water clocks achieved a degree of perfection not approximated again until the seventeenth century, when another bout of mechanism broke out.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 32-3.

“Accordingly, when several centuries later Galen (129-199 C.E.) mounted a highly rhetorical attack on Erasistratus, accusing him (falsely) of not being a teleologist at all, but a blind materialist, he converted Aristotle’s maxim, ‘Nature does nothing in vain,’ into an a priori conviction that a purpose can be found for virtually every trait. Galen’s teleology is purely intentionalistic. There is for Galen no difference between a trait that comes into existence for a purpose and one that comes into existence through purely material causes, but is subsequently put to good use. Good use is all there is, and good use can include the utility of one species for another as among its reasons for existing, as horses exist, in his view, in order to serve human beings. But Galen happened to be the most influential medical writer for the next millennium and a half. Accordingly, when he wrapped himself in Aristotle’s mantle, Aristotle’s teleology came to be interpreted in such a way that its emphasis shifted from internal, developmental teleology to external use-oriented teleology.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 34.

“In the first sense [of the meaning of “mechanism”], mechanistic biology enumerates a series of movements, each of which evokes its sequel, all necessitated a tergo, and all conceived as movements of nature. It is as if Aristotelian efficient and material causes were to function without the correlates of end and form. In the second sense, as we have already seen happening in Galen’s reading of Aristotle, living things become machines, designed for an end externally imposed.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 36.

“However [in the seventeenth century], partly because of the problems involved in describing, if not ‘explaining,’ the mystery of transubstantiation, whereby bread and wine allegedly become the body and blood of Christ, and especially through the influence of Duns Scotus and his school, matter had come to acquire a quasi-independence. (The bread and wine still look and taste like bread and wine, so their matter must be somehow independent of the Divine form that they now presumably express.) In Aristotle’s system, prime matter certainly did not exist independently.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 39.

“… it was a Christianized Aristotelian metaphysic with its attendant physical and logical works that caught the attention of Renaissance and early modern, as well as medieval, thinkers. The biological focus of Aristotle’s own thought had all but disappeared. This the ‘Aristotelian’ tradition of Descartes’s own day offered a severely modified version of Aristotle’s own life-centered vision.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 42.

“In fact, Descartes has discovered, there is only one kind of physical change: local motion. Birth and death, qualitative alteration, growth, are all reducible to this one, measurable, manageable type: the change in position of bodies relative to one another…. The very phenomenon of life, archetypical for ordinary people, is and must be overlooked and abolished.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 48.

“Descartes is opposing the Scholastic invocation of substantial and qualitative kinds of change. Nor do we need any but what an Aristotelian would call material and efficient causes in explaining the processes we observe. Again, for Descartes, the father of the bete-machine, there really is nothing alive.

“Harvey, in contrast, is himself an Aristotelian of a sort…. But, philosophically, he is much more conservative. In particular, he relies heavily on teleological reasoning. ‘Nature always does that which is best.’ Note, this is Aristotelian, internal teleology, not the external variety invoked either by Galen or, for that matter, by Descartes, who has to take it that God has made the ingenious machines whose operation he is analyzing. Harvey, too, does indeed sometimes invoke machinery, likening the heart beat to the firing of a gun. But his machinery is always in the service of purposes within the organism, not imposed from without.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 59.

“One of the most conspicuous obstacles to the definitive triumph of mechanism was the problem of explaining reproduction and development in its terms. On that view, animals are machines, like watches. As Fontenelle put it in a much quoted passage, ‘Put a male and female dog-machine side by side, and eventually a third little machine will be the result, whereas two watches will lie side by side all their lives without ever producing a third watch.’ An increasingly widespread answer to this problem was the doctrine of preformation. Another name for it was ‘evolution,’ not in the post-Darwinian sense, but in the literal meaning of ‘unfolding.’” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 83.

“From early in his decades as a natural historian, Buffon had announced his doctrine of ‘organic molecules.’ All the living world, he believed, was composed of living, though not yet organized, units, whose assemblage in various patterns produced the vast variety of kinds of living things that we in fact find in the world around us….

“It was a notion common to many naturalists of Buffon’s time that the parts of living things are already like the wholes in which they were contained.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 84.

“However, if we take organic molecules in that generalized sense – as minute bodies of which all plants and animals are composed – the confinement of their aggregation to a given species presents a puzzle. Why do the organic molecules of dogs produce dogs, or horses, horses, or of elm trees, elm trees: If organic molecules can all mix with one another, how do we get reproduction confined to a single species? For this purpose, Buffon had to introduce another notion, that of the ‘internal mold’ (moule interieur), which, on the analogy of crystal formation, presumably guides and limits reproduction….

“Even internal molds, will not quite do the job, however. Something more is needed, especially in sexual reproduction, where, in Buffon’s view, we have two sources that have to be brought together in the proper order. So, in addition to organic molecules throughout the body, and the internal mold that organizes them appropriately for a given species, we need ‘penetrating forces’ to mediate the proper arrangement.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 86,87.

“Mechanism was widely accepted by naturalists of the period, but usually with Divine Providence prominent off, or sometimes on, stage. Buffon, however, although he occasionally paid lip-service to the Deity, was plainly trying to give to nature itself wider powers than were permissible to the religious sensibilities of such writers as Haller or Bonnet. At the same time, if his explanations were mechanistic, they could be so only in an expanded sense of that term – that is, in the sense that no teleological reasons were invoked.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 87-8.

“To put the problem simply, Kant thought that the doctrine that causes must precede their effects is in considerable tension with our experience of organisms. For in an organism – a ‘natural purpose,’ as he calls it, for reasons we will explore later, – each part is reciprocally means and end to every other. This involves a mutual dependence and simultaneity that is difficult to reconcile with ordinary causality.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 94.

“… Kant says that organisms are – or at least must be grasped by us as – self-formative, bootstrapping operations, in which each part appears to be the joint product of all the other parts. This is what Kant means when he says that an organism is ‘a product of nature in which everything is both an end and also a means’ and in which the parts are ‘reciprocally cause and effect of form’….

“In this connection, Kant denies that organisms are even like the self-moving machines envisioned by Descartes. ‘A machine has only motive force,’ he writes, ‘whereas an organism has self-formative force’…. Precisely because they are not self-formative, moreover, the parts of an artefact must be ‘the product of a rational cause distinct from the matter of the thing, that is, distinct from the thing’s parts’. They compel an inference to a designer. The complex reciprocal causality of living things, on the other hand, requires us to disavow the very notion of an external agent.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 99.

“But where, other than our own experience as designers, makers, and choosers, could we ever acquire the idea of a being in which ‘the concept of the whole determines the form of the parts’ as fittingly, usefully, efficiently, even beautifully as we clearly observe in the case in organisms?…

“Kant’s way of putting this crucial point is to say that even if we do not and cannot know that organisms are ‘purposes’ – objects brought into existence in accord with an antecedent concept – we must admit that they cannot appear to us except as ‘purposive’.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 101.

“All along Kant has been asking in his ‘Critique of Teleological Judgment,’ not whether there are any living things, but whether there are any natural purposes. It is now clear that the answer is yes. Organisms are natural purposes. Kant says they are purposes in order to register our utter dependence in ‘grasping’ them and ‘cognizing’ them on an analogy between organisms and our own means-end reasoning activity, as we have just noted. The stress here is epistemic. Still, organisms are not merely purposes for Kant. They are, ontologically considered, natural purposes – the only case, in fact, in which Kant can finds (sic) natural purposes among objects in the world.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 102.

“While Kant seem willing to envision at least two kinds of causality, purposive and mechanistic, he certainly appears to have limited the term ‘explanation’ exclusively to the latter.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 107.

“Given the way organisms are ‘grasped’ by us and ‘cognizable’ by us, the antimony of teleological judgment holds instead between the following statements:
“(3) All products of material nature and their forms must be judged to be possible in terms of merely mechanical laws
“and
“(4) Some products of material nature cannot be judged to be possible in terms of merely mechanical laws. (Judging them requires a quite different causal law, namely that of final causes.)…

“The first tells us that ‘we ought always to reflect in terms of the principle of mere mechanism of nature, and hence ought to investigate this principle as far as we can, because unless we presuppose it in our investigation of nature, we can have no cognition of nature at all in the proper sense of the term’ (We can have no cognition in the proper sense because explanation, it would seem, depends on mechanical causality.) ‘None of this,’ however, Kant goes on,
“‘goes against the second maxim – that … in dealing with certain natural forms (and, on their prompting, even with all of nature) we should probe these in terms of … the principle of final causes. For this leaves it undecided whether in the inner basis of nature itself, which we do not know, the physical-mechanical connection and the connection in terms of purposes may not, in the same things, be linked in one principle.’” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 113; subquote: Kant, Immanuel. 1793. Critique of Judgment. p. 388.

“But the very fact that we must identify and learn about organisms by reflecting on them as ‘natural purposes,’ and must regard mechanistic laws as subserving those purposes in the way in which means serve the ends of an agent, presupposes that ‘in nature’s supersensible substrate,’ mechanism and teleology might be fused. For in using one maxim to compensate for the deficiencies of the other, we must be presupposing the possibility of a deeper unity in which both frames are brought together to an intuitive intelligence.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 115.

“The term ‘biologia’ goes back at least as far as the Wolffian philosopher Michael Christoph Hanov’s Philosophia Naturalis, the third volume of which, published in 1766, names it as the part of physics that studies living things. Lamarck, too, used the term; in an unpublished manuscript, written in French in 1800, he speculated about a discipline he called biologie, which would find the exact point at which the ‘corps vivant’ was unified with the ‘corps bruts’ by ‘fluides invisibles’. But it was Blumenbach’s student, the Goettingen professor Georg Reinhold Treviranus, who, in a six-volume text that began to appear in 1802, gave the term ‘Biologie’ both wider currency and the sense that it has borne ever since. In the title of his Biologie, oder Philosophie der lebenden Nature fuer Naturforscher and Aertze, Treviranus names a comprehensive science that would gather together information about living things from a variety of special sciences, such as physiology, systematics, and comparative anatomy. Treviranus’s Biologie, it would seem, is no longer part of physics, as it still was for Hanov; physics is now restricted to the study of inanimate, or life-less, objects.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 123.

“The British establishment, Tory and Whig, repudiated both the would-be political absolutism of the Stuarts and the religious ‘enthusiasm’ of the Puritans. They did so by combining respect for science (on terms laid down by the Royal Society) with a religious view of the world that was to be kept self-consciously moderate by the demand that revealed religion, with its potentially fanatical, even regicidal, appeal to faith, must be built upon and constrained by natural religion. Natural religion – the religion that all decent, reasonable human beings were presumed to be capable of arriving at and cultivating, even in the absence of revelation — was backed in turn by the argument for the existence of a creator God from the design of the natural world….

“Under these conditions, any threat to the mutual support that science, natural theology, and revealed religion were supposed to afford one another might well reopen wounds that were assumed to have been healed. Unfortunately, geology posed just such a threat. For the discovery of ‘deep time,’ in which species loss was more than occasional, episodic, or marginal, threatened to push religion and science apart again….

“This [massive extinctions] didn’t sound much like Genesis I. To make matters worse, this growing split was occurring just when populist, evangelical religion, born in part of the miseries of urbanization and early industrialization, was formally severing its ties with the established churches – Anglican in England, Presbyterian in Scotland – in the name of an emotional, faith-based pietism,…” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 159, 160, 161.

“According to Lamarck’s hypothesis of transformisme, expressed in his 1809 Philosophie Zoologique, lineages under pressure from a shift in their conditions of existence only appear to go extinct. Rather than dying out under the pressure of geological change, they can be presumed to have transmuted themselves into new forms by way of an inherent tendency in matter to complexify combined with the efforts of organisms to adjust to new environmental circumstances. As we remarked, it is a striking view for an evolutionist – not to have believed in extinction!” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 177.

“Owen had come to believe that biological order consists of systematic transformations of ‘archetypes’ that are presumed to dwell as Platonic ideas in the mind of God, but that appear successively in time as each Cuvierian embranchement is structurally adjusted both to their environments and to the demands of phylogenetic progress. Perhaps just because he held this rather heterodox view, rather than a version of the traditional argument from design, Owen was vehemently opposed to evolution on naturalistic terms.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 181; reference: Owen, Richard – anatomist of mid nineteenth century, at time of appearance of book Vestiges in 1844 that gave a simplistic view of evolution, which was amply criticized and thereby scared Darwin from publishing for a number of years.

“The oldest versions of the argument for the existence of a creator God from apparent design assume a kosmos thoroughly permeated with end-directedness. Although the argument can be traced as far back as Plato’s Laws and Xenophon’s Memorabilia, the version transmitted to Europe through Cicero’s De Natura Deorum was the most influential. In this dialogue, which Hume used as his literary model for his Dialogues Concerning Natural Religion, the Stoic representative of the argument portrays the world as a single living substance integrated and organized by a ‘world soul.’ This being assumed, there was no pressing need to distinguish between external and internal teleology, or between the present use of a trait and its future utility; in the kosmos as a whole, no less than in the individual body, nature does nothing in vain. This organicist view was rendered problematic, however, by pluralism about substances and even more by Christian creationism, which made God transcendent to the world. Thomas Aquinas, in his ‘fifth way,’ still portrays elements and planets as moving in an orderly fashion because they are seeking an end-point, as an arrow seeks the target. But Aquinas infers that this could not possibly occur without the divine analogue of an archer. By this route, teleology came to mean intentional design by an agent who is separate from his product. Final causes were thereby removed from the organism, their primary locus for Aristotle, and ascribed to a maker – with the result that living beings were assimilated to craft-objects, and ultimately to machines.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 184-5.

“In fact, Darwin’s own stance with respect to teleology, or final cause, appears to be irredeemably ambiguous.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 208.

“Nevertheless, we cannot say – as many said and some still say – that Darwin abandoned teleology….

“True, any divinely ordained teleology has certainly been abandoned. Natural selection is the cause. Nor is Darwin’s teleology Aristotelian, as Cuvier would have been happy to acknowledge his variety of final cause to be. Aristotelian final causes require a fixed end-point. In Darwinian nature, on the contrary, it is past and present dynamic that dictates the immediate future. Moreover, chance has a more positive role in Darwin’s world than in Aristotle’s.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 211.

“Owen rechristened them ‘homologies,’ and distinguished them from analogies. By homologies he meant structures built on the same plan, examples of the same ‘archetype.’ Analogies, in contrast, are similarities of function without the same underlying identity of structure. What Darwin did, as he himself put it, was to make the archetype into a real (formerly) living ancestor, so that homology becomes a historical concept. Homologous structures are signs of common descent….

“Analogies, on the contrary, provide examples of what we call convergent evolution: They do the same work, but their ancestries are different.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 215; Owen, Richard – anatomist of mid nineteenth century.

“In apparent contrast to this emphasis [Lamarckian explanation for new phylogenies], many students of the fossil record took an opposite direction, and found, or claimed to find, in the phylogenies they were tracing, evidence of ‘orthogenesis’ – that is, an intrinsic tendency to develop, from one generation to another, and one species to another, in a given direction, without the stress on adaptive relations characteristic of either classic Darwinian or Lamarckian accounts….

“Whatever its raison d’etre, orthogenesis in a number of varieties was an influential position throughout a number of decades…. If Darwin had conquered the world for descent with modification, he certainly had not effected a similar victory for his theory of natural selection. Well into the twentieth century, evolution was conceived, even if only vaguely, in terms of the biogenetic law; development and evolution – later considered alternatives – were thought to be the same thing writ small or large.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 230, 231.

“The 1980s witnessed widely publicized expressions of doubt on the part of some paleontologists about Simpson’s assurance that ‘macroevolution’ – evolution above the species level – is merely the result of accumulated ‘microevolutionary’ change at the level of populations.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 248.

“A species, he [Dobzhansky] argued, is ‘a stage in a process’ in which ‘a once actually or potentially interbreeding array of forms becomes segregated into two or more separate arrays which are physiologically incapable of interbreeding’…. They come into existence, Dobzhansky argued, when the interbreeding populations of which they are made up have found a way not just to occupy, but to keep themselves on, an adaptive peak by blocking gene flow between themselves and other populations, while at the same time they maintain sufficient genetic variation within themselves to adapt to an environment that inevitably changes, often by the organisms’ exploitation of its resources.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 255.

“During the evolutionary debates of the 1980s, it was claimed by Gould and others that after an initial period of ‘pluralism’ about evolutionary forces that was dominated by Wright, the Synthesis had ‘hardened’ into an ‘adaptationist program’ according to which natural selection alone is more or less responsible for adaptation and for evolution.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 258.

“In a rather grand sense, most, if not all, the figures we have been considering [around the Modern Synthesis] had philosophies, in the sense of privately held metaphysical interpretations of the scientific theory that they shared. Thus, Wright, when asked to write about his metaphysical interpretation of evolution, proved himself to be a monistic idealist. Simpson, by contrast, was a rather dogmatic materialist. And Dobzhansky, for his part, was an orthodox Christian who worried about how a good God could come up with balancing selection, which sentenced to death a predictable number of homozygotes for a recessive lethal allele, presumably in order to preserve the balance that could lead to further evolutionary advance.

“It was not in such matters, however, that philosophical reflection on the Modern Synthesis centered. Private interpretations, where they were known at all, were off the table in journals such as Evolution, which was founded in 1947 by Mayr and others who were hoping to project the Synthesis as a mature, value-neutral science. Just because those who forged the Synthesis were seeking a professional status that had eluded the Darwinisms of an earlier day – compromised as they had been by Spencer’s ‘Social Darwinism,’ Galton’s and Fisher’s eugenics, and other such value-laden, ideological concepts – the Synthesis came under philosophical scrutiny of a different sort.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 259-260.

“The first occurrence of a mutation that enhances the reproductive prowess of an individual that happens to possess it does not, and cannot, count as an adaptation. For an adaptation is a trait that not only has the effect of enhancing fitness, or that is useful to its possessor in fighting life’s battles, but that has come to be by way of cumulative, directional selection over many generations, just because it has this effect. Thus, by definition, natural selection of a concerted kind is a necessary condition for a particular member of a populations having this or that particular adaptation.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 261.

“For fitness means relative adaptedness of one sub-population compared with another in a given environment, and the various ‘components’ that confer relative adaptedness consist in the myriad small advantages by which selection gives a reproductive advantage to one phenotype rather than another. Expected fitness, or relative adaptedness, is in this sense a dispositional property of organisms, a propensity to reproduce that is not undermined by occasions, such as a bolt of lightning, when the expected result fails to happen in a statistically irrelevant case.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 263.

“During the 1980s, we may conclude, the Modern Synthesis did not stay stable. It tended to bifurcate into genocentric formulations, which, with some help from the ‘selfish’ properties of the molecular gene, looked back to Fisher’s adaptationism, and, at the other extreme, into ‘expanded’ versions that sought to recover Wright’s convictions that natural selection can and does operate at various levels, and that resolute ‘pluralism’ about interactions among various evolutionary forces must be maintained. Advocates of the second orientation do not deny that something like genic selection exists.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 275.

“Simpson was aware of how important ‘putting an equal sign’ between micro- and macroevolution was to efforts to present the Modern Synthesis as a general, complete, adequate theory of evolution. ‘If the two prove to be basically different,’ he wrote, ‘the innumerable studies of microevolution would become relatively unimportant and would have minor value in the study of evolution as a whole.’…

“Nonetheless, Simpson thought that cladogenesis – what happens when lineages branch at speciation events – took place against a background of ‘anagenesis’–that is, the slower, cumulative, largely adaptive evolution in the ‘phyletic’ mode that is presumably constantly going on, albeit at different rates, between branching events…. According to the Synthesis of the 1940s, speciation events occur as temporal and spatial dots in an ocean of ongoing adaptive change….” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 276.

“When Eldredge and Gould proposed their thesis of ‘punctuated equilibrium’ in 1972, then, their innovation was not to assert that speciation is rapid, or even ‘punctuated’…. Rather, Eldredge and Gould’s innovation was to deny that much anagenetic evolution occurs between branching points. Evolution, they claimed, is concentrated in comparatively rapid events of speciation….

“Eldredge and Gould’s claim was about pattern, not causes, and it was offered on empirical grounds. In the fossil record of marine invertebrates, for example, morphological change appears typically to have occurred within 5,000 to 50,000 years of speciation in species that lasted anywhere from 5 to 10 million years. To be sure, there is plenty of adaptation in the phyletic mode going on within that larger time. The point, however, is that it doesn’t seem to be going anywhere with respect to phylogeny; it consists of ‘oscillations around some modal value for phenotypic features examined’…. Punctuated equilibrium promotes itself as superior to the Synthesis in its way of dealing with the absence of evidence for intermediates. The evidence is missing, Eldredge and Gould argue, because the process of collinear change leading from one species to another does not actually exist.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 276, 277, 278.

“When it comes to conceptual considerations, however, perhaps the most important and controversial aspect of punctuated equilibrium is this: It has been taken by its sponsors to support the general idea, examined in the previous section, that selection operates at a variety of levels, some above the level of the individual organism. In particular, they take it to support the idea that selection operates at the level of species.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 278.

“Eldredge postulates that the species-level traits in question are the often quite subtle set of adaptations that lead local representatives of a species (‘avatars’) to recognize one another as good to mate with (and not good to eat)….

“Gould’s view is different. He argues that the properties in virtue of which species, qua species, are selected must be properties by which species compete, not with different species within an ecological community, but with very closely related species within their own clade. Species vary within a clade in terms of their ability to last longer in phylogenetic time (in virtue, perhaps, of a Dobzhansky-like ability to retain variation useful in changing environments); or to speciate more prolifically, or more often, thereby acquiring a better chance of driving species-level selection in a certain direction to form a trend; or perhaps in other ways. For Gould, such traits are components of fitness that are not resolvable into the properties of organisms or trait-groups.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 279-280.

“Waddington asserted that the causality of genes is negligible until it is acknowledged that interactions between the cytoplasm and the nucleus during different stages of development activate genes. Given this interactive approach to development, traits that are permitted by underlying genes but require much reinforcement at the phenotypic level, are reliably heritable in part because what Schmalhausen called ‘stabilizng selection’ narrows down the range of phenotypes that are possible for each genotype.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 281-2.

“What seems to be happening today is that the developmental gene concept, the gene concept of classical population genetics, and the molecular concept of the gene as a coding section of DNA, instead of drawing closer, as reductionists had expected, are actually pulling further apart….

“The Modern Synthesis was formed on the basis of population, not molecular, genetics. Its makers knew nothing of neutral alleles, selfish DNA, selfish genes, coding and non-coding sectors of the genome (exons and introns), structural versus regulatory genes, gene duplication, or gene splitting.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 285, 286.

“After Darwin, however, the situation has changed. Perhaps we should say it changed even after, or at the time of, the notorious Vestiges, whose many reprintings, as well as critiques, suggested a public ready for some transformist message, if a more cautious one than the Scottish journalist had offered. Whatever the correct reading of this story, and of Darwin’s role in it, it is certainly the case that since 1859 there has been a rampant ‘species problem’ – and it has not yet petered out.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 292.

“For Cuvier, who is following what he conceives to be the spirit of Aristotelian comparative anatomy, it is the total ‘conditions of life,’ the unique style of this kind of organism’s existence: its morphology, physiology, behavior, relationship to other organisms, and to its ecological niche; it is that inimitable whole that the naturalist is trying to understand. No little list of properties would suffice to capture it. If we want to call this a kind of essentialism, it is not the sort that can be itemized in lists of properties.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 292-3.

“Evolutionary theory, and, by now, usually the theory of natural selection, is there in the background of any contemporary biologist’s thought. But for an ecologist or a physiologist or a molecular biologist, it is not necessarily an evolutionary question that is being asked or an evolutionary answer that will ‘ultimately’ provide an answer.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 302.

“Two alleged solutions [to the problem of the nature of biological function] are still invoked, and their consequences are still subject to controversy. One answer, put forward by Larry Wright, proposes an ‘etiological’ concept of function. According to Wright, ‘the function of X is Z’ means:

“(i) Z is a consequence (result) of X’s being there
“(ii) X is there because it does (results in) Z….

“So any time we want to investigate the function of any biological organ or process, we are asking how natural selection produced it. As we have seen, however, that is not to give a teleological answer. On the contrary, it is to give a causal-statistically deterministic answer as to how something that looks telic, an adaptation, arose. The question may be metaphorically teleological: What was it designed for? But the answer will eventuate from a purely causal story of how one thing succeeded another. Yet Wright, and his later disciples, insist that their kind of explanation is teleological. Moreover, it gives us no clue as to the answer to the different, and more substantive, functional question, ‘How does it work?’…

“The common alternative to “Wright functions’ is a view put forward in 1975 by Robert Cummins…. … Cummins concludes: ‘To ascribe a function to something is to ascribe a capacity to it which is singled out by its role in an analysis of some capacity of a containing system’. This approach has the advantage of allowing us to ask of some process how it works. As Cummins points out, it also cleanly separates the question of function from that of teleology. In the case of artefacts, we can indeed ask why a feature is there, and can answer in terms of its artificer’s reason for putting it there. In natural systems, however, Cummins points out, such a ‘design’ answer is doomed to failure. We can only give a straight causal answer, and any ‘what for’ consideration is irrelevant.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. pp. 315-6.

“Cummins himself, however, has recently come to the defense of his original position, defending the CR [causal role] concept and arguing with devastating effect that the etiological view, or neo-teleology, as he calls it, is a non-starter. The neo-teleologist asks, for example, of a bird’s wing, why is it there, and answers, because it enables flight – and therefore selection produced it. But the trait or traits that make flight possible have to come into existence before the function eventuates. So neo-teleology has its history backward. Admittedly, selection itself produces nothing; it helps spread whatever happens to be there. Yet neo-teleology fares no better, Cummins argues, in explaining why traits spread. It wasn’t wings that were selected; it was just slightly more efficient wings as against their slightly less efficient competitors…. Nor will it do to try to save neo-teleology by identifying having a function with adaptiveness, since adaptiveness is a matter of degree, while having a function is not.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 319.

“As a result, deliberate self-regulation–from personal action to global geoengineering schemes–is either happening or imminently possible. Making such conscious choices to operate within Gaia constitutes a fundamental new state of Gaia, which we term Gaia 2.0.” Lenton, Timothy & B. Latour. 2018. “Gaia 2.0: Could humans add some level of self-awareness to Earth’s self-regulation?” Science. 361(6407): 1066-1068. p. 1066.

“Closure of a recycling loop triggers a self-perpetuating feedback process: The participants in the recycling loop are no longer limited by what comes into their world, but rather by how efficiently they can recycle resources. For example, coral reefs and the Amazon rainforest thrive on recycling in otherwise low-nutrient conditions.

“If, by contrast, we consider the state of the technosphere in the Anthropocene, an audit made by Gaia would question the purported quality of many innovations and note that from an engineering point of view, they perform poorly. Humans currently extract fossil energy, rock phosphate, and other raw materials from the crust far faster than they would normally come to the surface, and then dump the waste products on land, in the atmosphere, and in the ocean. Compared to Gaia, this is a very badly coupled and unsustainable set of inventions.

“This does not mean that humans should stop inventing but rather than engineering should shift attention to become as smart as Gaia in achieving nearly closed material cycling powered by sustainable energy.” Lenton, Timothy & B. Latour. 2018. “Gaia 2.0: Could humans add some level of self-awareness to Earth’s self-regulation?” Science. 361(6407): 1066-1068. p. 1066.

“The challenge is to design and incentivize a transition to a circular economy.” Lenton, Timothy & B. Latour. 2018. “Gaia 2.0: Could humans add some level of self-awareness to Earth’s self-regulation?” Science. 361(6407): 1066-1068. p. 1067.

“Some of Earth’s climate self-regulation mechanisms are purely physical and chemical, but many involve biology. On time scales of hundreds of thousands of years, changes in global temperature are counteracted by biologically amplified changes in the removal of CO2 by silicate weathering. On intermediate time scales of millennia, the dissolution of carbonate sediments on land and the ocean floor increases CO2 storage in the ocean. On even shorter time scales of years to centuries, land and ocean carbon sinks roughly halve the rate of CO2 rise and climate change.” Lenton, Timothy & B. Latour. 2018. “Gaia 2.0: Could humans add some level of self-awareness to Earth’s self-regulation?” Science. 361(6407): 1066-1068. p. 1067.

“Creating an infrastructure of sensors that allows tracking the lag time between environmental changes and reactions of societies is the only practical way in which we can hope to add some self-awareness to Gaia’s self-regulation.” Lenton, Timothy & B. Latour. 2018. “Gaia 2.0: Could humans add some level of self-awareness to Earth’s self-regulation?” Science. 361(6407): 1066-1068. p. 1068.

“An Aristotelian essence [from Aristotelian Essentialism or AE] is (a) comprised of a natural set of intrinsic properties which (b) constitute generative mechanisms for particularised morphological development which (c) are shared among groups of organisms, delineating them as members of the same ‘kind’.” Austin, Christopher. 2017. “Aristotelian Essentialism: Essence in the Age of Evolution.” Synthese. 74:2539-2556. dx.doi.org/10.1007/s11229-016-1066-4. p. 2539.

“Dispositional properties are inherently causal properties – they are responsible for the coming about of particular states of affairs (‘manifestation states’) upon the occurrence of some other state of affairs (‘stimulus conditions’). These properties function as ontological ‘switches’ of sorts, causally mediating the influence of certain activating conditions to produce particular states of affairs.” Austin, Christopher. 2017. “Aristotelian Essentialism: Essence in the Age of Evolution.” Synthese. 74:2539-2556. dx.doi.org/10.1007/s11229-016-1066-4. p. 2543.

“When a dispositional property is realised by a particular system then, the pathway from ‘stimulus’ to ‘manifestation’ often ‘reaches over’ a wide, multi-stage causal gap – thus, when such a gap is reliably and repeatedly bridged (upon the appropriate conditions being realised), we are afforded evidence of the existence of these properties.

“In abstracting to these end states, we not only abstract away from the particulars of that pathway – that is, the various links comprising the causal chain between those states – but also the various particular ways in which that pathway might be traversed. Accordingly, because there are many distinct instances of a particular type of stimulus condition which might lead to distinct instances of a particular type of manifestation state, the two states which define a disposition are determinables, not determinates.” Austin, Christopher. 2017. “Aristotelian Essentialism: Essence in the Age of Evolution.” Synthese. 74:2539-2556. dx.doi.org/10.1007/s11229-016-1066-4. p. 2544.

“… my claim is that the advent of evolutionary developmental biology has afforded us a unique view of that realm [AE’s ontology], one whose requisite ontology is dispositional, and whose foundational principles just are those of AE….” Austin, Christopher. 2017. “Aristotelian Essentialism: Essence in the Age of Evolution.” Synthese. 74:2539-2556. dx.doi.org/10.1007/s11229-016-1066-4. p. 2545.

“… I think it’s easy to see that AE is consistent with evo-devo: the fundamental ontological postulates of the latter – ‘developmental modules’ – can be conceptualised as instances of the ontological cornerstones of the former. In other words, from the Aristotelian point of view, developmental modules are dispositional properties.” Austin, Christopher. 2017. “Aristotelian Essentialism: Essence in the Age of Evolution.” Synthese. 74:2539-2556. dx.doi.org/10.1007/s11229-016-1066-4. p. 2546.

“The completed map of the human genome shifted biology’s attention from a primary focus on genes to seeing entire organism in information terms, constituted as much by data as by the physical structures that carry the relevant codes. The sites of biological invention also shifted almost as radically [to informatics] as in the move from the field to the laboratory a hundred years earlier.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. p. 32.

“In the twentieth century, science instrumentalized life in two ways, by learning to manipulate it and by profiting from its manipulation.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. p. 37.

“Both strategies of detachment – from collective, cross-disciplinary enterprise to individual achievement, and from economic or political interest to the purity of curiosity-driven research – can be traced, in part, through the discourses of discovery in the sciences. We begin with some landmark moments in the postwar history of the life sciences, at each of which credit for unusual perspicacity was either claimed by or accorded to individuals rather than to institutions or collectives. Helped along by individualized rewards such as a Nobel Prize, this personification of scientific achievement contributes to the sense that science is driven by powerful minds that can decipher life’s meaning on their own. Turning to science’s demands for freedom from state supervision, we see how the presumption that discovery means progress, coupled to claims of effective self–policing, has warded off substantial controls on biotechnoogy, in spite of intensifying entanglements between research, politics, and money.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. p. 40.

“He [sociologist Robert Merton 1973] identified four norms that constitute the ethos of science: communalism, universalism, disinterestedness, and organized skepticism. Unpacked, these terms mean that scientific knowledge is held in common; it is also invariant across contexts of use and application (universal), produced without regard for personal interests (disinterested), and held in check through systematic peer criticism (organized skepticism). That characterization of science still holds considerable public appeal, not least as an aspirational model for scientists, despite repeated demonstrations of a process that is in practice far more messy, contested, tribal, and driven by the rewards of the market.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. p. 55.

“This phrase [‘law lag’] encodes a very particular sense of the hierarchical relationship between science and law as regards the protection of life: on this view, progress indisputably lodges with science, while law must constantly extricate itself from outdated principles to give science its due respect. Science produces what is new and worthwhile in our understanding of life: the law trails behind, updating our values to keep pace with altered knowledge. The concept of the law lag thus carries with it, almost as a mathematical corollary, a linear notion of progress that places scientific discovery always ahead of norms-making, and thereby cordons off the domain of inquiry as if it can move ahead without interference from the domain of values.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. p. 69.

“That move, Woese said, had unmoored biology from its holistic urge to understand life in its fullness: ‘But the physics and chemistry that entered biology was a Trojan horse, something that would ultimately conquer biology from within and remake it in its own image. Biology would be totally fissioned, and its holistic side would be totally quashed.’ Thus hollowed out, Woese lamented, biology had ground to a halt as a fundamental science, ‘its vision of the future spent, leaving us with only a gigantic whirring biotechnology machine.’ The way forward lay in biology reclaiming ‘nonlinear’ phenomena such as emergence, evolution, and form, ‘to understand the world, not primarily to change it.’” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. pp. 142-3; reference Woese, Carl. 2004. “A New Biology for a New Century.’ Microbiology and Molecular Biology Reviews. 68(2):173-186.

“Further, the report presumes that the sciences and technologies whose integration makes up the New Biology can make progress on their own, without involving the social and human sciences, not to mention law and humanistic thought. The implicit assumption is that big problems may originate in the social world – such as overconsumption or scarcity – but solutions will be found in altogether different fields of endeavor, with no need for exchange between the producers of New Biological understandings and the eventual consumers of its proposed solutions. Third, the vision of progress outlined in the New Biology report makes little or no concession to possible value conflicts among interest groups, across nations, or among divergent philosophical schools about the endpoints of biological intervention or concepts such as ‘wise stewardship of our planet.’ In ethics as in science, the world is taken as flat, with everyone presumed to value the same outcomes to the same degree.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. pp. 150-1; “New Biology” refers to the report A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. 2009. National Research Council. Washington, DC: National Academies Press.

“Systems thinking permeates the report’s language and proposed solutions. Nonetheless, the systems that the New Biology addresses remain fixated on measurable, physical parameters, failing to take on board how human societies’ attempts to understand and make sense of their own condition loop back and reshape the very challenges that confront all life on the planet.” Jasanoff, Sheila. 2019. Can Science Make Sense of Life? Polity. p. 168.

“ITSNTS theory… was initially motivated by the now frequent claim that microbial community activities (‘functions’) are more stable or ecologically resilient than are the taxonomic compositions of the assemblages carrying them out, a phenomenon demanding evolutionary explanation.” Doolittle, W. Ford & S.A. Inkpen. 2018. “Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.” PNAS. April 17. 115(16):4006-4014. p. 4008.

“Together, evolutionary recruitment of capable taxa and their periodic reassembly, re-producing the nitrogen cycle or any of these less global processes, promote their persistence and evolution as processes.” Doolittle, W. Ford & S.A. Inkpen. 2018. “Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.” PNAS. April 17. 115(16):4006-4014. p. 4008.

“ITSNTS thus offers an alternative to luck and the anthropic principle for rationalizing Life’s long tenure on this planet, recasting ‘fortuitous benefits’ as persistence-promoting adaptations of processes, not of collectives of things.” Doolittle, W. Ford & S.A. Inkpen. 2018. “Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.” PNAS. April 17. 115(16):4006-4014. p. 4009.

“… ITSNTS theory might integrate persistence-based and reproduction-based ENS [evolution by natural selection] as extremes on a seamless spectrum. It is not so much that Nature holds two distinct kinds of evolving entities in either the domain of things or the domain of processes: there is a spectrum in both. But there are two distinct ways of thinking about variation-and-selection, one emphasizing reproduction and the other persistence.” Doolittle, W. Ford & S.A. Inkpen. 2018. “Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.” PNAS. April 17. 115(16):4006-4014. p. 4011.

“With fine-grained individuation (many types of nitrogen cycles, individual organisms in a species) differential reproduction makes sense, but as the grain ges coarser (nitrogen versus sulfur cycles, for example, or entire species or higher clades in the domain of things), differential persistence of processes becomes more satisfying as an explanation, and the role of reproduction as just one mechanism for promoting it becomes more obvious.” Doolittle, W. Ford & S.A. Inkpen. 2018. “Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.” PNAS. April 17. 115(16):4006-4014. p. 4011.

“Before being the name of a hypothesis, Gaia was the name of a new entity, defined as ‘the biosphere and all of those parts of the Earth with which it actively interacts’ – where the ‘biosphere’ meant ‘the total ensemble of living organisms’ and ‘the Earth’ refers to the entire planet as an object in the solar system. The Gaia hypothesis proposed that living beings could collectively regulate aspects of their global abiotic environment: the chemical composition of the atmosphere and oceans, and potentially also the climate.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. pp. 248-9.

“‘Life’ designates a new biological entity, localised in space and time comprising the total ensemble of all the living beings stemming from their last common ancestor, which biologists designate as a ‘clade’. This is distinct from ‘life’ (small l), the class designating the properties common to all living beings….

“Gaia is more than just Life in that it includes the effects of Life on habitability. Indeed, the Gaia hypothesis proposed that Life would not have survived without affecting its own habitability conditions.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. p. 250.

“Life has profoundly altered atmospheric composition and hence the Earth’s longwave energy fluxes and has significantly changed planetary albedo and hence the Earth’s shortwave energy fluxes, thus exerting considerable leverage on the overall energy balance. This agency must come from the informational quality of Life. Thus, the energetic and entropic views of Life are very different.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. p. 251.

“To trace Gaia’s boundaries thus requires (1) identifying all living beings (bacteria, horses, etc.) on Earth, (2) tracing carefully the chemical and material interactions and connections between these living beings and what is outside their membranes, (3) establishing which of those connections are relevant to habitability (or to Life’s persistence) and (4) recognising Gaia as the entity isolated by the resulting network of connections.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. p. 253.

“Oxygen at ~21% of today’s atmosphere is almost entirely a biological product, which would have a surface concentration of only ~10-12 atm in the absence of Life. The concentration of methane in this oxygen-rich atmosphere is a factor of ~1030 greater than expected at equilibrium, as are the concentrations of hydrogen and ammonia. This extraordinary order (negative entropy) in atmospheric composition can only be explained by an input of free energy via photosynthetic Life. An estimated ~0.7 TW is required just to maintain the O2-CH4 coexistence.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. p. 256.

“Carbon dioxide is extraordinarily scarce in the Earth’s atmosphere when compared to Mars and Venus (which have atmospheres dominated by CO2). Current human activities notwithstanding, Life has turned CO2 from a dominant component of the atmosphere to a trace gas, by locking up organic carbon in sedimentary rocks and by accelerating the weathering of continental silicate rocks and the resultant deposition of carbonate sediments. In the absence of Life, atmospheric CO2 would be up to ~10- to 100-fold higher producing a radiative forcing of ~10-20 W m-2.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. p. 256.

“Nitrogen has an essentially biological cycle in which organisms are responsible for all the key transformations. The input of bio-available nitrogen has been increased by a factor of ~40 by biotic nitrogen fixation (prior to human activities) relative to the small abiotic source from lighting strikes. Nitrogen uptake in net primary production is ~100-fold larger still, indicating a global nitrogen cycling ratio of ~100.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. p. 257.

“Furthermore, by producing an oxygen-rich atmosphere, an ozone layer, and the strong thermal stratification of the stratosphere, Life has created an effective ‘cold trap’ at the tropopause that prevents water reaching the upper atmosphere where it can be split apart and hydrogen lost to space. That said, before causing the rise of atmospheric oxygen, early methanogens likely enhanced hydrogen loss to space by increasing atmospheric methane concentration.” Lenton, Timothy, S. Dutreuil & B. Latour. 2020. “Life on Earth is hard to spot.” The Anthropocene Review. 7(3):248-272. pp. 259-260.

“This rapidly expanding body of work generally referred to as ‘transition studies’ includes two quite different schools of thought. … there are those interested in the different dimensions of sustainability transitions (STs), including socio-technical transitions, socio-metabolic transitions, techno-industrial transition, long-term development cycles and now most recently ‘deep transitions’….

“The second group of authors ‘posit[s] a profound cultural, economic, and political transformation of dominant institutions and practices’. … this group envisages a post-development, non-neoliberal, post/non-capitalist, biocentric and post-extractivist future and includes those who write from the global North about the commons, transition towns, degrowth, the ‘Great Transition’, the ‘Great Turning’, the ‘Great Work’, ‘Enlivenment’, transition from an age of Separation to an Age of Reunion and the transition from ‘Enlightenment to Sustainability.’” Swilling, Mark. 2020. The Age of Sustainability: Just Transitions in a Complex World. Routledge. p. 5.

“After all, it’s the quest for certainty that is the greatest threat to democracy.” Swilling, Mark. 2020. The Age of Sustainability: Just Transitions in a Complex World. Routledge. p. 7.

“Whereas Ostrom was interested in the way communities collaborate to govern common resources (e.g. land, water, forests), the more radical wing of the commons movement is interested in the governance of two types of converging spaces: the social commons (new modes of collaboration) and the knowledge commons (essentially codes, design and interconnected IT infrastructures).” Swilling, Mark. 2020. The Age of Sustainability: Just Transitions in a Complex World. Routledge. p. 64; reference: Ostrom, Elinor. 1990. Governing the Commons. Cambridge UP.

“A commons-centric society’ is a profoundly relationsl society, … The primary organizing principle of such a society is ICT-enabled mutual coordination that effectively hardwires relationality as a mode of economic production. As Bauwens et al. put it, ‘What market pricing is to capitalism and planning is to state-based production, mutual coordination is to peer production.’” Swilling, Mark. 2020. The Age of Sustainability: Just Transitions in a Complex World. Routledge. p. 66; reference: Bauwens, M., V Kostakis & A. Pazaitis. 2019. Peer to Peer: The Commons Manifesto. London: U of Westminister Press.

“Of course, long before there was biology there was ‘psychology,’ in the sense of the study of the soul, which was in turn understood as the principle of life. One crucial element in the eventual rise of biology was the elimination in the early seventeenth century of psychology from the study of the natural world, and the consequent need to replace the soul that used to animate nature with something else. This replacement took the form of the concept of ‘life,’ but the challenge for many seventeenth-century thinkers was to find a way to study life, or to ‘do biology,’ without allowing this to be simply a continuation of psychology under a new name.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 3.

“By the end of his philosophical career, Leibniz would come to the view that everything is biological, save for perception, which for its part underlies the biological without itself admitting of biological explanation.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 4.

“Overall, the place occupied by biology in Leibniz’s philosophy is closer to the one it enjoys in Aristotle than in Descartes….” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 8.

“It is clear that most of Leibniz’s philosophical engagement with the problems of biology may be characterized as a radical rejection of the central tenets of Descartes’ doctrine of the body-machine…. Yet at the same time Leibniz never denies the enormous debt of his own philosophy to Cartesian mechanism.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 10.

“Descartes believed that on the traditional Aristotelian picture, natural beings, in view of their capacity to strive toward their appropriate ends, partake too much of the divine, and thus that Aristotelian natural philosophy in the end amounts to a sort of animism that is at clear odds with Christian theology.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 10.

“Early on, Leibniz would agree with Descartes that animals are in fact machines, but he would come to believe that there are certain respects in which they are fundamentally different from the ordinary machines made by human beings. Later, he would come to believe that only animal bodies are machines, while the animal itself is a corporeal substance, over and above its organic body, the latter being distinguished from the ordinary mechanical body in that it consists, as Leibniz often puts it, in machines within machines ad infinitum.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 10.

“In particular, Leibniz agreed with Hobbes that Descartes’ conception of the physical world as consisting on the one hand in bodies defined as res extensa, and on the other hand in a fixed quantity of motion, certainly would not be adequate for explaining the complex activities of certain kinds of body, particularly animate ones. In this connection the young Leibniz is very happy to draw on Hobbes’s notion of conatus, which the latter defines in his De corpore of 1654 as ‘a motion through a space and time which is less than is given, i.e. is determined, whether by being displayed, or by being assigned a number; in other words, it is a motion through a point. Thus, for Hobbes, the conatus is the instantaneous propensity for motion even though, since it occurs in an instant, it cannot itself be said to be a motion…. Without such an added element in body, Leibiz thought, along with Hobbes, there could be no accounting for motion. In Descartes, by contrast, motion was a mere posit and could in no way be deduced from the concept of body itself.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 13.

“Hobbes distinguishes, further, between vital and animal motion, circulation and respiration being examples of the former, and running and swimming of the latter. In both cases, conatus or something analogous–namely, volition–plays a role. Volition is conceived as an infinitesimal beginning of a bodily motion.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 13.

“Leibniz does not entirely accept Descartes’ collapse of the Aristotelian ontological divide between the natural and the artificial insofar as he believes that the animal body is a natural machine or, which is the same, a divine machine whose infinite complexity and consequent indestructibility are enough to place it in a different ontological category from the ordinary products of human artifice. Ultimately, as we will see, it is from this infinitely complex structure that Leibniz believes its vegetation and motion can be derived: it is this structure that constitutes the organic body’s ‘material plastic nature,’ which Leibniz proposes as an alternative to the vitalist account of motion in the body as arising from an immaterial principle quite distinct from the body. This material plastic nature is ultimately nothing other than the derivative force of the organic body, which for its part results from the infinite aggregation of immaterial monads, all of which themselves come equipped with primitive active and passive force.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 14.

“Leibniz seems to agree that the ‘common people’ are justified in ridiculing the Cartesian view: ‘In Holland people are now disputing loudly and passionately about whether beasts are machines, and even the common man amuses himself with it, and ridicules the Cartesians, who imagine that a beaten dog cries in much the same way as an accordion when touched.’ Leibniz continues with his familiar take on the problem according to which the pure mechanism of the animal body does nothing to prove the absence of a soul: ‘Although I grant the Cartesians that all the external operations of beasts can be explained mechanically, I nevertheless believe that beasts have some knowledge, and that there is something in them which is not actually extended, and which can be called a soul, or, if you like, a substantial form’” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 53; subquotes: Deutsche Akademie der Wissenschaften (ed.) Gottfried Wilhelm Leibniz: Saemtliche Schriften und Briefe. II i 860-861.

“By appeal to fermentation, for example, Descartes believes himself able to account not just for the heat of the heart but also digestion and a number of other bodily processes…. In all of its manifestations, fermentation may be defined as calorification from corruption, and Descartes holds it responsible for digestion, respiration, conception, and certain components of fetal development, among other phenomena.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 78.

“Leibniz takes up the view that with respect to animal economy the principle of life is ‘igneous,’ [the process describing the activity effects of fermentation] but he denies strongly that this igneous principle is a soul. Instead, it is the body-machine itself that is igneous, and the full account of this igneous body-machine, at least from the Corpus hominis on, requires no mention of the soul. One may doubt that there is much difference between saying that there is an igneous and corporeal soul, on the one hand (Willis’s view), and on the other that the body is moved by a vital, igneous principle while the soul is something to be invoked only quite apart from any corporeal function (Leibniz’s view).” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. pp. 80-1.

“Rather, Leibniz, Hoffmann, and Baglivi are unified, against Stahl, in the view that the motion of an animal arises in the final analysis from a principle inherent in the nerves or muscles of the animal body rather than from the soul. Leibniz agrees that the body contains the principles of its own motion, and this will be the major point of contention around which his debate with Stahl circles. The debate, at least as both of its participants understood it, was not about vitalism, a notion that would not even come to be meaningful until well after the deaths of both Leibniz and his opponent. Yet if we must categorize Leibniz anachronistically in terms of this doctrine, we may say with firm conviction that he is an antivitalist: for him, the growth, motion, and preservation of a living body can be exhaustively accounted for without appeal to the soul. The soul is not responsible for life.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 86.

“… here Leibniz seeks to radically separate animal economy from inquiry into the nature of life, which he now sees as synonymous with perception. An animal is alive, but none of the phenomena treated by animal economy can reveal this. An animal is alive in virtue of its capacity to perceive, which is a soul-based and not a machine-based activity.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 88.

“Leibniz denounces the soul-body relation imagined by Stahl as one of obedience through violence, whereas Leibniz envisions an ‘obedience through accord.’” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 90.

“Although every body is ensouled for Leibniz, the soul nonetheless has no bodily function. The soul perceives, and this is a supercorporeal function.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 90.

“Thus, Leibniz thinks, one of the following two hypotheses must be true. Either, as the ‘Cartesians’ hold–which is to say Malebranche and other occasionalists–God implicates himself in the affairs of the world in order to directly bring about the states of the body that are required by the appetites of the soul; or these two agree with one another by a preestablished harmony.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 91.

“Thus Leibniz writes that ‘the soul, considered in itself, tends through final causes towards the goal that the corporeal machine, considered in itself, attains through efficient causes.’ Leibniz believes that as with everything else in nature the states of a living body result directly from ‘internal movements and from the structure of the machine,’ but that ‘since the internal parts are unknown to us, it may be easier to understand [the effects] from the final causes than from the efficient ones.’ Everything in nature is governed by both final and efficient causes. For the science of animal economy, explanation in terms of efficient causes is more appropriate, yet because this science is at present underdeveloped, Leibniz thinks, physiologists must sometimes rest content with final causes…. Depending on the problem at hand, one may be of more interest than another. Where the most general description of an animal as a whole is what is at issue, final causes will tend to be of more interest; where the diagnosis of a particular, local illness is what is sought, correspondingly local, efficient causes will be more relevant.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. pp. 91-2.

“All organism is in truth mechanism, but more exquisite.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 97; quote of Leibniz taken from the preamble of Georgii Ernesti Stahlii Negotium otiosum: Seu Ekiamaxia adversus positiones aliquas fundamentales Theoriae verae medicae. 1720.

“By the seventeenth century the microstructure of biological entities was not quite fully known, nonetheless, as a result of the recent invention of the microscope the study of organic microstructure had become a central component of much investigation into, and reflection on, the living world. If Aristotle’s was a biological metaphysics, Leibniz’s was thoroughly microbiological….

“Aristotle had been committed to a view of nature on which it ‘flies from the infinite, for the infinite is unending or imperfect, and Nature ever seeks amend.’ For him, a living body does not have to be divided up very far in order to reach homogeneous parts, that is to say, among other things, parts of the living body that are not themselves living bodies. It is exactly this decomposability into homogeneous parts that for Aristotle qualifies living bodies as natural. For Leibniz, in sharp contrast, not only does nature not flee from the infinite, but it is also the involvement of the infinite in the composition of a body that makes it a machine of nature, which is to say, that makes it ‘organic’ in Leibniz’s very narrow, technical sense.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 97.

“… the German philosopher’s conception nonetheless amounts to a radical departure from the earlier subtle-anatomical conception of bodies as consisting in numerous little machines. The crucial difference lies in Leibniz’s introduction of infinity into his account of the assemblage of machines that make up the body: for him, an organic body is contrasted with a mere machine to the extent that there is literally no lower limit to its mechanical composition.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 98.

“… he [Leibniz] agrees nonetheless with Descartes that for the purposes of the science of animal economy the living being may be studied exhaustively as a ‘mere’ machine. Organics, in contrast, engages the animal at a deeper level, at which the animal body is not a ‘mere’ machine but a special kind of machine, a ‘more exquisite’ or ‘more divine’ machine, as Leibniz puts it. This is the machine of nature, or the organic body, whose exquisiteness resides in the fact that it remains a machine in its least parts, which is to say that there is no stage in its decomposition at which one arrives at nonmachinic [sic] components.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 100.

“Other than one singular occurrence of the term as a count noun, ‘organism’ is an abstract term, very close in meaning [for Leibniz] to ‘organization’ or, less ambiguously, ‘organizedness.’” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 105.

“As Leibniz writes to Samuel Clarke, similarly: ‘The organism of animals is a mechanism that presupposes divine preformation: what results is something purely natural, and completely mechanical. Everything that happens in the human body, and in the body of any animal, is just as mechanical as what happens in a watch.’

“Of the handful of occurrences of ‘organism’ in Leibniz’s corpus, this one perhaps best captures what Leibniz intends by it: organism is to natural machines what mechanism is to artificial machines, and this organism is not contrasted with mechanism, but rather is conceived as a variety of it.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 106; subquote: Gerhardt, C. (ed) Die philosophischen Schriften von G. W. Leibniz. Vol. 7. 1890. pp. 415-8.

“The organic body, then is a machine of nature, even if, taken together with the soul rather than separately, the whole thing is not a machine at all, but a corporeal substance.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 109.

“As Leibniz writes to Sophie Charlotte in 1696: ‘My fundamental meditations revolve around two things, to know unity and to know infinity. Souls are unities and bodies are multitudes’….

“This conception of unity plays an important role throughout Leibniz’s thought, and in his mature period becomes attached to the notion of monad: ‘Monas is a Greek word which means Unity, or that which is one. Composites are Multitudes; and simple substances, Lives, Souls, and Spirits, are Unities.’” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 110; subquotes: Letter to Sophie, November 4, 1696 from Gerhardt, C. (ed) Die philosophischen Schriften von G. W. Leibniz, vol 7 p. 542; vol 6 p. 598.

“As opposed to artificial machines, as we saw in the previous chapter, a machine of nature for Leibniz entails an infinity of machines that form a single unit. This very distinction seems to indicate that there is, an intrinsic connection between Leibniz’s notion of organic unity and this unity’s nested structure. As we have seen, the unity of a composite substance derives from the entelechy or dominant monad, which is at once its singular source of activity as well as its source of unity.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 139.

“In the decades following Leibniz’s death, monads were broadly reconceived after the model of the infinity of small polyps that made parthenogenesis possible. They had become living and physical building blocks of the natural world….

“To be sure, physical monadologists entirely abandoned the distinction that Leibniz considered so crucial between ‘atoms of substance’ on the one hand, from which bodies result but not from which bodies are built, and physical atoms on the other….

“The tremendous difference between the parthenogenetic model of organic body and Leibniz’s model is that the polyp, as conceived in the eighteenth century, is not in any sense a unified corporeal substance. Leibniz can thus be seen as representing a halfway point between a certain widespread premodern conception of biological entities, which sought to give an account of the entity’s unity or soul-based properties while by and large ignoring its microphysical make-up, and the modern conception, which would come to see the microphysical make-up as all there is to an animal, as the only feature of a living being that differentiates it from nonliving entities, while its unity would come to be seen as nothing more than a temporary, contingent supervenience upon the physical make-up. In this sense, we may say that Leibniz’s theory, focusing as it does on unity and on microstructure, straddles the boundary between the old metaphysical picture of animals and the modern biological picture that emerged out of it.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. pp. 155-6.

“By the mid-eighteenth century, a strict materialism would come to dominate, particularly in France but also to no small extent elsewhere in Europe, in the philosophical discussion of what a living being is…. … animals, including humans, would come to be seen as mere clumpings of matter that, for limited time, through a fortuitous arrangement of their parts, come to develop the capacity for sensation and motion, and, in some few cases, for self-awareness. On this materialist picture, there is no room for an ontological distinction between real, existent entities and phenomenal sem-entities. Leibniz’s insistence on a soul-based principle of unity for the explanation of all organized, living matter, rather than taking spirit itself as a supervenient property of organized matter, would come to be viewed by materialists such as La Mettrie as unjustifiable speculation. The living being would come for many in the eighteenth century to have no more reality than the reality of its parts.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 156.

“Accounts of fetal development as an end- or idea-driven process were doomed to fall into disfavor in the seventeenth century. However, it would prove much harder to eradicate immaterial, guiding principles of development from embryological explanation….” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 167.

“There is no contradiction between the universality of mechanism, on the one hand, and the nonmechanicity of generation on the other, in Leibniz’s view, insofar as animals are never generated at all, but have preexisted since the creation….” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 168.

“In sum, Leibniz saves his own mechanism by opting for a preformationist account of generation.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 169.

“… the agreement or sympathy between the soul and the body will come about in one of three ways.

“1. The ‘way of influence.’ This is the account of causation given by ‘common philosophy.’ However, since it is impossible to conceive of material particles or of immaterial qualities that can pass from soul to body or from body to soul, this view must be rejected.

“2. The ‘way of assistance’ or occasionalism. This account would make a deus ex machina intervene in a natural and ordinary matter where reason requires that God should help only in the way in which he concurs in all other natural things.

“3. The way of ‘preestablished harmony,’ according to which God has made each of the substances from the beginning in such a way that each agrees with the other entirely as if they were mutually influenced or as if God were always ‘putting forth his hand’….

“… we may discern a striking analogy between each of the prominent early modern theories of cause and a corresponding theory of animal generation:

“Theory of cause Theory of generation
“Cartesian interactionism Epigenesis
“Occasionalism Spontaneous generation
“Preestablished harmony Preformation”
Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. pp. 193, 194.

“As we have already seen, Descartes denied the end-directedness of natural phenomena, including embryogenesis, but it would not be until the second half of the seventeenth century that the link between this denial and the tenuousness of species would be made explicit: the end-blindness of nature now means that the tendency of horses to beget horses is no more natural than the occasional cat-rat, ape-man, mule, or monstrous mola. Even if Descartes never faced up to the problem for Locke mechanism cannot but militate in the direction of antiessentialism; in the domain of science with which we are concerned, this means that the revolution in embryology that brought about the abolition of formative faculties also brought about a crisis in the concept of biological species.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 240.

“The view that an individual can pass through various species is sometimes called ‘transformism,’ and it is particularly widespread among Platonically inclined philosophers of the early modern period. These thinkers tend to see individuals as the bearers of essences, and they take these essences to be so durable that they could survive even the transition of the individual from one species to another….

“Conway takes insect metamorphosis as confirmation of transformation as a general principle of nature….” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 241; reference: Conway, Anne. 1690. Principles of the Most Ancient and Modern Philosophy.

“He [Leibniz] maintains that because an animal is a machine of perpetual motion in part in virtue of its capacity for self-reproduction, classification of species in terms of their generative systems is less arbitrary than any other taxonomy based on the comparison of morphological features. Creatures are the creatures they are in virtue of their being generated from like creatures, and they bear real relations to members of other species in virtue of resemblances of their generative systems. This is what Kant would later call ‘the unity of the generative powers,’ that is, the inclusion of a group of scattered individuals in the same kind in view of their shared ancestry.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 246.

“In other words, artificial machines are only able to continue running because a certain kind of natural machine–a human being –tends to them by bringing them new fuel. But natural machines require no such attendance. And even if the individual animal will eventually cease functioning, in death it is still capable of a sort of perpetuity to the extent that it is capable of reproduction. Put two clocks in a room together and you will never get a third, little clock out of them; put two dogs together, and you might. This is not just a difference in the degree of complexity of the tasks that the different kinds of machine can accomplish; it is a difference that places the dog in a a separate ontological class.” Smith, Justin. 2011. Divine Machines: Leibniz and the Sciences of Life. Princeton UP. p. 250.

“Intensive studies of protein-protein interactions have shown that the internal cellular medium is an assembly of supra-molecular protein complexes, e.g., the analyses of the proteome of Saccharomyces cerevisiae have shown that at least 83% of all proteins form complexes (containing from two to eighty-three proteins), and their overall enzymatic structure is formed by a modular network of biochemical interactions between multienzyme complexes.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 1.

“In concordance with the structural and functional self-organization of enzymes, the cell can be considered a complex metabolic network which mainly integrates a large ensemble of dissipative metabolic subsystems, where multiple autonomous oscillatory and some quasi-stationary activity patterns simultaneously emerge.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 2.

“In order to research the functionality of the cellular metabolism, the dissipative metabolic networks (DMNs) were created. Essentially, a DMN is an open system formed by a given set of metabolic subsystems (self-organized multienzymatic complexes) interconnected by biochemical substrate fluxes and three classes of biomolecular regulatory signals: activatory (positive allosteric modulation), inhibitory (negative allosteric modulation) and all-or-nothing type (which correspond to the regulatory enzymes of covalent modulation). Therefore, each metabolic subsystem is connected with others by a structure composed of biochemical message flows. This dynamic process of biochemical interconnections between subsystems may be understood as metabolic synapses i.e., the functional connection processes among self-organized multienzymatic complexes through which biomolecular information flows from one metabolic subsystem to another.

“In the DMN, the emergence output activity (the connection pattern) for each metabolic subsystem can be either steady state or oscillatory with an infinite number of distinct activity regimes.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 2.

“… several studies implementing flux balance analysis in experimental data supported new evidence of this Systemic Functional Structure. Specifically, a set of metabolic reactions belonging to different anabolic processes which remain active under all investigated growth conditions was observed. The rest of the enzymatic reactions belonging to different pathways remain only intermittently active.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 2.

“Recently, it was possible to quantify the bio-molecular information flows in a single metabolic subsystem, and in a DMN in which the emergence of an effective connectivity structure was also observed. This functional structure of biomolecular information flows is modular and the dynamical changes between the modules correspond to metabolic switches which allow for critical transitions in the metabolic subsystem activities. According to these results, the Systemic Metabolic Structure is not only characterized by a metabolic core and self-organized multienzymatic complexes in an on-off changing state but also it shapes a sophisticated structure of effective information flows which provides integrative coordination and synchronization between all the metabolic subsystems.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 2.

“We have quantified essential dynamic aspects of a dissipative metabolic network among which we have found that the systemic enzymatic activities are governed by attractors with the capacity to store metabolic information patterns which can be correctly recovered from specific input stimuli (associative memory). As a consequence, the multienzymatic network has the capacity to learn, self-regulate and self-adapt to new external conditions.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 18.

“In light of our results, and, in addition to the relatively small amount of genetic information that characterizes most cells, the metabolic networks of living cells may have far more biomolecular information in the form of functional metabolic memories stored in the connectivity patterns of the self-organized multienzymatic subsystems.

“It has not escaped our notice that the possible duality in the storage system of molecular information in cells (structural-genetic and functional-metabolic) are of considerable biological interest.” De la Fuente, Ildefonso M., J. Cortes, D. Pelta & J. Veguillas. 2013. “Attractor Metabolic Networks.” PLOS ONE. March. 8(3):e58284. p. 18.

“The central challenge in understanding the mechanics of biological structures is that they are dynamic and constantly sculpt themselves: their building blocks consume energy and generate force, they come on and off on their own, and whole structures morph to take new shapes and functions. These structures thus have ‘emergent mechanics,’ which we define as mechanics that arise from the above complex dynamics and the interplay (feedback loops) between them. We contrast these to the mechanics of static structures that are frozen in space and time. The emergent mechanics of biological structures can be dramatically different from the mechanics of their constituent parts, and they often defy current mechanics frameworks and intuition.” Dumont, Sophie & M. Prakash. 2014. “Emergent mechanics of biological structures.” Molecular Biology of the Cell. November 5. 25:3461-5. p. 3461.

“Despite knowing much about their building blocks and architecture, we are (for the most part) unable to predict the mechanics of living structures in the most rudimentary sense. For instance, given an infinite choice of building blocks, we cannot a priori design a new, higher-order structure of a desired compliance or viscosity or of a given force generation capability. Even predicting whether a biological structure will be more liquid-like or solid-like can be a challenge. Why? Because biological structures are wildly dynamic: their structural components themselves can consume energy and can rapidly turnover while the whole structure persists and changes architecture.” Dumont, Sophie & M. Prakash. 2014. “Emergent mechanics of biological structures.” Molecular Biology of the Cell. November 5. 25:3461-5. p. 3462.

“In self-organization, order arises from self-driven ‘active’ parts that consume (dissipate) energy. This energy comes from metabolism, bringing biological processes out of equilibrium: this empowers living structures to transform themselves again and again, to generate autonomous motion, and to organize life. As a classic example, cytoskeletal structures constantly build, unbuild, and rebuild themselves to match changing needs, and their dynamics themselves generate force. This raises a simple paradox: how can biological structures be so dynamic and yet persistently generate force and maintain their mechanical integrity? The answer lies in understanding the emergent mechanics of these structures, and we lack both the conceptual framework and tools needed to understand them.” Dumont, Sophie & M. Prakash. 2014. “Emergent mechanics of biological structures.” Molecular Biology of the Cell. November 5. 25:3461-5. p. 3462.

“A first key challenge to understanding the mechanics of living structures is time: how does one describe the mechanics of a structure whose components constantly turn over and evolve and whose mechanically relevant time scales range from milliseconds (molecular motor stepping) to days (organism developing)?… A second key challenge is space: how does one describe the mechanics of a structure whose architecture and force transmission (load-bearing) paths evolve over time? Most biological structures are spatially nonuniform, and their mechanically interconnected length scales range from nanometers to meters. Thus the mechanical responses of individual elements depend on where they are located in the structure and the structure’s local and global architecture…. A third key challenge is that self-organizing structures can consume energy and actively generate force. How does one describe the mechanics of a biological structure whose response to force include changes in the production of force itself?

“Although these three challenges are significant, it is their combination that presents the grandest challenge to understanding emergent mechanics: temporal, architectural, and active force-generation dynamics all affect each other (feedback loops), raising the structure’s complexity to a level that defies traditional frameworks and everyday intuition.” Dumont, Sophie & M. Prakash. 2014. “Emergent mechanics of biological structures.” Molecular Biology of the Cell. November 5. 25:3461-5. p. 3462.

“In the specific context of mechanics, our goal should be focused on extracting the general mechanical design principles used by biological systems…. It is very likely the case that these mechanical design principles will be fundamentally new and as such may not have a known analogue in nonliving physical systems.” Dumont, Sophie & M. Prakash. 2014. “Emergent mechanics of biological structures.” Molecular Biology of the Cell. November 5. 25:3461-5. p. 3464.

“Labor and capital are inert and unproductive without exergy inputs.

“The essential truth missing from economic education is that energy is the stuff of the universe, that all matter is also a form of energy, and that the economic system is essentially a system for extracting, processing and transforming energy as resources into energy embodied in products and services.” Ayres, Robert. 2017. “Gaps in Mainstream Economics: Energy, Growth, and Sustainability.” pp. 39-53. Shmelev, S. (ed.). Green Economy Reader. Springer. p. 40.

“It is not enough to know how much exergy is ‘embodied’ in a specific product made using yesterday’s technology. It is more important to know how much exergy is embodied in the $ output of the economy as a whole, and how much exergy is embodied in each additional increment of output, at the margin. And, by the way, it is important to know how much $ output would decline if the availability of exergy were to decline.” Ayres, Robert. 2017. “Gaps in Mainstream Economics: Energy, Growth, and Sustainability.” pp. 39-53. Shmelev, S. (ed.). Green Economy Reader. Springer. p. 45.

“Energy (exergy) has also been under-valued in the real world for a long time. It is this undervaluation that has led to a consumption-based ‘throwaway’ economy, now threatened by its own waste products.” Ayres, Robert. 2017. “Gaps in Mainstream Economics: Energy, Growth, and Sustainability.” pp. 39-53. Shmelev, S. (ed.). Green Economy Reader. Springer. p. 46.

“But the two centuries of declining energy (and work) costs is now in the process of ending…

“On the other hand, the costs of energy efficiency technologies (EETs) and renewable energy technologies (RETs), has been declining and will continue to decline.” Ayres, Robert. 2017. “Gaps in Mainstream Economics: Energy, Growth, and Sustainability.” pp. 39-53. Shmelev, S. (ed.). Green Economy Reader. Springer. pp. 46, 47.

“Lotka postulated that Darwinian natural selection favors species ‘that maximize the rate of energy flux (power) through their bodies’, so Lotka’s energetic hypothesis–which he attributes to Boltzmann–is one form of maximization of the rate of entropy production.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 53; reference: Lotka, Alfred. 1945. “The law of evolution as a maximal principle.” Human Biology. 17(3):167-194.

“So, to summarize the contest between EGR [Einstein general relativity] and YGR [Yilmaz general relativity] from a cosmological perspective:

“ EGR implies that gravity is curvature; this makes it hard to fit into the QCD [quantum chromo-dynamics, standard model of nuclear forces] theory of forces. YGR merely suggests that gravity causes curvature of space.

“ The two theories agree that ‘dark matter’ must exist to explain the gravitational stability of galaxies and other cosmological objects; neither offers any clue as to what it might be….

“ EGR also requires ‘dark energy’ to explain the apparent acceleration of the expansion of the universe. YGR does not….

“ EGR implies that ‘black holes’ exist, which implies that point singularities are legitimate in physics; the BB [black hole] was a singularity. YGR does not require point singularities (hence no ‘black holes’)….

“ EGR is consistent with (and essential for) the BB theory. YGR is not consistent with BB. It requires something like ‘continuous creation’ of mass throughout space-time (which is why it does not require dark energy).” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 84; reference: Yilmaz, Huseyin. 1986. Quantum mechanics and general relativity. New York: New Techniques and Ideas in Quantum Measurement Theory.

“… though quite a few of the known elements are utilized by living organisms, the majority, especially the elements heavier than iron, are not.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 103.

“The oceans contain about 5000 times as much carbon dioxide as the atmosphere, which means that the atmospheric level depends, above all, on the solubility of CO2 in the oceans. That, in turn depends on the surface temperature of the water.

“The warmer the water, the less additional CO2 it can absorb. As warming occurs, less of the ‘new’ CO2 emitted each year (by combustion of fossil fuels) is removed, leaving more as a greenhouse gas (GHG) in the atmosphere and accelerating the warming process. But, warmer water temperatures would also increase surface evaporation, rainfall and erosion rates. Clay minerals washed into the sea would then react with the dissolved CO2 causing it to precipitate as CaCO3 (limestone) and thus tending to re-stabilize the system.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 114.

“The interior of the Earth is gradually cooling, as the radioactive elements continue to decay. One long-term consequence of that cooling is that the Earth’s crust grows thicker, volcanism decreases, and tectonic activity gradually declines…. This slows down the rate at which carbonates in the sediments can be reduced (‘cooked’) to release their CO2 in the reducing environments of the magma. In a few words, the rate at which carbon dioxide is recycled to the atmosphere by volcanism is slowing down…. More and more of the earth’s carbon stock is being sequestered in biologically unavailable forms.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 115.

“Here I should make reference to three alternative theories of what may happen in the future. One is the Gaia theory, which says that life tends to co-evolve with the planet, so as to maximize its stability and resilience against perturbations. The opposite theory, which has been called the Medea theory (Note: Medea was the legendary Greek wife of Jason (seeker of the golden fleece), who killed her own children) argues that life is inherently suicidal, in that it tends to exploit all available resources until they are exhausted. One might call it the ‘Easter Island’ theory….

“The third theory, Thanatia, is not a theory of what will happen or would happen without human intervention. It focuses on the specific process that would lead to a ‘dead’ Earth, in which all available exergy resources have been used up by human economic activity, vis a vis the present state.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 117, 118.

“The reason this ‘trick’ [transfer of electrons in cells by ATP and ADP] works is (1) that the PO4 combination (with or without an extra electron) is extremely stable and very hard to break up. It is also quite insoluble. Moreover, (2) a single PO4 does not readily combine with other organic groups, except the lipids. But (3) PO4 groups do combine tightly, in pairs, with the nucleotide base, adenine (which consists of five linked HCN molecules), forming ATP. Finally (4), a single PO4 will combine (weakly) with ADP in preference to a lipid…. The essential point is that ADP/ATP play no role except as a carrier of electrons, via a detachable PO4, from one site to another.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 128.

“Moreover, oxygen began to accumulate in the atmosphere once again, probably because the oxygen photo-synthesizers increasingly out-competed other organisms…. A new biological ‘use’ for the oxygen was badly needed. Without such a mutation, all living organisms would eventually have been poisoned by their own waste products….

“What happened was a mutation that enabled organisms to oxidize glucose directly. This ‘invention’ is what we call respiration. It is very hard to pinpoint exactly when it took place, but based on indirect evidence it appears some prokaryotic bacteria had developed the chemistry of respiration by 2 billion years ago….

“Sometime between 1.5 billion years ago and 1 billion years ago, the basic energy metabolism of the biosphere, and subsequently the atmosphere, stabilized as an early version of the carbon cycle.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 151-2, 153.

“The metabolic advantage of respiration over fermentation is enormous, and it translates directly into better performance at the cellular level. The respiration process generates 18 times more free energy (exergy) from glucose than anaerobic fermentation, because it oxidizes the lactic acid and ethanol that fermentation leaves behind.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 153.

“It is much more efficient, in energy (exergy) terms, to construct new proteins by decomposing the proteins from dead biomass into their component amino acids, that to start from photosynthesized glucose as the primary producers must do. This, of course, is the survival strategy of the grazers, the parasites and the saprophytes. It is also the strategy of higher level predators in the food chain.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 159-160.

“Yet, paradoxically, the ecosystem as a whole does not necessarily maximize primary exergy consumption. On the contrary, it seems to maximize the life-cycles of organic molecules (such as amino acids) by minimizing entropy production per unit of exergy consumed.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 160.

“Some of the ‘structures’ created far from equilibrium by this process (waves, wind-driven gyres, typhoons [self-organizing processes in the biosphere]) tend to maximize local entropy production by increasing the rate of ‘destruction’ of thermal gradients. However, the exergy captured by photosynthesis and sedimentation simultaneously reduces the local rate of entropy-increase.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 168.

“However, 99.9% of the solar energy absorbed by the chlorophyll drives evapo-transpiration. Only a tiny fraction drives photosynthesis and produces glucose from CO2 and H2O. Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 169.

“In fact, the heat balance is complicated enormously by differences between the equator and the poles, differences in reflectivity (albedo) and absorption over different surfaces, and differences in cloud cover, among others.. The heat balance for the Earth as a whole, therefore, requires significant heat transfers from the sea to the land and from the equator to the poles. Since horizontal thermal conductivity is negligible, these transfers involve physical transfers, notably of water vapor in clouds and ocean currents.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 169-170.

“The water content of all living things on Earth–mostly trees–is about 1/9 of the water as vapor in the atmosphere, or 1.12 units of 103 km3 or 1120 cubic kilometers.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 171.

“It is important to realize that the oceans are by far the main storage system for heat in the short to medium term, having absorbed 93% of the increase in global heating between 1971 and 2010. They can absorb or emit heat much faster than solid rock, and can store much more (~1000 times as much) than the atmosphere.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 179.

“The only obvious negative feedback that could reverse warming over a period of years or decades would be sharply increased high-level cloud cover to increase the Earth’s albedo.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 184.

“There are two kinds of cycles, briefly characterized as ‘short’ (biological) and ‘long’ (geological)….

“The cycles differ markedly in terms of the physical and chemical form of the major inorganic reservoir, and the mechanisms for transfer from one reservoir to another. When an element passes from the bio-unavailable inorganic reservoir to the bio-available reservoir it is said to be mobilized…. When a nutrient moves in the reverse direction it is sequestrated. (In the case of carbon, the term is also used in connection with the accumulation of carbon or carbon dioxide in a reservoir from which CO2 cannot reach the atmosphere).” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 195.

“As I noted earlier, the only significant mechanism for phosphorus recycling to terrestrial life is geological. (A small amount is deposited on land in guano). This is because there is no phosphorus in the atmosphere and no gaseous form of phosphorus that could facilitate transfer from marine to terrestrial reservoirs.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 213.

“The atmosphere in that scenario [thermodynamic equilibrium] would consist almost exclusively (99%) of carbon dioxide and there would be no molecular nitrogen in the air because all the nitrogen would have reacted with oxygen to become nitrates. In that idealized world, water would constitute only 85% of ocean mass (compared to 96% in the actual ocean), sodium nitrate would constitute 1.7% of the ocean mass (which is many times greater than the atmospheric mass), and sodium chloride would constitute 13% of ocean mass (as compared to 3.4% in the actual ocean). Life could not exist in that hypothetical world, if only because of the excess salinity of the oceans.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 216-7.

“The ‘skin’ of the habitable Earth is a composite consisting of the Earth’s magnetosphere, the two (and sometimes three) Van Allen radiation belts, and–since oxygen accumulated in the atmosphere–the ozone layer. These are penetrable to solids (e.g. meteorites and comets) but they minimize penetration by high energy cosmic rays, solar wind (protons) and UV radiation.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 224-5.

“A much larger percentage of that input [solar exergy that reaches the Earth surface] drives the weather-climate system, without which the biosphere could not exist.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 226.

“Yet a large part of economic theory–and virtually all theories of economic growth–assumes that the economic system is always in equilibrium, even though ‘growth in equilibrium’ is an oxymoron. Equilibrium, after all, whether in physics or economics, is a state where nothing happens. The assumption of equilibrium is mainly for reasons of convenience (i.e. computability). However, in reality, this assumption is often dangerously false, especially in terms of analyzing phenomena such as ‘bubbles.’” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 368.

“The aggregation process involves three different simplifications. One is the assumption that all objects in the economic system belong to a finite number of categories, or sub-categories. Thus all workers may be assumed to belong to the category ‘labor’, or ‘manual labor’ notwithstanding great differences within the category. Capital stock may be subdivided into active components (machines) and passive components (buildings, pipes, infrastructure). There are other ways to subdivide.

“The second simplification is the assumption that the objects in the category are characterized in terms of some measurable quantity of interest, such as monetary value, or an input (e.g. of money or labor or exergy) or an output (e.g. work done or tonnes of product). The third simplification is that there is a natural time period–such as an hour or day or month–within which the objects belonging to the category can be regarded as fixed. In other words, it is important to be able to assume that changes only occur between periods. It is also assumed that the time periods of no-change are so short that incremental changes between successive periods are very small (i.e. they can be regarded as differentials).” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 369.

“Externalities were rare in the eighteenth century, but they are more and more important–even dominant–in economic life today….

“Externalities–third party effects–were not explicitly recognized by economists until the twentieth century. The formal definition of an externality is a cost (or benefit) incurred by a party who did not participate in the action causing the cost or benefit (a third party). In the older literature an example of a negative externality might have been a fire in a farmer’s haystack caused by the sparks from a passing steam locomotive. A real positive externality might be the pollination services performed by the bees of a bee-keeper for neighboring farmers. The most familiar externalities today are pollution and climate change, but ‘busts’ and ‘bubbles’–and subsequent financial crashes–are also major externalities….” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 374.

“An underlying theme of several of these papers [on the disconnect between private and public welfare] was that negative incentives resulting from competition and congestion are increasingly important in modern society as compared to the importance of cooperation in a Jeffersonian society.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 374.

“Starting with a disaster of some sort–e.g. a forest fire in the ecological case or a war or depression in the human case–the system grows fast, at first, because most of the barriers that were present during the previous ‘climax’ phase, have been eliminated. But as growth continues, more and more of those growth inhibitors also reappear. In the case of the ecosystem, the growth inhibitors are the longer-lived but slower growing shrubs and deep-rooted trees that capture the most water and the most sunlight. In the case of a firm or a nation, the inhibitors are competitors, government regulations, and long-term investors, such as pension funds and insurance companies, favoring dividends rather than growth.

“As time passes, those organizations combine to ‘lock in’ a given development path and prevent or discourage departure from that path (innovation)….

“Similarly, in democratic societies, all sorts of organizations form to promote or prevent laws, regulations or initiatives contrary to the interests of the group.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 379.

“Mancur Olson’s theory amounts to a cyclic model of organizational and economic behavior, just as Holling’s cyclic model explains patterns of ecological succession.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 380; references: Olson, Mancur. 1982. The Rise and Decline of Nations: Economic Growth, Stagflation and Social Rigidities. Yale UP; Holling, C.S. 1986. “The resilience of terrestrial ecosystems: Local surprise and global change.” Clark, William & R.E. Munn (eds). In: Sustainable Development of the Biosphere. Cambridge UP.

“The key insight of his work [Brian Arthur’s] is that self-reinforcing mechanisms, analogous to auto-catalysis, resulting from positive feedbacks in non-linear systems, are common to physics, chemistry and biology as well as economics. In all of these domains they can lead to multiple equilibria (complexity).” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 381; reference: Arthur, Brian. 1994. “Increasing returns and path-dependence in the economy.” Kuran, Timur (ed.) In: Economics, Cognition and Society. U of Michigan Press.

“Conventional economic theory is largely built around declining marginal returns which are negative feedbacks, resulting in an approach to equilibrium. This is why neoclassical economics cannot explain growth as an endogenous process. Clearly, economic growth does not occur in equilibrium. Hence economists have been forced to assume that growth results from exogenous factors, especially technological innovations (e.g. Schumpeter). Brian Arthur has shown that growth–and other economic phenomena–can be explained by invoking positive feedbacks, such as increasing returns to scale or to learning and experience.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 381; reference: Arthur, Brian. 1994. “Increasing returns and path-dependence in the economy.” Kuran, Timur (ed.) In: Economics, Cognition and Society. U of Michigan Press.

“Could large scale industrialization have occurred without coal and other hydrocarbon resources? I answered that it could not. But to dig deeper, does that mean that supply (of cheap coal) then created its own demand – or, more accurately, enabled demand? Or was it demand that created (i.e. induced) supply, as most economists assume today?…

“Imagine an alternate counter-factual eighteenth century universe in which there were no fossil fuels to energize the industrial revolution. Population was increasing, slowly but inexorably. In England trees were being cut to provide charcoal and timber for barrels, houses and ships. Forest land was being converted to cropland to feed more people. Common lands in England were being fenced and enclosed to produce wool for export. In that alternate universe, without coal or oil, the economy would be dependent entirely on the energy supplied by food and animal feeds, plus fire-wood….

“Actually, without the economic growth that did occur, the price of food would have consumed all the available income of the workers. People would have had to starve or freeze. Malthus’ thesis would have been proven correct.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 386.

“That future world [with no more fossil fuels] will have to be almost entirely electrified, apart from a fraction utilizing hydrogen. The electric power will come from a variety of sources, including flowing or falling water, wind, tidal or wave motion, solar energy, thermal energy from the earth, and heat from nuclear fission (or fusion). Solar energy may be captured by photosynthetic plants (biomass), by lenses or mirrors or directly by photo-voltaic cells.

“Some of that electric power may be used to produce hydrogen by electrolysis of water. The hydrogen, in turn, can be converted back into electricity (via fuel cells) for cars or trucks, or used directly as fuel in gas turbines for aircraft. Electrolytic hydrogen will also be needed to manufacture ammonia (for fertilizer), and other chemical intermediates currently produced from natural gas. But products currently made from ethylene, propylene, butylene, butadiene, benzene, xylene and other petrochemicals (including synthetic rubber, synthetic fibers and most plastics) will largely disappear unless a new chemistry based directly on carbon dioxide and methanol can be developed quickly….” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 388.

“But in some domains, notably transportation and chemistry, the eventual electrification, while technically feasible (and clean), may be less efficient and may consume more of the total energy available, than is now the case.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 389.

“Was industrialization and economic growth (the chicken) the root cause of increased demand for energy? Or was it the other way around? Was industrialization and economic growth an indirect consequence of the availability (declining prices) of energy resources (‘the egg’)? I think the availability of low-cost energy resources (the egg) definitely came first, back in the eighteenth century.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 389.

“The point is that there is no third category of payments in the national accounts. There are no payments ‘to energy’ or ‘resources’ or ‘natural capital’, as such, because there is no economic agent to receive that money and then spend it on something else. Payments from people always go to other people wearing different hats…. Thus energy (and exergy), from this perspective, are ‘produced’ by enterprises employing some combination of labor and capital.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 390.

“Without doubt, education and social learning are both important in today’s world. But I doubt that either education or social learning played a significant role in eighteenth century Europe, contrary to the popular idea that the ‘scientific revolution’ initiated by Copernicus, Galileo, Newton et al. somehow triggered the industrial revolution. Instead, I see resource discoveries, in response to scarcities, together with invention (by trial and error) of ways to use the new resources, as the major drivers of technological change until the last decade of the twentieth century.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 391.

“To summarize: it is evident that the discovery of coal and subsequently petroleum both incubated and financed a great many of the technologies upon which contemporary society depends. The mechanism that triggered economic growth was always the same: a technological improvement made the resource itself cheaper, or made a product made from the resource cheaper and better. That triggered increased demand. In some cases, it created whole new products and industries, as exemplified by the examples of cheap steel, internal combustion engines, electrification, electronics and information technology. Those inventions and innovations vastly increased the productivity of our economy, in the literal sense of increasing output per worker-hour.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 399.

“It is indisputable that the world economy, at least through the first three quarters of the twentieth century, depended essentially on technologies ‘incubated’ by the discovery and exploitation of coal and petroleum, not to mention other natural resources.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 399.

“Moreover, most of the products and industries that drove nineteenth century economic growth–the steam engine and the railroad, iron and steel, gas-light, coal-tar chemicals and electric power generation from steam turbines–were direct consequences of the use of coal. Similarly, the main driver of twentieth century growth, except for electrification, has been the internal combustion engine (and motor vehicles), direct consequences of the availability of liquid fuels from petroleum. All were due to overcoming various technological challenges.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 408.

“… it is useful to think of capital in energetic terms by making a distinction between ‘active capital’ and ‘passive capital.’ For animals the active components are muscles, the digestive system, the cardio-vascular system and the brain, while the passive components are bones and skin. In the economy the active components are human workers (actually only their eyes, hands and brains) plus information processing equipment (computers, telephones, etc.) and power-projection equipment consisting of engines, motors, generators, and machines with moving parts. Passive capital in the economy consists of structures that exist mainly to support, contain and protect the active capital equipment. The latter also includes ‘infrastructure’ (roads, rails, bridges, tunnels, harbors, pipelines, electrical transmission lines). It also includes knowledge and intellectual capital.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 423.

“Money also moves through the economy, much like oxygen in the blood. Money can be active (financing investment) or passive (repayment of debt).” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 423.

“The difference between work, in the technical sense, and useful work arises from the existence of human intention and control.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 429.

“As a starting point, it is useful to distinguish two kinds of wealth. One is created by humans: it is economic wealth. Part of it is passive, although it may be replicated: literature, music and art–or pure knowledge–that contributes to quality of life or happiness. The rest is productive ‘capital’, both passive and active. Financial wealth is ‘active’ if it can be exchanged for ‘real’ wealth in a marketplace, or if it enables the production of ‘real’ goods….

“The other kind of wealth can be characterized as ‘gifts of nature’. Some of it is passive, but exchangeable and monetizable, like minerals in the ground, or rights to exclusive access (e.g. to water rights, salmon fishing, rights on Scottish rivers, hunting licenses for scarce animals, or access to beaches). Another part is cultural and social. These things can be enjoyed but they do not produce more of themselves. There is an important category of wealth that is non-exchangeable and monetizable (no markets) but that contributes to health and productivity: clean air, clean water, and the waste assimilation (and detoxification) capacity of natural systems. To that might be added our culture, our ‘rights’ (such as free speech, equal opportunity), our safety and security provided by the State, public health, public education, and infrastructure, ranging from roads and streets to parks and schools.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 431.

“Liquid assets are cash or assets that can be sold for cash quickly in an existing market. Again, the existence of the market is fundamental. When there is no market, there is no financial wealth.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 431.

“Neither definition [of capital] adequately accounts for intellectual capital such as skills, patents, copyrights, art or old movies. Nor does it properly take into account empty buildings, undistributed corporate profits sitting in overseas banks, or underground reserves of coal, oil, gas or other potentially valuable minerals.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 434.

“My point is that economic wealth in the real world is based on productive assets (active capital) and is not closely related to economic activity or income. The cathedrals constructed at great cost in the Middle Ages consumed wealth but created GNP. They are tourist assets today. The religious wars after the Reformation consumed immense wealth and produced none, but they did constitute economic activity.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 437.

“The seemingly endless dispute between Keynesians and anti-Keynesians boils down to an argument between those who trust governments despite plenty of evidence of poor decisions by politicians, and those who don’t trust governments but trust ‘the market’, despite plenty of evidence of market failures and even criminal behavior.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 457-8.

“His [Mancur Olson’s] theory basically argues that political stability contains the seeds of its own destruction, very much like climax forests. Borrowing another metaphor from biological evolution, political stability is like oxygen photosynthesis: the longer photosynthesis goes on, the more it poisons the air with toxic oxygen. In the economy, it permits the formation of destabilizing networks of narrowly focused special-interested groups, such as cartels, lobbying organizations, political splinter groups and ideologies. Those narrow interest groups working against each other gradually impede decision-making, and choke off growth.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 458.

“The core point of the Minsky-Keen thesis is that banks do not just lend the money of their depositors. They create money and debt simultaneously, as pointed out earlier. Debt tends to grow faster than output. This means the banks also create imbalances.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 458-9; reference: Keen, Steve. 2011. “A monetary Minsky model of the Great Moderation and the Great Depression.” Journal of Economic Behavior and Organization. 86:221-235.

“It is qualitatively clear that economic growth cannot continue without limit for a variety of reasons, already touched upon. What is lacking is an endogenous anti-growth mechanism that can be incorporated in growth models. Currently, profit maximization or cost minimization and utility maximization are found virtually everywhere in economic models, large and small….

“There is no mechanism in the current models to reflect the anti-growth forces (such as debt accumulation, oligopoly, and externalities) that also exist….

“Another anti-growth trend has received almost no attention from economists. That is the declining ‘ore grade’ of all natural resources.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. pp. 462-3.

“… the ‘cowboy economy’, which our grandfathers or their grandfathers enjoyed, in contrast to the ‘space-ship economy’ where our children and grand-children will actually need to live. In a spaceship economy, products that deliver a service need to be designed for very long–virtually infinite–lifetimes. Re-use, refurbishing, renovation, and remanufacturing must be central features of the economic system of spaceship Earth.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 469.

“Consider the energy (actually exergy) return on energy invested, or EROI. The point is that EROI for petroleum has been declining rapidly; it was over 100:1 in 1930 and (globally) is now down to about 20:1. For deep-water wells, oil sands and shale fracking, the EROI is much lower. That is physics, not economics. But a lower EROI (10:1 or 5:1) means the magnitude of energy expenditure needed to keep the overall level of consumption steady doubles, and doubles again. When EROI for hydrocarbons gets close to 1:1, the fossil fuel game is over.” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 473.

“The loss of rare by-product metals that are not now being recoverd from mining of major industrial metals is a serious and unnecessary depletion problem for the planet Earth. Moreover, the waste is quite unnecessary. The technology to recover most of the rare by-product metals is well established. The problem is that prices are not high enough, at present, to justify the additional investment….

“For argument’s sake, I wonder if a stockpile of scarce by-product metals could become an actual currency base, in parallel with conventional paper money and the new ‘bitcoins.’” Ayres, Robert. 2016. Energy, Complexity and Wealth Maximization. Springer. p. 478.

“The result [of author’s college education in biology] was that the ensuing, increasingly unmemorable, and mostly irrelevant vocabulary of biology became more important than the subject itself. In the end, my formal education in college had the not-unexpected result of expunging from me virtually all of the wonders of biology that had inspired me as a child. Wonder gave way to a formalized language and ritualized culture of science. It is a philosophical cult that is ingrained in most aspiring scientists so rigidly that core questions, such as What is life? When did life originate? and How does it work? become distant memories, if every they were asked in the first place.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 7.

“… the evolution of microbial nanomachines allowed organisms across the planet to become connected via their internal machinery in a giant electron circuit. This circuit is based largely on transfers of hydrogen to and from four of the six principal elements: carbon, nitrogen, oxygen, and sulfur.

“To connect the metabolism between organisms requires some kind of ‘wires,’ and the ocean and the atmosphere are the two major ‘wires’ on Earth.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 87.

“I estimate there are only about 1500 core genes required for the synthesis of all the nanomachines in nature. All of them occur in microbes. That estimate may be a bit conservative–but let’s assume that even if it is off tenfold, it means that of the approximately 60 million to 100 million genes in nature, only between 0.0015% and 0.025% of them contain critical information for life….

“Because the genes encoding for the parts of the core nanomachines are so highly conserved, I refer to them as ‘frozen metabolic accidents.’” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 96.

“Sex helped reduce the prevalence of horizontal gene transfer.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 106.

“The evolution of eukaryotes is the story of horizontal gene transfer on an immense scale–wholesale invasion of one organism by another.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 107.

“If the gas mixture in our guts is not at equilibrium with the atmosphere of the planet, then it follows that the ensemble of all the consortia of microbes in the guts of all animals are not in equilibrium with metabolic pathways on the planet.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 114.

“Microbes create a global market for electrons that is stabilized by the integration of the metabolism of hundreds of billions of consortia spread across the planet–from the surface films on lakes to hundreds of meters into the sediments and rocks in the deep sea. The metabolism of Earth is an outcome of a consortium of consortia in which an individual consortium is dispensable, but the machines for all electron transfer reactions are distributed nonrandomly, depending on opportunity and accessibility of resources. Nature’s insurance policy is to spread the risk primarily by investing in a global microbial electron hedge fund. The investment is in the potential of nanomachines to operate based on the availability of any molecule in the environment that can serve as either a source of or a sink for electrons.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 114.

“To form a multicellular animal, cells had to evolve four basic traits. They needed a shared power supply. They had to adhere to each other in precise way. They had to share functions communally for the organism, rather than only for themselves. And they had to reproduce that template again and again and again. These four traits had to function together, like a choreographed theater performance.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 128.

“The burial of organic matter in the ocean’s sediments, and the attendant rise of oxygen in Earth’s atmosphere, was dramatically hastened with the evolution of phytoplankton. Unlike their prokaryotic ancestors, which barely sank in the oceans because they were so small (the viscosity of water helped keep them suspended), eukaryotic phytoplankton could sink rapidly. Their evolution and subsequent death and burial in the sediments of the ancient oceans led to a long-term sequestration of organic matter and, as a consequence, helped give a boost in Earth’s oxygen concentration. The boost in atmospheric oxygen occurred about 700 million years ago, approximately 1.7 billion years after the Great Oxidation Event.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. pp. 129-130.

“Cellulose does not require any nitrogen or phosphorus–only carbon, oxygen, and hydrogen, all of which are abundant. Additionally, cellulose and its derivatives are difficult for most microbes to break down… Cellulose gives plants structural support on land, and when land plants die, some of the cellulose is incorporated into the soil and some is washed to the ocean, where it becomes incorporated into sediments.

“Like the burial of single-celled photosynthetic eukaryotes 500 million years earlier, the evolution and death of land plants boosted the oxygen concentration in Earth’s atmosphere–big time…. It is estimated that because of the rise and death of large land plants that were the forerunners of modern trees, the concentration of oxygen in Earth’s atmosphere 350 million years ago was about 35%–or about 67% more than at present.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 141.

“The list of alterations of microbes and other organisms attempted every day [by synthetic biologists] is virtually endless. Most of these efforts are noble attempts to develop a future that is sustainable for humans, but the lack of understanding of the unintended consequences for the evolutionary trajectory of life on Earth is very seldom considered.” Falkowski, Paul. 2015. Life’s Engines: How Microbes Made Earth Habitable. Princeton UP. p. 172.

“And overwhelmingly, the natural and social sciences are currently producing a slew of what I have provisionally called pantheologies. Despite their steadily secular self-identification, these sciences are generating rigorous, awestruck, and even reverential accounts of creation, sustenance, and transformation–processes that are wholly immanent to the universe itself.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. xix.

“By ‘the table, and the law as table,’ Foucault has in mind the whole chart of oppositions that Aristotle ascribes to Pythagoras, and that Western philosophy keeps extending and expanding: namely, the ‘table’ that opposes mind to body, human to animal, male to female, the unchanging to the changing, the rational to the irrational, the spiritual to the material, perfection to imperfection, light to darkness, activity to passivity, etc. As deconstructive thinkers have been pointing out for decades, the first of each of these terms maintains its historical privilege by denigrating and repudiating the second, which turns out to be its condition of possibility. And strikingly, the first set of terms includes all the characteristics that Western metaphysics has traditionally associated with God, while the second set includes the characteristics associated with the world, or creation, or nature. God is said to be anthropomorphic, unchanging, rational, and masculine while the world is coded as animal-vegetal, changeable, irrational, and feminine.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. pp. 2-3.

“To be sure, there are numerous reasons one might opt for panentheism rather than pantheism; panentheists might hold an a priori commitment to the ontological distinction between God and the world, or they might worry that pantheism’s identity forecloses difference, or both of these at once. As such, panentheists call upon the ‘en’ to ensure the separation between God and world that enables their relation.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 4.

“In his reading of American transcendentalism, Richard Hardack argues that the transcendental movement emerged as a white, romantic appropriation of Native American ‘animism’ on the one hand and African possession traditions on the other. In Emerson and Melville, Hardack shows, the landscape that becomes divine becomes in the same breath primitive, feminine, and racialized–specifically, black.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 7; reference: Hardack, Richard. 2012. Not Altogether Human: Pantheism and the Dark Nature of the American Renaissance. U of Massachusetts Press.

“Meanwhile, at the other end of the theological spectrum, we find even the apocalyptic horseman Richard Dawkins deriding pantheism as a ‘sexed-up atheism.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 20.

“For the monist, [William] James explains, the world is one ‘tremendous unity,’ in which ‘everything is present to everything else in one vast instantaneous co-implicated completeness’. For the pluralist, by contrast, the things of the world are ‘in some respects connected, [and] in other respects independent, so that they are not members of one all-inclusive individual fact’. Monism tell [sic] us that everything is connected to everything else, whereas pluralism affirms that connections come and go–that ‘a bit of reality when actively engaged in one of these relations is by that very fact engaged in all the other relations simultaneously’. Monism is the ‘philosophy of the absolute,’ of idealism and ‘the all-form,’ whereas pluralism opts for empiricism and ‘the each-form,’ thinking that ‘there may ultimately never be an all-form at all’….

“But James sides with pluralism for a host of ethical, political, and psychological reasons: if we affirm a messy plurality rather than a perfect totality, then ‘evil’ calls for a practical response rather than a speculative explanation; differences of opinion are signs of health rather than pathology; and our everyday experiences amount to ‘intimacy’ with the universe itself.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. pp. 21-2; references: James, William. 1996 [1908]. A Pluralistic Universe. U of Nebraska Press. pp. 37, 322, 55, 34.

“If it is the case as Philip Clayton suggests, that ‘no philosophically adequate form of pantheism has been developed in Western philosophy,’ then the absence is even more striking in the case of pluralist pantheism–if there even is such a thing…. Far from dreaming up such a position ex nihilo, then, this study seeks to show it is already in subtle formation….” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 24; reference: Clayton, Philip. 2000. The Problem of God in Modern Thought. Grand Rapids: Eerdmans.

“Young writers like Goethe, Herder, and Fichte suddenly appealed to Spinozist pantheism as an alternative to what they saw as superstitious theism on the one hand and a cold, mechanical deism on the other. Thus, Beiser proclaims, ‘the scapegoat of the intellectual establishment became its hero,’ and ‘pantheism became, as Heine later put it, ‘the unofficial religion of Germany.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 34; reference: Beiser, Frederick. 1987. The Fate of Reason: German Philosophy from Kant to Fichte. Harvard UP. pp. 44-5.

“Among the many errors of the tragically confused commonfolk, the most fundamental, according to Spinoza, is their anthropocentrism. ‘They imagine Nature to be so limited,’ he laments, ‘that they imagine man to be its chief part.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 42; reference: Spinoza, Baruch. 1998. Theological-Political Treatise. transl. Samuel Shirley. Indianapolis: Hackett. p. 73.

“Both with and against Descartes, Spinoza argues that there are not two substances, but one. Calling upon his predecessor’s own definition of substance, Spinoza reasons that if a substance is that which relies on nothing outside itself, then ‘there can be, or be conceived, no other substance but God.’ Rejecting Descartes’ analogical compromise, Spinoza insists that thought and extension are in no sense ‘substances. Rather, insofar as they rely on God for their existence, they must be attributes of God Godself, who alone can be called a substance, according to Descartes’ own definition…. Substance must therefore be infinite, and this infinite substance, at once mental and corporeal, is both what we commonly call ‘God’ and what we mean when we say the word ‘nature.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 45; subquotes: Spinoza, Baruch. 1992. “Ethics.” pp. 31-223. Feldman, Seymour (ed.) Ethics, Treatise on the Emendation of the Intellect, and Selected Letters. Translated by Samuel Shirley. Indianapolis: Hackett.

“In Aristotle’s demythologized cosmogony, we similarly find matter lying in wait for another principle to discipline, order, and shape it; as he explains, it is matter’s ‘own nature to desire and yearn for [form].’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 66; subquote: Aristotle. 1984. “Physics.” Barnes, Jonathan (ed.) Complete Works of Aristotle. Princeton UP. 1.9.192a16-17.

“Humanity’s chief error in this regard is its conviction that the harmonious order of the universe–its tides and crops and seasons–are evidence of one or more all-powerful deities who made the world ‘for our sake,’ and who did so in excess of all existing physical principles, which is to say ‘out of nothing’. Insofar as people perceive the world to be an unmatchable gift, they feel perpetually indebted to the gods who gave it. And insofar as they perceive the divine function to be supernatural, they believe the gods to lie beyond the bounds of earthly power, reason, or morality. In an effort to repay those inscrutable gods, or to win their favor, people thus deceived will enact endless rituals, no matter how pointless, demeaning, or even murderous….

“The surest way to end this madness, Lucretius suggests, would be to realize that the world is not nearly as well ordered as we have been led to believe. Rather than marveling at the regularity of its sunrises and sunsets, or of its evaporation and rain, we might reflect instead upon its arid land, hostile plants, ‘savage beasts,’ or ‘rocky crags and desolate fens’–not to mention death, disease, and misery. ‘My point,’ Lucretius summarizes, is that the universe was not created for our sake / By powers divine, since as it stands it is so deeply flawed.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. pp. 73-4; subquotes: Lucretius. 2007. The Nature of Things. Translation: A.E. Stallings. Penguin. 2.172, 1.150, 5.198-226.

“Far from having been wrought by eternal providence, he explains, the world was born in a series of random collisions that just happened to give rise to things as they are: ‘by trying every motion and combination, they at last / Fell into the present form in which this universe appears.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 74; subquote: Lucretius. 2007. The Nature of Things. Translation: A.E. Stallings. Penguin. 1.1026-27.

“And indeed, it is certainly the case that each of them affirms the cosmic immanence of creation, as well as the identity of the creator with the world itself. That having been said, the creative agent for Lucretius is utterly lacking in a quality that is central to Spinoza’s theo-cosmology (and to that of the Stoics, for that matter): namely, reason. Whereas Spinozan thought, like the Stoic nous, is inherent to the material order, it is simply absent for the Epicureans; ‘for certainly the elements of things do not collect / And order their formation by their cunning intellect,’ reasons Lucretius, ‘Nor are their motions something they agree on or propose. There is no plan, no goal, no mind in matter–just particulate bumblings that occasionally form remarkable things by the sheer power of accident, enacted through infinite time.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. pp. 74-5; subquote: Lucretius. 2007. The Nature of Things. Translation: A.E. Stallings. Penguin. 1.1021-23.

“Theologically speaking, then, what this ‘strictly physical’ dialogue [by Bruno 1548-1600 when he was burned at the stake] has done is to call each of the divine faculties down into nature itself–all the while pretending not to speak of God. It is precisely by bracketing the ‘supreme first principle’ that Bruno goes on to render such a principle irrelevant, leaving us with an omni-formed, ensouled matter as the creator and end of all things. Insofar as this created creator is both intellectual and extended, Bruno’s ‘cause and principle’ of the universe looks less like the riot of Epicurean atoms than the ‘multi-unitary’ Spinozan substance it goes on to influence–whether directly or indirectly. And indeed, just as Spinoza will proceed to do, Bruno argues that each of the particular things of the world is a mode of this cause and principle; in his words, ‘the uniform substance is one… which manifests itself through innumerable particularities and individuals, showing itself in countless, concrete, individual substances’. Again, Bruno is not as careful as Spinoza will be (in the wake of Descartes) with respect to his use of the term ‘substance.’ Nevertheless, the conviction is the same: the manifold animals, vegetables, and minerals around us are all physical and ideational expressions of the same substance, which does not exist independently of its expressions and for that reason is many in its oneness–or in Filoteo’s words, ‘multi-modal.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 84; references: Bruno, Giordano. 1998 [1584]. “Cause, Principle and Unity.” Blackwell, Richard (ed.) Cause, Principle and Unity and Essays on Magic. Translated by Richard Blackwell. Cambridge UP.

“Far more recently than [pre-Socratic] Anaxagoras, Nicholas of Cusa [1401-1464] had taught this same precept as a theological principle: God is present everywhere throughout the boundless universe, he argued, and as such God is as fully present in a mustard seed as in a man. This radical indwelling is, in fact, what it means for Cusa to call God ‘creator’ in the first place: ‘creating,’ he ventures, ‘seems to be not other than God’s being all things.’ And to the extent that God is the being of all things and things dwell reciprocally in God, it can in fact be said that ‘all are in all and each are in each.’

“Although the logic is nearly indistinguishable from Cusa’s, Teofilo [from Bruno’s dialogue] does perform two major but subtle departures from his more orthodox predecessor. First, as we will continue to see, he effectively eliminates the Cusan difference between God and the universe, entreating us by virtue of this entangled animacy not to ‘look for the divinity outside of the infinite world and the infinity of things, but inside this world and those things.’ Second, he qualifies the Cusan-Anaxagoran proclamation of ‘all things in all things’ with a pre-Spinozan principle of particularity: ‘Everything is in everything,’ Teofilo affirms, ‘but not totally or under all modes in each thing.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. pp. 85-6; subquotes: Bruno, Giordano. 1998 [1584]. “Cause, Principle and Unity.” Blackwell, Richard (ed.) Cause, Principle and Unity and Essays on Magic. Translated by Richard Blackwell. Cambridge UP. pp. 82, 90.

“Considering Bruno’s August place in this scientific lineage, it is perplexing that so few of his teachings have been incorporated into the purportedly secular domain of inquiry to which he purportedly gave birth. Although he can perhaps be credited with circulating Copernican cosmology and contributing to its eventual victory over geocentrism, almost none of Bruno’s own ideas was adopted by his alleged successors. Neither Galileo nor Bacon nor Newton nor Einstein believed the universe to be infinite, much less filled with infinite, inhabited worlds. None of them embraced his turn to theurgy and necromancy to describe the interactions of bodies. And absolutely none of them proclaimed the divine animacy of all things by virtue of the spiritual-material world soul. Rather, modern science ‘freed’ the material world from its ecclesiastical imprisonment only to intensify matter’s traditional degradation.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 88.

“A person for the Ojibwa is a being who can act, speak, move, and change–and as such, the sun is not a thing or an object, but rather a person ‘of the other-than-human class’….

“As such, their [rocks and animals] animacy is not a matter of belief but rather of relation; to affirm that this tree, that river, or the-bear-looking-at-me is a person is to affirm its capacity to interact with me–and mine with it. As Tim Ingold phrases the matter, ‘we are dealing here not with a way of believing about the world, but with a condition of living in it’…. Hence Graham Harvey’s redefinition of ‘animists’ as ‘people who recognise that the world is full of persons, only some of whom are human, and that life is always lived in relationship with others.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 93; references: Ingold, Tim. 2011. “Rethinking the Animate, Re-Animating Thought.” Ethnos: Journal of Anthropology. 71(1):9-20. p. 10; Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. xi.

“In her most recent work, Haraway proposes the term ‘Chthulucene’ as an immanent elsewhere to the Anthropocene and Capitalocene, each of which manages to reaffirm the untrammeled power of the particularly white, over-developed human agents at their centers, and to make them once again in the image of God. Reminding us that ‘the Greek chthonios means ‘of, in, or under the earth or seas,’’ Haraway configures the Chthulucene as the ongoing project of the irreducibly terrestrial. ‘The Chthonic ones are precisely not sky gods,’ she insists, ‘not a foundation for the Olympiad… and definitely not finished.’ They are, rather, earthly creators, working from the messy middle of things to make the multispecies kinship structures that amount to worlds. In this work, Haraway’s ‘chthonic ones’ are led not by Man, but by those fungal, bacterial, vegetable, and animal earth-others, who know best how to become-with one another in order to compose and decompose cosmoi….

“In their ongoing cosmogonic labors, the chthonic ones therefore allow us to begin to form a fully immanent, nonanthropic vision of divinity: what we mean by god(s) in a Harawayan register would be nothing more or less than the sympoietic world(s) in ongoing (de)composition.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. pp. 135-6; references: Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 53.

“Indeed, there is no ‘problem of evil’ for those non-monotheistic cosmogonies that affirm a proliferation of shape-shifters, tricksters, and demiurges; their answer to the question of the origin of evil is simply that there have been competing interests among limited beings from the very beginning–and that the beginning has always been in the middle of things…. ‘Evil’ in such frameworks is therefore not a mystery to be explained but rather a concrete reality to negotiate and try to overcome.” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 177.

“Because the Christian tradition cannot abide death, it explains death as the consequence of sin rather than the result of nonnegotiable physical processes. ‘In Indian religions,’ by contrast, ‘death is a natural occurrence and not a special punishment from an arbitrary God.’ Death in this context is a sadness to be mourned, but not ‘an occasion for probing the rationale of whatever reality exists beyond ourselves.’” Rubenstein, Mary-Jane. 2018. Pantheologies: Gods, Worlds, Monsters. Columbia UP. p. 178; subquote: Deloria, Vine Jr. 1969. Custer Died for Your Sins: An Indian Manifesto. NY: Macmillan. p. 120.

“In his execution [Giordano Bruno’s in 1600] there was an unconscious symbolism: for the subsequent tone of scientific thought has contained distrust of his type of general speculativeness.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 1.

“The Greek view of nature, at least that cosmology transmitted from them to later ages, was essentially dramatic. It is not necessarily wrong for this reason: but it was overwhelmingly dramatic. It thus conceived nature as articulated in the way of a work of dramatic art, for the exemplification of general ideas converging to an end. Nature was differentiated so as to provide its proper end for each thing.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 7-8.

“It is a great mistake to conceive this historical revolt [the Scientific Revolution] as an appeal to reason. On the contrary, it was through and through an anti-intellectualist movement. It was the return to the contemplation of brute fact; and it was based on a recoil from the inflexible rationality of medieval thought.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 8.

“Their [great tragedians of ancient Athens, Aeschylus, Sophocles, Euripides] vision of fate, remorseless and indifferent, urging a tragic incident to its inevitable issue, is the vision possessed by science. Fate in Greek Tragedy becomes the order of nature in modern thought.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 10.

“Let me here remind you that the essence of dramatic tragedy is not unhappiness. It resides in the solemnity of the remorseless working of things.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 10.

“I do not think, however, that I have even yet brought out the greatest contribution of medievalism to the formation of the scientific movement. I mean the inexpugnable belief that every detailed occurrence can be correlated with its antecedents in a perfectly definite manner, exemplifying general principles. Without this belief the incredible labours of scientists would be without hope. It is this instinctive conviction, vividly poised before the imagination, which is the motive power of research: – that there is a secret, a secret which can be unveiled.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 12.

“In the background the Byzantine Empire, under Justinian, in three ways determined the character of the early Middle Ages in Western Europe. In the first place, its armies, under Belisarius and Narses, cleared Italy from the Gothic domination. In this way, the stage was freed for the exercise of the old Italian genius for creating organisations which shall be protective of ideals of cultural activity….

“In the second place, the codification of the Roman law established the ideal of legality which dominated the sociological thought of Europe in the succeeding centuries….

“Thirdly, in the non-political spheres of art and learning Constantinople exhibited a standard of realised achievement which, partly by the impulse to direct imitation, and partly by the indirect inspiration arising from the mere knowledge that such things existed, acted as a perpetual spur to Western culture…. No account of the rise of the European scientific mentality can omit some notice of this influence of the Byzantine civilisation in the background. In the sixth century there is a crisis in the history of the relations between the Byzantines and the West; and this crisis is to be contrasted with the influence of Greek literature on European thought in the fifteenth and sixteenth centuries.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 13-4.

“In particular, we owe it to St. Benedict that the monasteries were the home of practical agriculturalists, as well as of saints and of artists and men of learning. The alliance of science with technology, by which learning is kept in contact with irreducible and stubborn facts, owes much to the practical bent of the early Benedictines.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 15.

“Science has never shaken off the impress of its origin in the historical revolt of the later Renaissance. It has remained predominantly an anti-rationalistic movement, based upon a naive faith. What reasoning it has wanted, has been borrowed from mathematics which is a surviving relic of Greek rationalism, following the deductive method. Science repudiates philosophy. In other words, it has never cared to justify its faith or to explain its meanings; and has remained blandly indifferent to its refutation by Hume.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 16.

“Now the scientific philosophy of this age [seventeenth century] was dominated by physics…. As a matter of fact, these concepts are very unsuited to biology; and set for it an insoluble problem of matter and life and organism, with which biologists are now wrestling.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 41.

“Furthermore, this fact that the material is indifferent to the division of time [in classical physics] leads to the conclusion that the lapse of time is an accident, rather than of the essence, of the material. The material is fully itself in any sub-period however short. Thus the transition of time has nothing to do with the character of the material.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 50.

“This is the famous mechanistic theory of nature, which has reigned supreme ever since the seventeenth century. It is the orthodox creed of physical science. Furthermore, the creed justified itself by the pragmatic test. It worked. Physicists took no more interest in philosophy…. But the difficulties of this theory of materialistic mechanism very soon became apparent. The history of thought in the eighteenth and nineteenth centuries is governed by the fact that the world had got hold of a general idea which it could neither live with nor live without.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 50.

“It is at once evident that the concept of simple location is going to make great difficulties for induction. For, if in the location of configurations of matter throughout a stretch of time there is no inherent reference to any other times, past or future, it immediately follows that nature within any period does not refer to nature at any other period…. In other words, the order of nature cannot be justified by the mere observation of nature. For there is nothing in the present fact which inherently refers either to the past or to the future. It looks, therefore, as thought memory, as well as induction, would fail to find any justification within nature itself.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 51.

“I also express my conviction that if we desired to obtain a more fundamental expression of the concrete character of natural fact, the element in this scheme which we should first criticise is the concept of simple location…. To say that a bit of matter has simple location means that, in expressing its spatio-temporal relations, it is adequate to state that it is where it is, in a definite finite region of space, and throughout a definite finite duration of time, apart from any essential reference of the relations of that bit of matter to other regions of space and to other durations of time.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 57-8.

“In the second half of the [eighteenth] century, Lavoisier practically founded chemistry on its present basis. He introduced into it the principle that no material is lost or gained in any chemical transformations. This was the last success of materialistic thought, which has not ultimately proved to be double-edged.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 60.

“The things which are grasped into a realised unity, here and now, are not the castle, the cloud, and the planet simply in themselves, but they are the castle, the cloud, and the planet from the standpoint, in space and time, of the prehensive unification. In other words, it is the perspective of the castle over there from the standpoint of the unification here. It is, therefore, aspects of the castle, the cloud, and the planet which are grasped into unity here.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 69-70.

“For each volume of space, or each lapse of time, includes in its essence aspects of all volumes of space, or of all lapses of time. The difficulties of philosophy in respect to space and time are founded on the error of considering them as primarily the loci of simple locations. Perception is simply the cognition of prehensive unification; or more shortly, perception is cognition of prehension.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 71.

“Thus a prehension has simple location at the volume A in the same way as that in which a man’s face fits on to the smile which spreads over it.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 71.

“It is necessary to understand that space-time is nothing else than a system of pulling together of assemblages into unities. But the word event just means one of these spatio-temporal unities. Accordingly, it may be used instead of the term ‘prehenshion’ as meaning the thing prehended.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 72.

“It is the defect of the eighteenth century scientific scheme that it provides none of the elements which compose the immediate psychological experiences of mankind. Nor does it provide any elementary trace of the organic unity of a whole, from which the organic unities of electrons, protons, molecules, and living bodies can emerge. According to that scheme, there is no reason in the nature of things why portions of material should have any physical relations to each other.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 73.

“… the two attitudes [in Western mentality] involved are inconsistent. A scientific realism, based on mechanism, is conjoined with an unwavering belief in the world of men and of the higher animals as being composed of self-determining organisms. This radical inconsistency at the basis of modern thought accounts for much that is half-hearted and wavering in our civilisation.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 76.

“The remaining pair of new ideas to be ascribed to this epoch are both of them connected with the notion of transition or change. They are the doctrine of the conservation of energy, and the doctrine of evolution.

“The doctrine of energy has to do with the notion of quantitative permanence underlying change. The doctrine of evolution has to do with the emergence of novel organisms as the outcome of chance.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 100-1.

“The conservation of energy provided a new type of quantitative permanence. It is true that energy could be construed as something subsidiary to matter. But, anyhow, the notion of mass was losing its unique preeminence as being the one final permanent quantity. Later on, we find the relations of mass and energy inverted; so that mass now becomes the name for a quantity of energy considered in relation to some of its dynamical effects. This train of thought leads to the notion of energy being fundamental, thus displacing matter from that position. But energy is merely the name for the quantitative aspect of a structure of happenings; in short, it depends on the notion of the functioning of an organism. The question is, can we define an organism without recurrence to the concept of matter in simple location?” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 101-2.

“… in truth, a thoroughgoing evolutionary philosophy is inconsistent with materialism. The aboriginal stuff, or material, from which a materialistic philosophy starts is incapable of evolution.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 107.

“But the whole point of the modern doctrine [of evolution] is the evolution of the complex organisms from antecedent states of less complex organisms. The doctrine thus cries aloud for a conception of organism as fundamental for nature.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 107.

“But if the enduring pattern is wholly derived from the direct aspects of the various temporal sections of the event in question, then th endurance is an important intrinsic fact… Let us use the term physical endurance to express endurance of this type. Then physical endurance is the process of continuously inheriting a certain identity of character transmitted throughout a historical route of events. This character belongs to the whole route, and to every event of the route. This is the exact property of material. If it has existed for ten minutes, it has existed during every minute of the ten minutes, and during every second of every minute. Only if you take material to be fundamental, this property of endurance is an arbitrary fact at the base of the order of nature; but if you take organism to be fundamental, this property is the result of evolution.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 108.

“On the organic theory of nature there are two sorts of vibrations which radically differ from each other. There is vibratory locomotion, and there is vibratory organic deformation; and the conditions for the two types of changes are of a different character. In other words, there is vibratory locomotion of a given pattern as one whole, and there is vibratory change of pattern.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 131.

“Modern philosophy is tinged with subjectivism, as against the objective attitude of the ancients. The same change is to be seen in religion. In the early history of the Christian Church, the theological interest centred in discussions on the nature of God, the meaning of the Incarnation, and apocalyptic forecasts of the ultimate fate of the world. At the Reformation, the Church was torn asunder by dissension as to the individual experiences of believers in respect to justification. The individual subject of experience had been substituted for the total drama of all reality. Luther asked, ‘How am I justified?’; modern philosophers have asked, ‘How do I have knowledge?’ The emphasis lies upon the subject of experience. This change of standpoint is the work of Christianity in its pastoral aspect of shepherding the company of believers. For century after century it insisted upon the infinite worth of the individual human soul. Accordingly, to the instinctive egotism of physical desires, it has superadded an instinctive feeling of justification for an egotism of intellectual outlook. Every human being is the natural guardian of his own importance.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. pp. 140-1.

“The ancient world takes its stand upon the drama of the Universe, the modern world upon the inward drama of the Soul.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 141.

“The Greek gods who surrounded Aristotle were subordinate metaphysical entities, well within nature.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 173.

“In formal logic, a contradiction is the signal of a defeat, but in the evolution of real knowledge it marks the first step in progress towards a victory.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 187.

“Religion will not regain its old power until it can face change in the same spirit as does science.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 189.

“The worship of God is not a rule of safety–it is an adventure of the spirit, a flight after the unattainable. The death of religion comes with the repression of the high hope of adventure.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 192.

“The moral discipline [at the time just before Descartes] had emphasised the intrinsic value of the individual entity. This emphasis had put the notions of the individual and of its experiences into the foreground of thought. At this point the confusion commences. The emergent individual value of each entity is transformed into the independent substantial existence of each entity, which is a very different notion….

“Also the independence ascribed to bodily substances carried them away from the realm of values altogether. They degenerated into a mechanism entirely valueless, except as suggestive of an external ingenuity. The heavens had lost the glory of God. This state of mind is illustrated in the recoil of Protestantism from aesthetic effects dependent upon a material medium. It was taken to lead to an ascription of value to what is in itself valueless. This recoil was already in full strength antecedently to Descartes. Accordingly, the Cartesian scientific doctrine of bits of matter, bare of intrinsic value, was merely a formulation, in explicit terms, of a doctrine which was current before its entrance into scientific thought or Cartesian philosophy.” Whitehead, Alfred North. 1967[1925]. Science and the Modern World. NY: The Free Press. p. 195.

“The idea of life as a movement of fluid and solid parts of the organism, a movement that in itself leads necessarily to its own cessation, was standard in the eighteenth century [including for Lamarck].” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 60.

“At the same time, he [Lamarck] incorporated in his thinking much that was commonplace in his day. When he dropped his view of life as a vital principle, and when he came to believe that life in the simplest animals depended upon external stimuli rather than an incomprehensible vital force, he continued to think of life in terms of organic motion. Life remained, in his view, essentially a function of the contained fluids and the containing solids of the organized body. And in the mechanical effects of fluids moving within the living body, he found that he had an explanation not only of the phenomena of growth and development but also of organic mutability.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. pp. 61-2.

“The role of subtle fluids in plant and animal life was discussed throughout the 1780s and 1790s. There were debates concerning the reality of the effects of electricity on plant growth…. There was disagreement over the cause of animal heat (Lamaarck found that Lavoisier’s idea that respiration was a kind of combination was too extraordinary to be true, but both men explained animal heat in terms of subtle fluids–‘fire in the state of expansion’ in Lamarck’s case, ‘caloric’ in Lavoisier’s).” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 68.

“But it could not go unnoticed that the two most prominent naturalists of the eighteenth century, Linnaeus and Buffon, both set forth explanations of organic diversity involving the production of new species over time. Linnaeus proposed that God had brought certain living things into existence at the Creation and that from these, through hybridization, numerous other living things were produced. Buffon proposed that a certain number of primordial forms arose by spontaneous generation when the earth’s surface became fit for life and that the ‘degenerations’ of those forms that had been spontaneously generated in the fifth epoch of the earth’s history had resulted in all the different forms alive in the eighteenth century.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 92.

“In 1797 Lamarck thus had a basically mechanical explanation for the organic motions of plants and a similar explanation, aided by the special faculty of irritability, for animals…. The creative action of fluids in action was not prominent in his writings of 1797, but five years later, in his first major exposition of his evolutionary views, it was central.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 102.

“His [Lamarck’s] supposition that all the different minerals were produced gradually as the elements disengaged themselves from the remains of living things appears to be virtually the inverse of his later idea that all the different organic species were produced gradually as the ‘power of life’ and modifying circumstances caused simple, spontaneously generated forms to become increasingly complex and diversified.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 102.

“The step Lamarck had taken in coming to believe in spontaneous generation was critical for the development of his view of evolution. Others before him had believed in spontaneous generation without believing in evolution…. Given his long-held thoughts on the general linear arrangement of nature’s productions, … it becomes possible to appreciate the feeling he expressed in 1802 that ‘once the difficult step [of admitting spontaneous generation] is made, no important obstacle stands in the way of our being able to recognize the origin and order of the different productions of nature.’” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. pp. 139-140.

“Lamarck’s statements of his two-factor theory appear unambiguous: once life was generated in simple form at the bases of the plant and animal scales it became diversified as the result of (1) the ‘power of life’ or ‘cause that tends to make organization increasingly complex’ and (2) the modifying influence of particular circumstances.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 147.

“In the 1800s, when Bichat’s work was lending special strength to the vitalist position, Lamarck was adamant in his insistence that life was not a ‘special being’ or ‘some sort of principle, the nature of which is unknown.’” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 151.

“The reason Lamarck gave in 1815 for nature’s plan not being as simple as he had initially supposed was that ‘accidental causes have necessarily modified [the plan] here and there.’ Nature was unable to form a single series because ‘the circumstances in which she has been forced to operate have really made her produce at least two.’ The second cause of organic change had thwarted the tendency of the power of life to increase organic complexity in a regular fashion. In discussing how this second cause of organic change operated, Lamarck set forth the views for which he is most widely remembered today….

“‘The principal circumstances [nature employs in bringing into existence all her productions],’ he had explained as early as 1800, ‘arise from the influence of the climates, from the variations in temperature of the atmosphere and of all the surrounding milieux, from the diversities of places, from … habits, movements, actions, finally from the means of living, conserving oneself, defending oneself, reproducing, etc, etc.’ In 1800, having enumerated the principal ‘circumstances’ at nature’s disposal, he described the mechanism of organic change as follows: ‘Now, as a result of these diverse influences, the faculties extend and strengthen themselves through use and diversify themselves through new habits long conserved; and imperceptibly the conformation, the consistency, in a word the nature and the state of the parts as well as the organs partake of the consequences of all these influences, conserving and propagating themselves through generation.’” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. pp. 164-5.

“He looked upon the simplest animals (the ‘insensitive’ animals, or animals lacking a nervous system) as being in much the same situation as plants. The causes of activity of these animals, he supposed, were external to them. He referred to the insensitive animals as ‘totally passive machines.’ By contrast, in the ‘sensitive’ animals (the invertebrates with a nervous system), the ‘productive force of movement’ was internalized. The primary cause of the behavior of these animals was instinct, which was the product of a certain sentiment interieur, or inner feeling…. The sentiment interieur was something that functioned in a wholly mechanical fashion.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 167.

“It was easy enough for Lamarck to explain how an organ could be strengthened or weakened through use or disuse. It was not so easy for him to explain how new organs arose in the first place. He maintained that each class of animals was characterized by a distinct plan of organization, and he was quite specific in identifying what the distinct plan of organization for each class was. His attempts to explain how nature moved from one plan of organization to the next, however, were feeble.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. pp. 177-8.

“‘If I discover that nature herself… creates organization, life, even feeling; that she multiples and diversifies, within bounds that are not known to us, the organs and the faculties of the organized bodies whose existence she sustains or propagates… must I not recognize, in this faculty of nature …. the execution of the will of her sublime author, who has been able to will that she have this faculty?’” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 185.

“The guiding idea of Cuvier’s [who disliked Lamarck’s work and considered anatomy too finely structured to be able to evolve or change] work as a comparative anatomist was the functional integrity of the living organism. This idea found expression in his two anatomical rules: the ‘correlation of parts’ and the ‘subordination of characters [hierarchy of functions].’” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 193.

“In France at the beginning of the nineteenth century, Lamarck was by no means the only naturalist toying with the idea of organic mutability. Indeed, of the zoologists at the Museum d’Histoire Naturelle in the early 1800s, only Cuvier was clearly unsympathetic with the idea of organic mutability.” Burkhardt, Richard. 1977. The Spirit of System: Lamarck and Evolutionary Biology. Harvard UP. p. 202.

“… the necessary simplicity of the early universe relative to its present state means that this cannot account for all causes.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 305.

“The Turing machine is a fundamental concept in computer science: it is a conceptual machine that can in principle compute anything that is computable. So when a Turing machine was created using the plastic building toy Lego, it became possible, in principle, to make the word processor from Lego. Clearly, a word-processor is a phenomenon that is not determined by what it is made from. We shall use the term ‘transcendent complex’ (TC) for such entities because they transcend the particular method of implementation used. Their properties are that (1) they arise from the interaction among elements and (2) they may be realised in multiple ways, because they depend only on certain functions of the elements, not their whole nature. TCs are therefore multiply realisable. This concept has been described as classes of functional equivalence.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 308-9.

“Elements within an ensemble do not really interact with the TC of that ensemble; they interact only with each other. What makes the interactions act as something larger, controlling the behaviour of the elements, is the additional functionality provided by the particular configuration that gives rise to the TC. The configuration of the ensemble is one that instantiates functional information so that a TC emerges. The TC is the aggregate of this functional information, and it appears at the scale of organisation of the ensemble.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 309.

“Physical information is independent of the components used to embody it in the physical world, but its existence still depends on there being something physical to instantiate it. Additionally, physical information creates phenomena that do not belong to the component parts instantiating it. Therefore physical information is a TC [transcendent complex].” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 310.

“We can go further, since functional information is a functional relation between particular structures of physical information. That is to say: functional information is the phenomenon of function arising from one information structure providing the context for another.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 310.

“To understand it better, let’s simplify even further and think of a remote control that just switches a lamp on and off….

“The design gives the control information a context, without which it would have no ‘meaning’ in the sense that it would not be functional. To be precise, functional information is that which causes a meaningful difference: we can now interpret that as meaning it has causal power. The pure information and the regulated system of which it is a part are inseparable. This idea can be generalised to any control system: the information causes physical effects only because it is embodied within the physical system that gives it the context necessary for it to become functional. We may even go so far as to say that design is the embodiment of functional information in the physical form of a system.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 312.

“A functional equivalence class is by definition the ensemble of entities sharing in common that they perform some defined function. But a phenomenon can be functional only in a particular context, since function is always context dependent. This context is provided by the TC, which organises one or more of the members of one or more functional equicvalence classes into an integrated whole having ‘emergent properties’. The TC is an information structure composed of the interactions among its components. In practice, these make up the material body, which embodies the information that collectively constitutes the TC. It must be described in terms of functional equivalence classes because it is multiply realisable.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 316.

“The formation of a three-dimensional network of atomic interactions [in biopolymers such as proteins] is effective cause for the ability of the molecule to carry a function. However, evolution does not select for the three-dimensional shape [e.g. exact molecular structure] per se; rather, it selects the function embodied in the structure.” Farnsworth, Keith, George Ellis & L. Jaeger. 2017. “Living through Downward Causation: From Molecules to Ecosystems.” pp. 303-333. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 320.

“Norms are, in their most developed form, facts about shared ideals, about what the group believes – or, more formally, a coarse-grained representation and lossy compression of the idiosyncratic beliefs and desires held by individuals. We need not all believe exactly the same thing in order to share a norm; norms constitute a new set of group-level facts.” DeDeo, Simon. 2017. “Major Transitions in Political Order.” pp. 393-428. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 406.

“In the original account of broken windows, … minor norm violations led to an increasing likelihood of future violations (a single broken window in an abandoned building attracts more). Here, we find the reverse effect: norm-conformant actions lead to an increasing likelihood of future norm conformance.” DeDeo, Simon. 2017. “Major Transitions in Political Order.” pp. 393-428. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 411.

“Yet because of the reinforcing nature of norm bundles, shifts in behavior are rarely due to the emergence or strengthening of a single norm in isolation. Rather, when studying long-term norm-driven change, we expect signals of multiple, conceptually distinct – but bundled – norms working together.” DeDeo, Simon. 2017. “Major Transitions in Political Order.” pp. 393-428. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 417.

“GPT [general process theory] is a mono-categorial ontology that postulates only one type of entity, called ‘general process’ or, to allow for occasional transnumeral references, ‘dynamics’. According to GPT, all there is–that is, all the different sorts of entities we speak about in common sense and in science (including in the humanities)–is one variety or other of a general process or dynamics. The main task of GPT is to differentiate this basic entity type into subtypes that can form the ontological correlates for true sentences of (part of) some theory T (in common sense or in science).” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 115.

“General processes are modeled on ‘subjectless’ or ‘pure’ activities, as these are denoted by sentences that merely affirm the presence of a dynamic feature, such as ‘it is snowing’, ‘it is itching’, ‘the fire is spreading’, ‘photosynthesis occurs everywhere in your garden’.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 115.

“Subjectless activities qualify as a model for the postulated ontological category of ‘general processes’ or ‘dynamics’ to the extent that the inferential role of statements about subjectless activities illustrates the seven category features in terms of which general processes are defined. These seven categorial features [of subjectless activities] are as follows:

“(i) Statements about subjectless activities do not license the inference that there is one unique and discrete spatial location or temporal period where the denoted activities occur. A subjectless activity is an entity occurring somewhere in space and time; in other words, an entity that is concrete, yet general or non-particular, as these category features are commonly defined….

“(ii) Non-particular entities cannot be individuated in terms of their space-time location, as particular entities typically are. Instead, as subjectless activities illustrate, they are individuated in terms of their typical functioning within a dynamic context…. we individuate items in terms of what they commonly ‘do’, engender, or are involved in.

“(iii) Subjectless activities are occurrences in their own right rather than modifications of persons or thing-like things. Unlike properties and relations, they are independent in the sense that sentences such as ‘it is snowing’, … do not entail either statements about determinate single snowflakes, … or statements about any sort of medium or carrier for these activities.

“(iv) Subjectless activities are temporally extended and, like things, they are good illustrations of the category feature of being an enduring entity, that is, an entity that persists through time by being ‘identical’ in time.

“(v) Quite unlike things and much like stuffs (water, wood, etc.), subjectless activities are not countable in the sense that they do not necessarily occur in space and time pre-packaged into discrete spatio-temporally extended units that afford our common practices of counting. Since subjectless activities are individuated or differentiated in terms of their functional features, we can also count them in this way. For instance, metabolism and photosynthesis are two activities, and so are C3 photosynthesis and C4 photosynthesis.

(vi) In our reasoning about (subjectless) activities we ‘zoom in and out’. We accept that there are highly generic and also highly specific activities. For example, we may say that in a tobacco plant the following activities occur: photosynthesis, C3 photosynthesis, C3 photosynthesis in a tobacco plant, C3 photosynthesis in a tobacco plant on a window sill directed eastward, C3 photosynthesis in a tobacco plant on a window sill with spatial coordinates <x, y, z> at time t’, and so on. In other words, (subjectless) activities are a good model for entities that are said to be concrete, yet more or less indeterminate….

“(vii) Subjectless activities are not changes. Constitutive ‘phases’ of a subjectless activity–for example, the change of place of every single flake that constitutes the dynamicity of the snowing–contribute to the activity’s occurring, but not as temporal stages or phases….

“In sum, then, guided by familiar patterns of common sense reasoning, we can claim that subjectless activities can serve as a model for an entity that is concrete, non-particular, enduring, more or less indeterminate, dynamic, and individual in the sense of being functionally distinct from others.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. pp. 115-7.

“GPT is a domain theory that postulates one basic category or entity type and one basic relationship that holds among such entities, namely the relationship of ‘being part of’ in its most basic sense of ‘belonging with’, which in everyday speech is used with any entity type. In order to capture the sense of this notion of ‘being part of’, one cannot, however, resort to any of the standard mereological systems of so-called classical extensional mereology or to their intensional modifications, for these systems axiomatize part-whole relations that are informationally richer (e.g. ‘is a spatial part of’, ‘is a material part of’, ‘is a functional part of’, etc.).” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 117.

“… using the basic, not very informative part relation of ‘is part of’, which supports only weak axioms, it is possible to introduce other, more informative varieties of parthood (spatial parts, material parts, functional parts, morphological parts, etc.) by stipulating additional conditions.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 118.

“The most basic concepts of common sense and scientific reasoning, ‘thing’, ‘stuff’, ‘event’, ‘state’, ‘activity’, ‘field’, ‘organism’, and so on, are associated with characteristic inferential patterns pertaining to how the item in question occurs in space and time…. In GPT this is achieved through a systematic extension of the predicate of homeomereity–that is, like-partedness. Aristotle observed that our reasoning about stuffs can be accounted for if we assume that stuffs are ‘like-parted bodies … composed of [spatial] parts uniform with themselves’… Just as any spoonful of a puddle of water is like the whole, namely an expanse of water, so any minute of an hour of snowing is like the whole, namely a period of snowing. Thus we can formulate a generalized notion of homeomereity:

“Like-partedness or homeomereity: An entity of (proximate) kind K is homeomerous with respect to its spatial extent (temporal extent) iff all of its spatial parts (temporal parts) are of kind K.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 120.

“(Spatio-temporal) Self-containment or automereity: An entity E is automerous iff for any spatio-temporal region r (r > 0): if r is a subregion of a spatio-temporal region R in which all of E occurs, then r is a region in which all of E occurs.

“In other words, the entities denoted by sentences about stuffs and activities are not only like-parted in space and time, respectively. They are also literally the same individual; that is, they are recurrent in space and time, respectively.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. pp. 120-1.

“The participant structure of a general process or dynamic states what types of processes are involved in a complex dynamics, and in what role. There are three basic roles, labelled ‘agent’, ‘patient’, and ‘interagent’, but additional ones can be defined recursively. For example, for the ontology of biology, it would be of particular interest to introduce the role of an emergent constituting constrainer (ECC), as a special variety of interagent. Self-maintaining far-from-equilibrium systems like a candle flame, a hurricane, or a biological organism are complex dynamics that emerge from, and constrain, certain interactions and thereby constitute the dynamic system.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 125.

“Unlike Whitehead’s philosophy of organism, GPT is not a speculative metaphysics. For this reason, the conceptual tools of GPT are bound to appear as shallow reformulations of what we know anyway. In contrast, if we reconstruct biological concepts with the tools of Whiteheadian metaphysics, all terms acquire additional semantic content deriving from speculative principles. But precisely the interpretational austerity of GPT is, in my view, an advantage rather than a drawback, especially in a situation where philosophers of science wish to encourage a new way of visualizing a scientific domain.” Seibt, Johanna. 2018. “Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory.” Pp. 113-136. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 134.

“Accordingly, Plato reasoned as follows:

“The sensory world of our ordinary life experience is through-and-through processual.
“Reason demands stability: Whatever it grasps must be constant, unchanging, timelessly true.

“Therefore, if reason is to accomplish its work, there must be another realm, separate from the world of sense, an ideal realm where the demands of reason can be accommodated….

“While Aristotle’s metaphysics of substances and natural kinds was an emphatic substantialism, Aristotle’s metaphysics nevertheless also deployed a considerable array of processist elements. For, so Aristotle insisted, the ‘being’ of a natural substance is always in transition, involved in the dynamism of change. Dunamis (potency), energeia (activity), kinesis (motion), and metabole (change) are fundamental categories of Aristotelian metaphysics, and he conceives of his particulars developmentally–an acorn is less a stable thing than a stage of an evolving organism moving continually if all goes well, along its predestined journey toward its eventual condition as an oak tree….

“Aristotle’s position was accordingly something of a halfway house, seeing that his ontology was less one of substances pure and simple than one of substances-in-process.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. pp. 10, 11.

“Each of these monads is endowed with an inner drive, an ‘appetition’ which ongoingly destabilizes it and provides for a processual course of never-ending change. The whole world is one vast systemic complex of such active processual units…. Leibniz accordingly viewed the world as is an infinite collection of agents (monads) linked to one another in an all-pervasive harmony, with each agent, like a member of an orchestra, playing its part in engendering nature’s performance as a whole. On this basis, Leibniz developed a complex theory of nature as an integrated assemblage of harmoniously coordinated eventuations so that processes, rather than substantial objects, furnish the basic materials of his ontology.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. pp. 12-3.

“Bergson contrasted psychological duration with physical time. Physical time is a mathematicized spatial concept based on the timeline analogy, while psychological duration is a creature of experience that functions in our thought-life where we encounter ‘succession without distinction … an interconnection and organization of elements, each one of which represents the whole, and cannot be distinguished or isolated from it except by [the distorting transformation of] abstract thought.’ But the creative process typical of duration pervades nature and establishes the central role of change on the stage of natural existence.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 17.

“The building blocks of reality as envisioned in Whitehead’s classic Process and Reality are not substances at all but ‘actual occasions’–processual units rather than ‘things’ of some sort–with human experience affording their best analogon. Even as in conscious experience humans apprehend what goes on in their environment in a way that encompasses a low-grade mode of emotion, consciousness, and purpose. Thus Whitehead’s ‘actual occasions’ are, as it were, living units of elemental experience.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 20.

“In Whitehead, as in Leibniz, microcosm and macrocosm are coordinated, linked to one another in a seamless web of process. Whiteheadian entities, like Leibnizian monads, are infinitely complex and, in a way, boundless. Each represents a perspective on the world that reaches out to touch and, as it were, encompass the rest.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 21.

“As process philosophers see it, the supposed predominance and permanence of ‘things’ in nature is at best a useful fiction and at worst a misleading delusion.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 28.

“Thus, in general terms, process philosophy is predicated on two contentions:

“ In a dynamic world, things cannot do without processes. Since substantial things change, their nature must encompass some impetus to internal development.
“ In a dynamic world, processes are more fundamental than things. Since substantial things emerge in and from the world’s course of changes, processes have priority over things.

“Becoming and change–the origination, flourishing, and passing of the old and the innovative emergence of ever-new existence-constitute the central themes of process metaphysics.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 28.

“Process metaphysics is really less of a theory than a point of view taking the line that one must prioritize processes over things and activities over substances…. Process philosophy thus prioritizes change and development in all of its aspects over fixity and persistence.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 35.

“The distinction between owned and unowned processes also plays an important role in process philosophy. Owned processes are those that represent the activity of agents: the chirping of birds, the flowering of a bush, the rotting of a fallen tree. Such processes are ownership attributable with respect to ‘substantial’ items. Unowned processes, by contrast, are free floating as it were, and do not represent the activity of actual (i.e., more than nominal) agents: the cooling of the temperature, the change in climate, the flashing of lightning, the fluctuation of a magnetic field. From the process philosopher’s point of view, the existence of unowned processes is particularly important because it shows that the realm of process as a whole is something additional to and separable from the realm of substantial things.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 42.

“As process philosophers see it, processes are basic and things derivative–not least because it takes a mental process (of a separation and individuation) to extract ‘things’ from the blooming buzzing confusion of the world’s physical processes.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 44.

“After all, even on the basis of an ontology of substance and property, processes are epistemologically fundamental. Without them, a thing is inert, undetectable, disconnected from the world’s causal commerce, and inherently unknowable. Our only epistemic access to the absolute properties of things is through inferential triangulation from their modus operandi–from the processes through which these manifest themselves.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 46.

“In sum, processes without substantial entities are perfectly feasible in the conceptual order of things, but substances without processes are effectively inconceivable.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 46.

“Accordingly, process metaphysicians are given to conceptualizing nature in general–and physical nature in particular–in organic terms, owing to the tendency, at work everywhere in nature, for processes to cluster together in self-perpetuating systemic wholes.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 86.

“On the issue of purposiveness in nature, process philosophers divide into two principal camps. On the one side is the naturalistic (and generally secularist) wing that sees nature’s processuality as a matter of an inner push or nisus to something new and different. On the other side is the teleological (and often theological) wing that sees nature’s processuality as a matter of teleological directness toward a positive destination. Both agree in according a central role to novelty and innovation in nature. But the one (naturalistic) wing sees this in terms of chance-driven randomness that leads away from the settled formulations of an established past, while the other (teleological) sees this in terms of a goal-directed purposiveness preestablished by some value-geared directive force.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. pp. 99-100.

“To be sure, there are, in theory, both productive and destructive processes, degeneration and decay being no less prominent in nature than growth and development. Historically, however, most process philosophers have taken a positive view and have envisioned a close relationship between process and progress.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 102.

“In natural science, the driving force of innovation is provided by technology, for observation and experimentation both need to be technologically mediated….

“In natural science, then, we are embarked on a potentially limitless project of improving the range of effective experimental intervention….” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. pp. 145, 148.

“The neo-Platonic sympathies of the Church Fathers impelled Christian theology to adopt Greek philosophy’s stance that in order to see God as existent we must conceive of him as a being, a substance of some sort.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 154.

“Whitehead sees God in cosmological terms as an ‘actual occasion’ functioning within nature, reflective of ‘the eternal urge of desire’ that works ‘strongly and quietly by love,’ to guide the course of things within the world into ‘the creative advance into novelty.’ For Hartshorne, by contrast, God is less an active force within the world’s processual commerce than an intelligent being or mind that interacts with it. His God is less a force of some sort than a personal being who interacts with the other mind-endowed agents through personal contact and love. Hartshorne wants neither to separate God from the world too sharply nor yet to have him be pantheistically immanent in nature. He views God as an intelligent world-separated being who participates experientially in everything that occurs in nature and resonates with it in experiential participation.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 156; reference: Hartshorne, Charles. 1948. The Divine Relativity: A Social Conception of God. Yale UP.

“To be sure, process philosophers differ from one another regarding the notion of God. Some take an immanentist line and view the divine as a force or factor at work within the cosmic processes to make for an ongoing enhancement of intelligible order and appreciable value. Others take a more transcendentist line and view the divinity as a processual being or entity–a superprocess of sorts that works upon, rather than within, the world’s constitutive machine of processes.” Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. State University of New York Press. p. 162.

“While we recognize that the notion of individuality has been approached from different perspective (physiology, immunology, developmental biology, etc.) it is clear that the advocates of the holobiont concept discussed below are also concerned with evolutionary individuality.” Bourrat, Pierrick & Paul Griffiths. 2018. “Multispecies individuals.” HPLS. https://doi.org/10.1007/s40656-018-0194-1. p. 3.

“Taken together, proteomics studies appear to suggest that protein localization in the cell may be inherently uncertain or, at least, significantly more flexible and dynamic than is commonly believed.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 1

“Any protein structure exists in solution as a population of conformer families…. Moreover, the conformational landscape of the protein is not fixed. Binding of ligands, posttranslational modifications, temperature, pressure, solvent and other factors may drastically alter the conformational landscape by triggering a redistribution of conformers and changing heights of the energy barriers separating alternative conformers.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 3.

“The latest studies addressing the structure and dynamics of various enzymes suggest that the walk of a protein structure through its conformational landscape is actually not random, but proceeds along statistically preferred routes that, strikingly enough, happen to correspond to the conformational changes observed during actual enzymatic catalysis.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 3.

“Proteins performing multiple functions have come to be recognized as a phenomenon in itself under the cliche ‘moonlighting proteins’.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 4.

“The balance between order and disorder in protein structure, function, and interactions ensures that higher order macromolecular complexes and sub-cellular structures, and thus vital cellular functions, remain flexible and adaptive on relatively short timescales that are too fast to involve genetic mechanisms and that require rapid and efficient epigenetic adaptations.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 4.

“Steady-state macromolecular organizations are sustained by the flow of energy and matter passing through them, with their resident components entering and leaving organizations with widely different recruitment probabilities, residence times, and turnover rates.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 5.

“The problem is that, instead of clarifying the hypothetical evolutionary design, ever-advancing technology and methods make it ever more confusing and elusive, by generating massive amounts of the experimental data that is manifestly inconsistent with and difficult or impossible to assimilate within the mechanistic/clockwork image of the cell. Hence, the accumulation of paradoxes, controversies, inconsistencies, and contradictions that persist unresolved over time; hence the rise of technology-driven ‘discovery’ science and a decline of hypothesis-driven research – a sure sign of the failure of the conventional paradigm to serve as a theoretical framework enabling understanding and prediction of experimental outcomes.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 20.

“The present work shows that the experimental reality in molecular and cell biology becomes largely devoid of paradoxes, inconsistencies, and contradictions, and is thus best understood, if the conventional interpretational framework of classical physics is replaced by an alternative paradigm of biological organization, which is based on the concepts and empirical laws of nonequilibrium thermodynamics.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6 doi:10.1186/1742-4682-6-6. p. 20.

“… in biology, the specificity of an object of observation or experiment limits unpredictably any logical generalization. We know that nothing is as important for a biologist as his choice of material to study.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 11.

“Today, one would have to be quite uninformed of the methodological tendencies of biologists–even those biologists least inclined to mysticism–to believe that anyone can honestly boast of having discovered, by physico-chemical methods, anything more than the physico-chemical content of phenomena, whose biological meaning escapes all techniques of reduction.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 16.

“In positivism, there could be a history of myths but not a history of science.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 26.

“This [the facts of reproduction] leads Buffon to argue that there exists an infinite quantity of living organic parts [‘organic molecules’], which are of the same substance as organized beings. These organic parts, common to animals and plants, are primary and unalterable, such that the generation and destruction of organized beings is nothing other than the conjunction and disjunction of these elementary living beings.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 33.

“This aggregation of organic molecules by attraction obeys a sort of law of morphological constancy; this is what Buffon calls the ‘inner mold.’ Without the hypothesis of the inner mold added to that of organic molecules, the nutrition, development, and reproduction of the living are unintelligible….

“The inner mold is a logical intermediary between the Aristotelian formal cause and the ‘guiding idea’ of which Bernard speaks.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. pp, 34, 35.

“As is well known, Hume believed that his effort to enumerate and determine the simple ideas whose association with one another produces the appearance of a unity of mental life was authorized by Newton’s success…. Buffon’s biological atomism corresponds symmetrically to Hume’s psychological atomism.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 37.

“By the theoretical difficulties it raises, individuality obliges us to dissociate two aspects of living beings that are naively and immediately blended in our perception of these beings: matter and form. The individual is what cannot be divided in form, even as we sense the possibility of dividing its matter.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 42.

“Novalis reproaches universal suffrage for atomizing the popular will and for failing to appreciate the continuity of society (more exactly, of the community). Anticipating Hegel, Novalis and, some years later, Adam Heinrich Mueller consider the state a reality willed by God, a fact that exceeds the individual’s reason and to which the individual must sacrifice himself. If these sociological conceptions offer an analogy with biological theories, this is because, as has often been remarked, Romanticism interpreted political experience on the basis of a certain conception of life. That conception was vitalism. At the very moment when French political thought was offering Europe the social contract and universal suffrage, the French school of vitalist medicine was proposing an image of life as transcendent to analytic understanding. For this school, an organism could not possibly be understood as a mechanism; life is a form irreducible to any composition of material parts. Vitalist biology gave totalitarian political philosophy the means if not the obligation to inspire certain theories concerning biological individuality. The problem of individuality is itself indivisible.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. pp. 42-3.

“… we should not expect much from a biology fascinated by the prestige of the physico-chemical sciences, a biology reduced or reducing itself to the role of a satellite of these sciences. A reduced biology has as its corollary the effacement of the biological object as such–in other words, the devaluation of its specificity.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 59.

“… the term vitalism is appropriate for any biology careful to maintain its independence from the annexationist ambitions of the sciences of matter.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 60.

“Mechanism and Vitalism confront one another on the problem of structures and functions; Discontinuity and Continuity on the problem of the succession of forms; Preformation and Epigenesis on the problem of the development of a being; Atomicity and Totality on the problem of individuality.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 61.

“It is not without interest to consider vitalism to be the biology of physicians skeptical of the constraining power of remedies. In pathology, the Hippocratic theory of the natura medicatrix accords greater importance to the organism’s reaction and defense than to the morbid cause…. It is as important to predict the course of a disease as it is to determine its cause…. Medical vitalism is the expression of a distrust, shall we say an instinctive one, of the power of technique over life.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 62.

“If vitalism translates a permanent exigency of life within the living, mechanism translates a permanent attitude of the living human toward life. Man is here a living being separated from life by science and attempting to rejoin life through science. If vitalism, being an exigency, is vague and unformulated, mechanism, being a method, is strict and imperious.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 62.

“Was Aristotle’s vitalism not already a reaction against Democritus’s mechanism, as Plato’s finalism in the Phaedo was a reaction against Anaxagoras’s mechanisms?” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. pp. 66-7.

“A mechanism is a configuration of solids in motion such that the motion does not abolish the configuration.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 76.

“Schuhl has shown that within ancient philosophy the opposition between science and technics overlies the oppositions between freedom and servitude, and, more profoundly, between nature and art. Schuhl refers to the Aristotelian opposition between natural and violent movement. The latter is engendered by mechanisms in order to counteract nature and has the following characteristics: it exhausts itself quickly, and it never engenders a habit–that is to say, a permanent, self-reproducing disposition.

“Here we come across a rather difficult problem in the history of civilization and in the philosophy of history. In Aristotle, the hierarchy of freedom and servitude, theory and practice, nature and art parallels an economic and political hierarchy–the hierarchy, within the city, of free men and slaves. A slave, says Aristotle in the Politics, is an animate machine.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 80; reference: Schuhl, Pierre-Maxime. 1938. Machinisme et philosophie. Alcan.

“The construction of the living machine [by Descartes] implies, if one reads the text well, an obligation to imitate a prior organic given. The construction of a mechanical model presupposes a vital original, and, in the end, we may wonder whether Descartes is not closer here to Aristotle than to Plato. The Platonic demiurge copies the Ideas. The Idea is a model of which the natural object is a copy. The Cartesian God, the Artifex Maximus, works to equal the living itself. The model for the living machine is the living itself. The Idea of the living, which divine art imitates, is the living thing. And just as a regular polygon is inscribed within a circle, and in order to derive the circle from it, it is necessary to pass through infinity, so the mechanical artifice is inscribed within life, and to derive one from the other, it is necessary to pass through infinity–that is to say, God….

“In truth, one cannot, it seems, oppose mechanism and finalism, one cannot oppose mechanism and anthropomorphism, for if the functioning of a machine is explained by relations of pure causality, the construction of a machine can be understood neither without purpose nor without man.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. pp. 85, 86.

“… machines can be considered organs of the human species. A tool or a machine is an organ, and organs are tools or machines. Consequently, it is hard to see where the opposition between mechanism and finalism lies. No one doubts that a mechanism is needed to ensure the success of a given purpose, and inversely, every mechanism must have a sense, for a mechanism is not just an accidental series of interdependent movements. In reality, the opposition is between those mechanisms whose sense is manifest and those whose sense is latent. The sense of a lock or a clock is manifest; the sense of the pincers of a crab, so often invoked as marvels of adaptation, is latent.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 87.

“We must at least admit that, in the organism, a plurality of functions can adapt to the singularity of an organ. An organism thus has greater latitude of action than a machine. It has less purpose and more potentialities.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 90.

“Life by contrast [to a machine], is experience, that is to say, improvisation, the utilization of occurrences: it is an attempt in all directions. From this follows a massive and often neglected fact: life tolerates monstrosities. There is no machine monster.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 90.

“Since it is the result of an effort, adaptation is thus neither harmonious nor providential; it is gained and never guaranteed. Lamarckism is not mechanist, and it would also be inaccurate to call it finalistic. In reality, it is a bare vitalism. There is an originality in life for which the milieu does not account and which it ignores. Here the milieu is truly exterior, in the proper sense of the word; it is foreign, it does nothing for life… In Lamarck’s conception, life resists solely by deforming itself so as to outlive itself…. One sees how far one has to go to get from Lamarck’s vitalism to the French neo-Lamarckians’ mechanism.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 104.

“The fundamental biological relation, in Darwin’s eyes, is the relation of one living being to others; it prevails over the relation between the living and the milieu conceived as an ensemble of physical forces.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 105.

“Von Uexkuell and Goldstein agree on this fundamental point: to study a living being in experimentally constructed conditions is to make a milieu for it, to impose a milieu on it; yet it is characteristic of the living that it makes its milieu for itself, that it composes its milieu.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. pp. 110-1; reference: Goldstein, Kurt. 1934[1995]. The Organism: A Holistic Approach to Biology Derived from Pathological Data in Man. Zone Books.

“The milieu of behavior proper to the living (Umwelt) is an ensemble of excitations, which have the value and signification of signals. To act on a living being, a physical excitation has not only to occur but also to be noticed. Consequently, insofar as the excitation acts on the living being, it presupposes the orientation of the living being’s interest; the excitation comes not from the object but from the living. In order for the excitation to be effective, it must be anticipated by an attitude of the subject. If the living is not looking, it will not receive anything. A living being is not a machine, which responds to excitations with movements, it is a machinist, who responds to signals with operations. Naturally, this is not to contest that it happens through reflexes whose mechanism is physico-chemical. That is not where the question lies for the biologist. Rather, the question lies in the fact that out of the abundance of the physical milieu, which produces a theoretically unlimited number of excitations, the animal retains only some signals.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 111.

“The situation of a living beihng commanded from the outside by the milieu is what Goldstein considers the archetype of a catastrophic situation. And that is the situation of the living in a laboratory. The relations between the living and the milieu as they are studied experimentally, objectively, are, among all possible relations, those that make the least sense biologically; they are pathological relations. Goldstein says that, in the organism, ‘’meaning’ and ‘being’ are the same’; we can say that the being of an organism is its meaning.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 113; reference: Goldstein, Kurt. 1934[1995]. The Organism: A Holistic Approach to Biology Derived from Pathological Data in Man. Zone Books.

“… the milieu is the state in which nature has placed us; we are floating on a vast milieu; man is in proportion with parts of the world, he has a relation to all that he knows: ‘He needs space to contain him, time to exist in, motion to be alive, elements to constitute him, warmth and food for nourishment, air to breathe. He sees light, he feels bodies, everything in short is related to him.’ We thus see three meanings of milieu intervene here: medial situation, fluid of sustenance, and vital environment.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 117; subquote: Pascal, Blaise. 1941. Pensees. Random House. p. 92

“As Edouard Claparede writes: ‘What distinguishes the animal is the fact that it is a center in relation to ambient forces that are, in relation to it, no more than stimulants or signals; a center, that is to say, a system with internal regulation, whose reactions are determined by an internal cause: momentary need.’ In this sense, the milieu on which the organism depends is structured, organized, by the organism itself. What the milieu offers the living is a function of demand. It is for this reason that, within what appears to man as a single milieu, various living beings carve out their specific and singular milieus in incomparable ways. Moreover, as a living being, man does not escape from the general law of living beings. The milieu proper to man is the world of his perception–in other words, the field of his pragmatic experience, the field in which his actions, oriented and regulated by the values immanent to his tendencies, pick out quality-bearing objects and situate them in relation to each other and to him. Thus the environment to which he is supposed to react is originally centered on him and by him.

“Yet man as scientist and bearer of knowledge constructs a universe of phenomena and laws that he holds to be an absolute universe. The essential function of science is to devalorize the qualities of objects that comprise the milieu proper to man; science presents itself as the general theory of a real, that is to say, inhuman milieu. Sensory data are disqualified, quantified, identified. The imperceptible is presumed, and then detected and proven. Measurements substitute for appreciations, laws for habits, causality for hierarchy, and the objective for the subjective.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. pp. 118-9; subquote: Claparede, Edouard. 1928. Preface to Frederik Jacobus Johannes Buytendijk. Psychologie des animaux. Payot.

“Too often, scientists hold the laws of nature to be essentially invariant. They treat singular phenomena as approximate copies, which fail to reproduce these laws supposed lawful reality in its entirety. From this perspective, the singular–that is, the divergence, the variation–appears to be a failure, a defect, an impurity. The singular is thus always irregular, but that is at the same time perfectly absurd, for no one can understand how a law whose reality is guaranteed by its invariance or self-identity could be at once verified by diverse examples and powerless to reduce their variety, that is, their infidelity. This is because, despite modern science’s substitution of the notion of law for that of genus, the first of these concepts carries over from the second (and from the philosophy in which the latter held an eminent place) the meaning of an immutable and real type, such that the relationship of law to phenomenon (the law of gravity and the falling shard that killed Pyrrhus) is always conceived on the model of the relation between genus and individual (Man and Pyrrhus). We thus see, without any intentional paradox or irony, the reappearance of a famous problem of the Middle Ages, the problem of the nature of Universals.” Canguilhem, Georges. 2008[1965]. Knowledge of Life. Translated by Geroulanos Stefanos & Daniela Ginsburg. Fordham UP. p. 123.

“A biological individual is a functionally integrated entity whose integration is linked to the common fate of the system when faced with selective pressures from the environment.” Bouchard, Frederic. 2018. “Symbiosis, Transient Biological Individuality, and Evolutionary Processes.” Pp. 186-198. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 188.

“Biological individuals may be temporary ‘eddies in the constant flux of process’, but viewing them as genuine individuals is necessary for evolutionary explanations nonetheless.” Bouchard, Frederic. 2018. “Symbiosis, Transient Biological Individuality, and Evolutionary Processes.” Pp. 186-198. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 188; subquote: Dupré, John. 2015. “A process ontology for Biology.” Physiology News. 100: 33-4. p. 81[sic].

“If we accept that individuality is about functional integration and that functional integration is a question of degree, we must also accept that an individual’s degree of individuality may fluctuate over time.” Bouchard, Frederic. 2018. “Symbiosis, Transient Biological Individuality, and Evolutionary Processes.” Pp. 186-198. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 192.

“The global biogeochemical cycling of materials, fuelled by solar energy, has transformed the Earth system. This transformation of energy and cycling of materials by the biosphere can be seen as the ‘metabolism’ of the Earth system. It is fundamental to the remarkable productivity of the Earth’s biosphere, just as an individual organism’s metabolism is essential to its healthy existence.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. pp. 36-7.

“There is remarkable correspondence between the ratio in which the essential nutrients nitrogen and phosphorus are found in ocean water and the ratio in which they are required by marine organisms. This was first highlighted by the oceanographer Alfred Redfield in 1934 and the average N:P ratio of marine organisms is known as the ‘Redfield ratio’ in his honour. Traditionally phytoplankton have N:P = 16 whereas waters upwelling from the deep ocean have close to N:P = 15. So from the average organisms’ point of view there is a slight deficit of nitrogen relative to phosphorus in the ocean.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. p. 41.

“Key to Redfield’s feedback mechanism is the activities of nitrogen fixing organisms. Fixing nitrogen comes at a serious energy cost (in splitting the triple bond of N2), which means that nitrogen fixers tend to be outcompeted by non-fixers whenever nitrogen is available. Thus, when deep waters with N:P < 16 are physically upwelled to the surface ocean the nitrogen they contain gets used up by other phytoplankton, but when nitrogen runs out, on average, some phosphorus will remain. Nitrogen fixing organisms then have the opportunity to grow using this remaining phosphorus and fixing nitrogen directly from the atmosphere. The activity of nitrogen fixers adds fixed nitrogen to the ocean, so they limit their own spread. However, fixed nitrogen is continually being removed by the activities of denitrifying organisms that thrive wherever oxygen runs out at depth in the ocean. This allows some nitrogen fixers to persist as a small fraction of the surface community.

“The result is a negative feedback mechanism operating on the input of nitrogen to the ocean and keeping it in balance with the outputs. This feedback enables the nitrogen content of the ocean to track variations in the phosphorus content, which can be driven by, for example, fluctuations in weathering.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. pp. 41-2.

“… cloud water needs something to condense on…. In particular, marine phyloplankton release a gas called dimethyl sulphide–or DMS for short–which is the major source of cloud condensation nuclei (CCN) over remote, unpolluted parts of the ocean today (and prior to human industrial pollution was even more important as a global source of condensation nuclei). Increasing the number of CCN in a cloud distributes the same amount of water over a larger number of smaller droplets, which makes the cloud whiter–meaning it reflects more sunlight. This biological production of CCN cools the Earth by several degrees.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. p. 52.

“The challenge for early life was to evolve the means of recycling the materials it needed to metabolize–in other words, to establish global biogeochemical cycles.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. p. 63.

“Intriguingly, the first evidence for oxygenation of parts of the deep oceans appears 580 million years ago, shortly before the appearance of Ediacaran fossils at depth in the ocean. However, there had been oxygen in the shallow waters of the ocean for more than a billion years before this. It may be that evolution caused oxygenation rather than vice versa. By increasing the efficiency of carbon removal from the water column and phosphorus removal into sediments, the rise of sponges and algae may have oxygenated the ocean, improving conditions for ongoing animal evolution. Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. p. 72.

“There have been three revolutionary transformations in the history of the Earth system: the inception of life and biogeochemical cycling; the origin of oxygenic photosynthesis and the Great Oxidation; and the origin of complex life out of the Neoproterozoic environmental turmoil. These revolutions share common features. They were caused by rare evolutionary innovations. They involved step increases in energy capture and material flow through the biosphere, accompanied by increases in the complexity of biological organization and information processing. They relied on the Earth system having some instability, such that new metabolic waste products could cause catastrophic upheavals in climate and biogeochemical cycling. They ended only when blind evolution was able to close the biogeochemical cycles again, recycling the waste materials and establishing a new stable state for the Earth system.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. p. 73.

“… several subsystems of the Earth system are thought to exhibit alternative stable states and tipping points. An archetypal example is the Atlantic Ocean’s overturning circulation. I have dubbed those parts of the Earth system that can exhibit tipping points ‘tipping elements.’ Amongst them are several candidates that could be tipped by human-induced global change. They can be divided into those involving abrupt shifts in modes of circulation of the ocean or atmosphere, those involving abrupt shifts in the biosphere, and those involving abrupt loss of parts of the cryosphere.” Lenton, Tim. 2016. Earth System Science: A Very Short Introduction. Oxford UP. pp. 100-1.

“… it is not at all clear that either O [self-organizational or metabolic theories of life] or R [reproductive theories of life] provides a scientifically fruitful, theoretical foundation for exploring deep-seated questions about life. Moreover, even supposing that they do, the perennial problem of goal-directed self-causation remains, for both O and R seem to presuppose it.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. pp. 21-2.

“Individual organisms are the paradigmatic living things. Evolution-based definitions of life, however, have trouble classifying them as such. Organisms do not evolve as individuals; they merely live and die…. For our purposes, the important point is that metabolism-based definitions of life construe the individual organism as the basic unit of life whereas evolution-based definitions take groups of related organisms (populations, species, or lineages) as the basic unit of life.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 24.

“Functional properties are peculiar insofar as they are instantiated by an entity before the ends that functionally define them actually occur. That is, they are intrinsically goal-directed. The concept of intrinsically goal-directed processes represents a problem for contemporary scientists and philosophers of science whose concept of causation holds that causes precede their effects without anticipating them. For this reason, functional capacities are rarely if ever taken as basic in science.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 30.

“The scientific project of defining life is founded upon a failed theory of the meaning and reference of natural kind terms and hence ought to be abandoned.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 59.

“Unlike the present-day chemical concept of water, however, the biological concept of life will almost certainly continue to change in unanticipated ways. For modern biology does not have a truly general theory of life analogous to the chemist’s molecular theory of chemical substance.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 60.

“Scientific definitions of life tend to reflect the diverse backgrounds of their authors, with biochemists emphasizing biochemical aspects of life in their definitions, physicists emphasizing thermodynamic aspects of life in their definitions, and computer scientists emphasizing informational aspects of life in their definitions.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 74.

“The primary function of all definitions is classification. Scientific theories, in contrast, have a variety of functions other than classification. As mentioned earlier, these functions include explaining and predicting phenomena falling under a theory, but they also include guiding and constraining the search for relevant evidence and interpreting data once it is acquired. The ability to come up with an intuitively appealing classification scheme – to sort things into distinct, highly plausible, categories – does not guarantee the capacity to realize these other functions, which are far more critical to the scientific success of a theory.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. pp. 78-9.

“… the scientific project of defining life rests not only upon misconceptions about a close logical relationship between definitions and scientific theories but also upon ignoring the important functions served by scientific theories….

“Scientific theories are far more open ended and fluid than definitions, which is what allows them to be applied to novel and unanticipated empirical phenomena.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 79.

“It [the term ‘shadow biosphere’] is intended to capture the idea that (like all life) shadow microbes [life on Earth with a novel chemistry] would leave as yet unrecognized traces (in essence, shadows) in their environments as they extract matter and energy and release waste products.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 195.

“… much of contemporary biological thought is still implicitly wedded to a defective, neo-Aristotelean, theoretical framework for life based on animals and plants.” Cleland, Carol. 2019. The Quest for a Universal Theory of Life: Searching for Life As We Don’t Know it. Cambridge UP. p. 217.

“I think of life as a sort of balancing act in an ever-changing environment.” Wolff, Robert. 2001. Original Wisdom: Stories of an Ancient Way of Knowing. Inner Traditions. p. 25.

“Both doctors and patients believe that healing comes from drugs, from outside intervention, forgetting that until recently healing was always what the body did, perhaps aided or stimulated by a healer.” Wolff, Robert. 2001. Original Wisdom: Stories of an Ancient Way of Knowing. Inner Traditions. p. 54.

“Laurens van der Post writes that what sets the Bushman apart from other indigenous peoples is that they could not be ‘tamed.’ In Africa, if an aborigine is jailed, he died ‘for no good reason,’ as white historians would write….

“Laurens van der Post suggests that these preagricultural people had not been caught in what he calls ‘the tyranny of numbers,’ the idea that there is strength in numbers.” Wolff, Robert. 2001. Original Wisdom: Stories of an Ancient Way of Knowing. Inner Traditions. pp. 113, 114.

“The idea of the commons has been popularly associated with natural resources and local inhabitants who want to govern and protect localized commons for their own use, as with the common pool resource institutions that Elinor Ostrom studied and became well-known for. Drawing from, but also expanding on this notion, we see commons more generally as combinations of shared resources which are co-produced and managed by a community of stakeholders according to their own rules and norms. This definition aims to be objective, stressing the existence of a shared resource, which can be ‘immaterial’ such as a community and its activity; it emphasizes the intersubjective aspects, as it requires human choice and intervention; and it involves institutional/property arrangements. This definition does not idealize the commons as necessarily being egalitarian, nor universal, nor for the benefit of everyone. Commons exist in various scopes and scales, and include various forms of inequalities, reflecting broader societal structures and dynamics. Open source communities, for example, produce digital commons, which are qualitatively immaterial and global in scale. Alternatively, residents of a city may work together to manage and tend to commons such as parks, water systems or even energy production systems.

“Commons in a broader sense, however, become so by implication into a community of shared concern which has an interest in protecting and extending that which they mutually depend on for their survival and well-being. For example, left solidarity in the traditional working-class European context was understood as based on class, yet this could have been framed simply as a solidarity of common concern.” Bauwens, Michel & J. Ramos. 2018. “Re-imagining the left through an ecology of the commons: towards a post-capitalist commons transition.” Discourse. https://doi.org/10.1080/23269995.2018.1461442. p. 2.

“… the language and literature of the commons emphasizes a relational cross-implication of one commons in another. Yes we need a world where workers have dignity and power, but these same workers are commoners of the atmosphere as well, which they and their own future generations depend on for their well-being and survival. This ‘ecology of the commons’, which envisions dynamic solidarities and collaborations across ontologically different commons communities, is the conceptual position we take to consider the transformation of the left in this paper.” Bauwens, Michel & J. Ramos. 2018. “Re-imagining the left through an ecology of the commons: towards a post-capitalist commons transition.” Discourse. https://doi.org/10.1080/23269995.2018.1461442. p. 3.

“We describe the organization of ecological systems as panarchies. Panarchies are hierarchically arranged, mutually reinforcing sets of processes that operate at different spatial and temporal scales, with all levels subject to an adaptive cycle of collapse and renewal, and with levels separated by discontinuities in key variables. Dominant processes entrain other processes to their spatial and temporal frequencies. This entrainment (an interaction among process and structure dominated by one or a few processes within a range of scale) produces discontinuities (gaps) and aggregations (clumps) in animal community body-mass distributions and in distributions of other complex systems, such as urban systems and economic systems.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. p. 3.

“Moreover, in these systems, the dynamics of each set of the components within a range of scale follow an adaptive cycle of change. The adaptive cycle model proposes that the internal dynamics of systems cycle through four phases: rapid growth, conservation, collapse, and reorganization. As unorganized processes interact, some processes reinforce one another, rapidly building structure and organization. This organization channels and constrains interactions within the system. However, the system becomes dependent on structure and constraint for its persistence, leaving it vulnerable to either internal fluctuations or external disruption. The system eventually collapses, allowing the remaining disorganized structures and processes to reorganize or the structures and processes from neighboring, extrinsic systems to invade.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. pp. 4-5.

“Architecturally simple landscapes have few clumps in the body-mass distributions of animals living in them; complex landscapes have many clumps. For example, Schwinghamer and Raffaelli and colleagues show that architecturally simple marine sediments have communities living within them that have three and perhaps four clumps in their inhabitants’ size distributions. Boreal forest landscapes are somewhat more complex; their mammal and bird communities show about eight clumps in body mass. Tropical forests systems are even more complex, and their bird inhabitants show an even greater number of clumps.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. p. 10; references: Schwinghamer, P. 1981. “Characteristic size distributions of integral benthic communities.” Canadian Journal of Fisheries and Aquatic Sciences. 38:1255-1263; Rafaelli, D., S. Hall, C. Emes & B. Manly. 2000. “Constraints on body size distributions: An experimental approach using a small-scale system.” Oecologia. 122:389-398.

“It takes the kind of extreme disturbances seen over paleoecological time and space scales to change the pattern of aggregations and discontinuities in body-mass structure significantly. Eleven thousand years ago, for example, all the very large herbivores, such as giant ground sloths and the shovel-tusked elephants, became extinct in North and South America in less than one thousand years. Lambert and Holling analyzed two reconstructed fossil data sets from either side of the North American continent to identify the body-mass structure before and after that massive extinction pulse. The data demonstrate a significant body-mass structure that remained entirely unchanged for animals less than 41 kg, even though extinction occurred among those species. Replacement by new species of similar sizes maintained the structure despite species turnover. At greater than 41 kg, the body-mass structure was entirely transformed, and the largest clump of animals, with masses greater than 1,000 kg, was eliminated entirely.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. pp. 11-2; reference: Lambert, W.D. & C.S. Holling. 1998. “Causes of ecosystem transformation at the end of the Pleistocene: Evidence from mammal body mass distributions.” Ecosystems. 1:157-175.

“Species in different body-mass aggregations forage at different scales, so they begin to utilize budworm only when budworms are at an appropriate level of aggregation-that is, only when the scale of the budworm resource matches the scale of the insectivores’ foraging and environmental interaction. Small warblers, for example, respond to single budworms on branches, larger sparrows to aggregations of budworms on branches, and still larger grosbeaks to aggregations within crowns. Hence, as budworm population densities increase during periodic outbreaks, a strong biotic resistance develops that brings into play more and larger avian predator species with larger appetites and from more distant areas. All the bird species in question are foliage-gleaning insectivores and would be considered redundant in some models of the relationship between diversity and stability, but because each species interacts with its environment at a different scale, the different species are not really redundant, but instead provide a cross-scale reinforcement of function. When the regulation of budworms eventually fails, it does so suddenly and over large spatial scales of hundreds of kilometers, allowing the budworm to emerge as forest-structuring process as it defoliates and kills large areas of forest.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. p. 13.

“The effect of diversity of function is not redundancy in the sense that an engineer might replicate function to achieve engineering reliability. Rather, each species in the same size aggregation has a similar scale of resource exploitation, but at least a slightly different function and different responses to unanticipated environmental change. If the ecosystem were a theater, the species within an aggregation would be the stand-in actors who are prepared to replace each other in the event of unexpected external surprises and crises. Species in different aggregations also can engage in similar or related ecosystem functions, but because of their different sizes, they differ in the scale and degree of their influence. In our ecosystem theater, species in different clumps are the actors waiting in the wings to facilitate a change in pace or plot when needed.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. pp. 13-4.

“The same kind of imbricated redundancy is a common property of many biological phenomena. For example, body temperature in homeotherms is regulated by five different physiological mechanisms ranging from metabolic heat generation to evaporative cooling. Each operates over different ranges of temperature with different efficiencies and speed of feedback control. The result is remarkably robust regulation of temperature around a narrow range. In another behavioral example, migratory birds navigate with great success between summer and winter feeding areas over enormous distances by using at least four different signals for direction–magnetic, topographic, aural, and sidereal–each of which has different levels of precision and accuracy. It is the overlapping, reinforcing nature of those separate mechanisms that makes the total effect so robust.” Holling, Crawford S., G D Peterson & C R Allen. 2008. “Panarchies and Discontinuities.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 3-19. Columbia UP. p. 14.

“The interaction of process and pattern at one sale produces emergent organization at larger and slower scales.” Peterson, Garry. 2008. “Self-Organization and Discontinuities in Ecosystems.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 20-30. Columbia UP. p. 20.

“Transition between dynamic regimes can be found in many ecosystems that are as diverse as coral reefs (shifts between algal and coral dominance), woodlands (between forest and savanna), and arid lands (grassy to a shrub-dominated rangeland).” Peterson, Garry. 2008. “Self-Organization and Discontinuities in Ecosystems.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 20-30. Columbia UP. p. 22.

“An ecological process may impose a pattern on a landscape, it may be shaped by a pattern, or it may both shape and be shaped. The intensity of the feedback between landscape pattern and the processes that shape it fundamentally influences landscape dynamics. The degree to which an ecological process is shaped by its history can be thought of as the strength of the ecological memory of that process.” Peterson, Garry. 2008. “Self-Organization and Discontinuities in Ecosystems.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 20-30. Columbia UP. p. 23.

“Fire is a key structuring process in many ecosystems. Although the duration of a fire is much shorter than the life span of the vegetation it consumes, fire produces landscape patterns that persist for long periods. At small spatial scales, it homogenizes the landscape by killing above-ground growth of trees, thus producing patches of even-aged vegetation. At larger spatial scales, it produces heterogeneity by creating a mosaic of burned and unburned patches.” Peterson, Garry. 2008. “Self-Organization and Discontinuities in Ecosystems.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 20-30. Columbia UP. p. 24.

“Fire is representative of a larger group of contagious disturbance processes–including fires, insect outbreaks, and grazing herbivores–that spread themselves across a landscape. Unlike the extent and duration of noncontagious disturbances, such as ice storms, hurricanes, and clear-cutting, the extent and duration of a contagious disturbance event are dynamically determined by the interaction of the disturbance with a landscape. The size of a contagious disturbance depends, at least partially, on the spatial configuration of the landscape being disturbed. Changes in landscape pattern will alter the nature of a contagious disturbance regime, but will not alter a noncontagious disturbance regime.” Peterson, Garry. 2008. “Self-Organization and Discontinuities in Ecosystems.” In: Allen, Craig R. & C.S. Holling (Eds). Discontinuities in Ecosystems and Other Complex Systems. pp. 20-30. Columbia UP. p. 24.

Citations for the following book are additions to those from Biology, 2012 Quotes sections.

“Their [inorganic elements’] changing availability with the oxidising power of the environment as observed in geochemistry is in fact, we consider, the major driving factor in life’s evolution.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 56.

“The effect of light on organic chemicals can cause separation of charge, electrons from a residual positively charged molecules [sic], and further reaction can lead to separation of products, one oxidised, one reduced. This is the same photoreaction as we have described for the disproportionation of water to hydrogen and oxygen. It will be seen that this photoreaction has become the basic energy capture reaction of organisms leading to reduced organic molecules and molecular oxygen, an enormous energy storage.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 63.

“… individual molecules have ordered structure but no organisation. Study of ordered, even energised, structure alone, as in much of molecular biology, cannot describe living organisms since that study is mostly of static molecular structure, order, in isolated molecules (not of their states) and not of the essential controlled flow within boundaries, organisation.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 84.

“Everything we observe of chemical change is, following the lines of the previous discussion, seeking a cyclic steady flowing state in this basic ‘structured’ or constrained irradiated environment (fields due to gravity and radiation), overwhelmingly due to the input of light [following steady state examples of clouds and ozone layer].” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. pp. 98-9.

“It is clear that only if Z [in equation where X <–> Y + Z but where the paths and energy exchanges are different and written as bi-directional and curved arrows to represent cyclic and separated flows] unmodified or somewhat modified can, in some way, enter chemically, as well as physically perhaps and increasingly into the organised X <–> Y + Z [actually misprint has X <–> X but again with bi-directional, curved arrows between X and Y] cycle, that the system can evolve materially continuously towards a new energy retention state which will have a new eventual optimal value. This corresponds to chemical evolution of the system from X + Y to X + Y + Z in a cycle. As stated, evolution after introduction of novel chemicals, here S. proceeds to an increasing energy and chemical flow towards a final limit, a fully cyclic condition.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 101.

“Since the organised steady states present in life as well as in clouds or ozone layers are cooperative or at least interactive with the physical and chemical environment, on which they all depend, the whole can be represented schematically as heading towards an optimal cycle and Z [from above X <–> Y + Z chemical reaction but now with Z acting in additional new ways on original X, Y system] will be particularly effective if it acts in all three of the above ways, as catalyst, an absorber of energy and as a chemical part of the system….” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 102.

“Therefore, if we are to understand and manage life on Earth, it is necessary to study flow. Very importantly, in all cases it will evolve and will attempt to become completely cyclical, to avoid self-damage via waste. The cyclic condition is final when, as in equilibrium conditions, it can evolve no further. Such a cyclic condition would be an end point of evolution, a fixed maintained optimal system with fixed shape or form. We have described this condition as one of optimal retention of energy and rate of thermal entropy production with a flow system. A system can only change if energy or material input to it changes.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 119.

“While the genome is defined by a DNA sequence so that each base has a singular intensive property as in a computer code of symbols, by way of contrast, the protein content of a cell is an extensive property being concentration dependent and therefore varies under circumstances such as temperature and pressure although each protein also has a fixed sequence. In this respect the RNA content is also to be likened to the protein content or proteome, to the substrate content, the metabolome, and the metal ion content, the metallome. All these concentration-dependent terms are extensive thermodynamic properties of a cell system via the expression of the DNA but not of the DNA itself. Expression itself is a thermodynamic concept. By using the word chemotype, as opposed to genotype, we are therefore using an all-embracing thermodynamic concept based in part upon the concentrations of elements in the energised genome, the proteome, the metabolome and the metallome. As stated we are then forced to describe also the spaces (volumes) which are under consideration, the energy which is put into both compounds and concentrations since many of the elements are not in equilibrium with their surroundings, as well as the internal organisation, and any relationship to the environment. It is energy use which also typifies the dynamics of the system, the organised controlled flows due to pumps, synthesis and degradation and information transfer in confined spaces. The concept of a chemotype is then very different from that of a genotype since it is environmental, material- and energy-dependent. The DNA genotype allows the definition of a species but does not fit easily with the activity of an organism, particularly, the chemical activity within an organism. Note again the comparison between mankind and gorillas which are hardly distinguishable in genotype or general physical shape. This release from the dependence on sequence information in the genotype or on morphology in the discussion of evolution is extremely important as it allows us to see that it is not chance which guides evolution but a dominant thermodynamic drive towards equilibrium via energy degradation in sophisticated chemical pathways – organisms.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. pp. 130-1.

“The requirement for H, C, N, O and P is absolute in that only they were sufficiently available and functionally adequate to make kinetically stable reproducible polymers, soluble in water,….” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 132.

“… no life form (chemotype) has been found without several basic essential inorganic elements: Na, K, Ca, Mg, Cl, Mn, Fe, W(Mo) and Se…. In fact, they are all present in virtually all if not all life in rather similar free amounts in the cytoplasm, though in different amounts in compartments within later organisms and in different combinations generally…. There may be one or two other elements we should add to the initially required groups, e.g. some V, Zn, Ni and Co to a total of at least 15 and at the most 20 elements. Some of these additional elements, e.g. Ni and Co, have been much used in early life but are now less employed; others are more used now, e.g. V and Zn, or even introduced later, e.g. Cu and I. There are some other additional elements such as Si, B, Sr, and Ba which only have special value in particular later chemotypes.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 133.

“Note the considerable kinetic stability of the peptide bond, the phosphate diester and the other links of polysaccharides in water at pH 7. Later, we shall observe the reasons for the remarkable and essential catalytic properties of the proteins. The very limited number of non-metals capable of giving this required kinetic stability in combination makes it very improbable that there are in fact other possible element combinations for, or methods of synthesis of, biologically suitable polymers. For example, it is not possible to base stable linear polymers on sulfur or silicon monomers, and notice the much greater abundance of H, C, N, and O over S and P.

“We consider then that the effects of energy upon the non-metals once in a cell were inevitable eventual events leading to those products which were and are the most kinetically stable and therefore provided the best starting capability for retaining energy for a considerable period. All the further development of cell chemistry is then to be seen as further steps toward the optimal manner in which to generate energy flux through survival strength in a system of inevitable instability and decay.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 142.

“We can now summarise the combined network of communication between the active units of flow, stressing concentration dependence as well as sequences in information. Information about the concentrations of internally collected environmental ions and molecules, some with energy content, is transmitted via transcription factors to the DNA/RNA code which subsequently informs the amounts of synthesis of coded proteins related to the introduction and reactions of the collected units. The proteins carry in their structures the translated code for these initial and subsequent substrate syntheses. The substrates of these syntheses also inform by feedback, via their concentrations, the proteins which carry out these very syntheses, as well as the DNA/RNA. They also inform the membrane so that uptake starts or stops according to the needed concentration. Meanwhile, the membrane is informed externally about concentrations in the environment by selective interactive binding of its contents to the uptake machinery. The proteins in the membrane are governed in synthesis by these same environmental chemicals, through some indirect concentration-dependent interaction with the DNA/RNA transcription factors. Remember that the controlled levels of NTP are needed for DNA and RNA synthesis by protein catalysts, while proteins are synthesised by RNA catalysts. The whole synthetic activity is driven by the available energy, NTP in its internal concentration, which can also act as a source of information by binding, without energy transfer of reaction, to DNA/RNA or to the protein machinery, enzymes and pumps, to start or stop activity. A major information system is clearly the transfer of bound phosphate by enzymes, i.e. kinases, to both substrates and proteins and to water to provide energy. The whole is a thermodynamic irreversible system of controlled flows and it is homeostatically fixed in a given steady state.

“We see that the functional information in this network concerns concentrations and acts through selective binding constants, which being thermodynamically fixed factors, are only partly linked to a code.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 150.

“… only on their reduction, i.e. combination with hydrogen, can organic polymers such as proteins, lipids, nucleotides and sugars be synthesised…. Most of these reactions cannot be catalysed by C/N/O/H/S compounds, e.g. RNA or proteins per se, so certain available metal ions in combination with proteins were essential. The only elements capable of catalysing the reduction (or the oxidation) of these small molecules are transition metal ions.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 171.

“Electron-rich metal centres are very valuable in reductive catalysis since they form associations with electron-poor unsaturated organic molecules such as CO and CN-, donating electrons to them. Initially, there were not many available electron-rich inorganic mineral compounds other than those of nickel (and cobalt) sub-sulfides, i.e. FeS2, pyrite, and FeS. Electron richness is increased in all low-spin metal ion organic complexes, often kinetic traps, and we shall see that all three metal ions, Fe, Co and Ni, in such states evolved in complexes (porphyrins) and found uses a short while after the history of organisms began…. Later in evolution oxidising agents became available and electron deficiency rather than richness became valuable. We note how the metals manganese (zinc) and then copper increased in value as they became available, while nickel and cobalt became progressively less used.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 171.

“Apart from individual sites, series of metal ion sites provide electron conduction paths, vital in energy transduction in all organisms and leading to proton transfer, and Mg2+ in chlorophyll is essential for light capture.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 172.

“Now magnesium with potassium are also essential for the stability of the structures of DNA and RNA compensating its negative charge…. The folded forms and catalytic activity of RNA are absolutely dependent on Mg2+ for their structures and no known RNA is without this cation. Mg2+ and Ca2+ are also extremely valuable in stabilising membranes and walls. Under conditions of environmental and cellular organic chemistry no other cations can carry out these functions in which reasonable concentration, structural flexibility and very fast exchange (equilibria) are necessary.” Williams, R.J.P. & J.J.R. Frausto da Silva. 2006. The Chemistry of Evolution: The Development of our Ecosystem. Elsevier. p. 174.

“Unfortunately, a cell, unlike laboratory or industrial vessels, will burst if the concentration inside it is not kept commensurate with that outside it. Similarly, charge inside the vesicle must be close to neutrality or the electrostatic repulsion will cause rupture. Now, the metabolic paths of organic chemicals in water are largely made up of anions in order to maintain solubility. The anions are mostly carboxylates and phosphates, often of side chains of small and large molecules. To avoid osmotic and electrostatic breakdown the concentration and the total charge content of primitive cells of both environmental and organic ions had to be controlled to match closely their values in the neutral sea water external to the cell. The major osmotic component of the sea is sodium chloride and it was clearly necessary to expel this salt more than ten-fold from inside the cell to reduce cellular osmotic pressure. This leaves the electrostatic anion problem unsolved but it was resolved by admitting potassium ions. Potassium is the only sufficiently available ion in the sea for this purpose. At the concentrations of K+ inside the cells the equivalent amount of Na+ would bind considerable more strongly giving another reason for its rejection. Thus, gradients of Na+,K+ and Cl- became a fundamental feature of cell systems for all time. In fact, the almost fixed ionic composition of cell cytoplasm of the vast majority of organisms, ancient and modern, is a remarkable feature of evolution.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 174.

“In conclusion, we stress that the control of concentrations of about 12 metal ions is an essential requirement of all organisms and is a thermodynamic feature different in different chemotypes. The concentration of attention on the DNA and genetics in modern biochemistry is hiding fundamental features of life limited yet permitted by the environment. There is a ‘fitness’ of life in the environment.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 176.

“Nevertheless we do consider that there must be a general overall directional change in the organic chemistry of cells to match the changes in the environment and the inorganic element changes. It is this progression which leaves us with little doubt that there was but one way in which evolution could occur due to the very nature of the internal energised chemistry of cells and the effect of the selection of elements in them upon the environment which back interacted with the cells.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 183.

“The DNA evidence shows that the development of the numbers of related Mg2+, Ca2+, Zn2+ and Cu2+ proteins increased very rapidly with the evolution of multi-cellular eukaryotes but with relatively few completely novel protein structures and major functional changes. Through DNA analysis there are now well over 1000 known zinc and copper proteins in animals and over 500 Mg-dependent kinases in humans alone.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 342.

“A fast organic messenger molecule has to be degraded very shortly after release from binding at a receptor to allow rapid, repeated response and is therefore free for any length of time only at extremely low fixed concentration.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 349.

“To summarise the way in which the increase of oxidation using new elements and novel states of previously used inorganic elements, created in environmental conditions, enabled multi-cellular organisms to evolve new selective organic communication systems between differentiated cells, we note: (i) the increase in the cytoplasm of selected cells of iron oxidases, e.g. for steroids, thyroxine, retinoic acid and prostaglandins production; (ii) the increased use of oxidation outside selected cells and in vesicles by copper enzymes, e.g. adrenaline and hydroxylated peptides production; (iii) the involvement of oxidation of halides, e.g. in thyroxine synthesis as well as of even carbon and nitrogen (e.g. oxides CO and NO) employing haem iron enzymes in cells; (iv) the value of selected zinc receptors to monitor oxidised products and (v) the use of zinc peptidases to destroyed oxidised peptides. The developments apply to all multi-cellular chemotypes, but differentially to different cell types and organs. Only in animals is there a necessity for a vast range of transmitters. Oxygen increase together with that of the external availability of some metal ions in protein complexes was clearly essential for this evolution. We stress again that zinc and copper were released increasingly into the environment by oxidation of their sulfides only around one billion years ago.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. pp. 349-350.

“In a plant, such chemistry [use of catalysts for connective tissue by manganese in oxidized state] is not so dangerous since plants unlike higher animals do not have circulating cells, so that a disease such as cancer does not metastasise in them.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 353.

“The reason for the existence of large plants is then that they can take advantage of their organised ability to capture and use available energy (light) and materials by occupying previously unoccupied space, while that of large animals is their searching and scavenging abilities. They then increase synthesis and energy degradation rate, respectively, Note, for example, how higher organisms increase energy turnover in that ‘bacterial’ organelles for degradation (e.g. mitochondria) are linked with bacterial syntheses (e.g. chloroplasts) in a unity in the ecosystem through plants and animals.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 361.

“Because al the chemicals produced [in organisms] are unstable (in bond energy and/or gradient), it is not only the drive to optimal rate of energy absorption but also of optimal degradation of chemicals that is achieved in a fully cyclic system, and the activity therefore corresponds with an optimal rate of thermal entropy production by the system on reaching the final steady state….” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 365.

“The increased complexity of the total necessary set of chemical operations in later organisms made reliance on one another, especially earlier organisms, that is between chemotypes of organisms, unavoidable to gain efficiency. The later organisms are slower in reproduction but have organisational advantages that allow coexistent and cooperative survival with the earlier more numerous life forms. The final objective can only be achieved if all organisms within the environment work together in an ecosystem to retain energy to as great a degree as possible without further environmental waste, even though some, mostly similar, organisms, may compete with and even feed on one another.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 366.

“Clearly, what is desirable for a quicker response of a large organism for faster long-range communication is a charge carrier stored in a gradient, which does not bind, and hence does not cause chemical but only field change during transmission in the point of required action. Any chemical activity is a time and energy waste until the message reaches its action site. In the response, only a local part of a whole body needs to be informed from the senses, which have been activated through specific connections with the site to be made useful via an effective line of connections in an electrolytic system analogous to an electrical wire.”

“The observed system for this fast coordinated action is in fact the only one open to biological evolution – the use of the gradients of the very weakly binding ions generated of necessity by all cells from the beginning of life, that is of Na+, K+ and Cl-. Any transfer of such ions across membranes causes fast electrical potential, physical, change but no chemical change.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. pp. 369-370.

“However, the nerve message had to produce a response at termini, that is, for example at the locomotive organs, muscles, nerve relay junctions or any other organs that are capable of being activated. Therefore, there had to be at the nerve endings, the so-called synapses, an accessory system of messenger units, which could bring about action. The obvious choice was influx of calcium ions, which, stimulated by an Na+/K+ nerve current locally at synapses, could flow in pulses [for chemical effects], into and then out of a cell.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 371.

“As this central organisation grew it developed a novel feature. The effect of a nerve message to a bundle of central nerves in the brain came to bring about specific cell growth and storage of chemicals in them. These two features, nerve growth and storage with communication between them reflected experience of the environment (a memory)…. Quite differently from DNA and a computer code a bit is now not an all or nothing store but a (variable) concentration at a synapse and as a result it is much more prone to variation even error (and in the end perhaps to what we call imagination and even creativity?). Concentration storage gives memory a variable intensity factor dependent upon the size of and the concentration in the store, but a store can and does decay.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. pp. 374-5.

“In conclusion, higher multi-cellular plants, lower unicellular plants, multi-cellular and unicellular fungi and prokaryotes include several different chemotypes which cooperate in an organised ecosystem.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 385.

“The parallel stepwise chemical and organisational development of very different chemotypes, which became separated very early in evolution, and the fact that the time of these developments is not linked by any genetic relationship, is highly suggestive that for all organisms evolution is environmentally driven since environmental change came first and is common to all.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 387.

“We are then the poorest organisms as a chemical factory, and with the activity of our brains the fastest heat producers.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 397.

“Thus, human activity is in line in part with the proposition that evolution concerns energy degradation, but to make it fully compatible with long-term sustainability all our chemical products must cycle…. While we, mankind, operate on short-term basis, at best 5-10 years, biological or rather, to include the environment, ecological evolution is based on hundreds of millions of years. Unfortunately, the time scales of the two are so disparate that the two systems may well come into conflict rather than into cooperative activity.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 404.

“… the environmental sequence of states of elements in evolution followed their aqueous oxidation/reduction potentials as the concentration of oxygen increased…. A change, an increase in potential with the [oxidised]/[reduced] ratio, is then imposed on the whole environment where change is relative to the starting potential of the environment, say -0.2 V on the H+/H2 scale at pH 7.0. The critical changes in the equilibrated inorganic chemistry of the surface of the Earth occurred as the potential increased towards that of the ambient oxygen of today, that is + 0.8 V on the same scale.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. pp. 429-430.

“Evolution may be blind in its diversification of similar organisms (species) but it expands within a directed time cone of physical and chemical opportunity in an ecosystem, increasing and improving the retention and use of elements and energy….” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 442.

“Evolution is then blind in similar species production but it feels its way along a cone-like constraint of increasing variety with the direction fixed by major environmental features while the diversity of its ever-increasing small variations is not directed. All the time the efficiency of the whole ecosystem in the degradation of energy increases; while there is considerable cooperation between chemotypes and limited competition between species and individuals.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 447.

“Thus, historically the ages of the history of mankind are labelled Stone (physical, not chemical, but note bricks and mortar). Bronze (Cu, Sn), Iron, and finally Industrial or should it be called The Age of all the Elements, when evolution has entered a final stage. (Mankind could be considered as a very rapid succession of chemotypes and note that the order of elements used is that of availability as in all other stages of evolution.) The availability of the appropriate elements has followed the rise in working temperatures (i.e. intense use of energy) from 300 K (primitive) via 1,000 K (Iron Age) (coal) to 3,000 K (Al) in element production.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. p. 450.

“In order to achieve a high information content in multi-omic data, as a community we need to learn to adhere to standards, to conduct experiments in a highly systematic fashion, and to anticipate the integration of sophisticated mathematical approaches at the stage of experimental planning…. Multi-omic sciences has the potential to transform our understanding of biological systems and enable an excitingly fresh view on how the biological system is functioning.” Haas, Robert, A. Zelezniak, J. Iacovacci, S. Kamrad, S. Townsend & M. Ralser. 2017. “Designing and interpreting ‘multi-omic’ experiments that may change our understanding of biology.” Current Opinion in Systems Biology. 6:37:45. p. 43.

“There are unchanging principles of process and abstract forms. But to be actual is to be a process. Anything which is not a process is an abstraction from process, not a full-fledged actuality….

“… the contrary notion that what is actual or fully real is beyond change leads to a devaluation of life in the world…. But to understand that the process is the reality directs the drive to be ‘with it’ into immersion in the process.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 14.

“If the process constituting our world were a single smooth flow, the boundaries of events would have to be placed upon them by perception or thought, and there would be no real individuals. All of the ideas to be developed in later sections of this chapter depend on the notion of real individuals. The boundaries of most things which are ordinarily called ‘events’ are arbitrarily imposed from without, of course. Events such as elections, wars, storms, graduations, and dinners are of this type. But there are also events that have a unity of their own. As the next section will clarify further, this is an experiential unity. Events of this restricted type are true individuals. Whitehead calls them ‘actual occasions’ or ‘occasions of experience.’

“This doctrine, that the true individuals are momentary experiences, means that what we ordinarily call individuals, the sorts of things that endure through time, are not true individuals, but are ‘societies’ of such. Personal human existence is a ‘serially ordered society’ of occasions of experience….

“Besides the process of transition from occasion to occasion which constitutes temporality, there is another type of process. The real individual occasions of which the temporal process is made are themselves processes. They are simply the processes of their own momentary becoming. From the external, temporal point of view they happen all at once; yet at a deeper level they are not to be understood as things that endure through a tiny bit of time unchanged, but as taking that bit of time to become. Whitehead calls this becoming ‘concrescence,’ which means becoming concrete.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 15.

“The dual emphasis on the process of transition and the process of concrescence opens the way for the understanding of a variety of religious experiences. On the one hand, transition establishes the importance of time. One occasion succeeds another….Time flows asymmetrically from the past through the present into the future. There can be no denial of the reality of time nor can there be any doctrine of its circularity. Every moment is new and none can be repeated. The sense of history is undergirded. On the other hand, the experience of the ‘eternal now’ is also intelligible. In the process of concrescence itself there is no time. This means not that there is static actuality, but that the successiveness of transition does not apply. Every moment is a now, which in this sense is timeless.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. pp. 15, 16.

“Whitehead, like Teilhard, holds that all actualities have an inner reality as well as an outer one. Hence, the sense of kinship with all things, which has evidently characterized human experience at most times and places, is rationally supported [in contrast to dualism].” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 18.

“The idea that the experiencing processes are momentary is the basic difference of Whitehead’s philosophy from that of Leibniz. Like Whitehead, Leibniz saw the actual world as composed exhaustively of experiencing processes. These ‘monads’ did not, however, experience anything beyond themselves. Although Leibniz used the term ‘perception’ to describe their activity, he defined this perception as projection. The monads did not really enter into each other’s experiences. Each one was completely ‘windowless.’” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 20.

“Each of Whitehead’s occasions of experience begins, as it were, as an open window to the totality of the past, as it prehends all the previous occasions (either immediately or mediately)…. But as soon as this process is completed, the windows of the world are again open, as a new occasion of experience takes its rise… In such a stream of occasions, a ‘defining essence’ of that stream may arise, representing the characteristics that apply to each member of the stream. But this enduring stream with its stable essence is an abstraction in comparison with the individual occasions themselves, which alone are fully concrete individuals.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 20.

“Since God was said to be totally independent, with no real relations to any other actualities, it was natural to think in similar terms of the worldly actualities that God created, especially since some of them were said to be made in the divine image. Accordingly, the Leibnizian monads were totally independent of everything else, except God. On this point Leibniz is at one with Descartes, who had defined a substance as ‘that which requires nothing but itself to exist’” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 21.

“Whiteheadian process thought gives primacy to interdependence as an ideal over independence.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 21.

“Ecology, as the study of the interrelationships of things, has taught us that this view [the billiard ball model of the world’s being only efficient causation] is false. Interrelations are internal to things. Whitehead’s thought is thoroughly ecological.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 24.

“However, precisely how the present subject responds to its past, precisely how it incorporates the past feeling, precisely how it integrates the multiplicity of feelings into a unified experience–this is not determined by the past…. For each actuality is partially self-creative; it finally creates itself out of the material that is given to it….

“Final causation finishes what efficient causation had begun.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 25.

One aspect of God is a primordial envisagement of the pure possibilities. They are envisaged with appetition that they be actualized in the world. The actualization of novel possibilities generally increases the enjoyment of experience; for the variety of possibilities that are actualized in an experience adds richness to the experience, and the element of novelty lends zest and intensity of enjoyment.

“This means that the divine reality is understood to be the ground of novelty. This stands in tension with most religious philosophies, according to which deity (if it be the ground of anything in the world) is the ground of an established order. The God of process thought is also the ground of order, but this is a changing and developing order, an order that must continually incorporate novelty if it is not to become repressive of enjoyment. The positive appraisal of novelty resulting from this vision pervades process theology.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 28.

“There are not actual entities that first are self-contained and then have accidental relations to God. God-relatedness is constitutive of every occasion of experience…. It is God who, by confronting the world with unrealized opportunities, opens up a space for freedom and self-creativity.” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 29.

“Process theology rejects the notion of creatio ex nihilo, if that means creation out of absolute nothingness. That doctrine is part and parcel of the doctrine o God as absolute controller. Process theology affirms instead a doctrine of creation out of chaos (which was suggested not only by Plato but also by more Old Testament passages than those supporting the doctrine of creation out of nothing).” Cobb, John & D.R. Griffin. 1976. Process Theology: An Introductory Exposition. Louisville: Westminster John Knox Press. p. 65.

“There are three reasons why I use the Gaia hypothesis as one of my two organizing themes. First, by being rooted in questions of regulation and stability through identifiable biological, chemical, and physical processes, it gives a direction for relevant scientific research – for disproof of the hypothesis if nothing else. Second, this is the only concept I know that can, in principle, provide a global rationale for giving priority to rehabilitation, protection of ecosystems, and land use management. If CH4 production, for example, provides an essential negative feedback control for ozone concentration, then the recent 1-2% annual increase in CH4 content is important and priority should be given to considering major changes in its primary sources – i.e., wetlands, biomass burning, and ecosystems containing ruminants and termites. Finally, an examination of global change concerns not only science but policy and politics. In a polarized society where certitude is lacking, Gaia has some potential for bridging extremes by providing a framework for understanding and action.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. p. 294.

“Expectations [about ecological change] develop from two interacting sources: from the metaphors and concepts we evolve to provide order and understanding and from the events we perceive and remember. Experience shapes concepts; concepts, being incomplete, eventually produce surprise; and surprise accumulates to force the development of those concepts. This sequence is qualitative and discontinuous. The longer one view is held beyond its time, the greater the surprise and the resultant adjustment. Just such a sequence of three distinct viewpoints, metaphors, or myths has dominated perceptions of ecological causation, behavior, and management.

“Equilibrium-centered view: nature constant….

“Multiple equilibria states: nature engineered and nature resilient….

“Organizational change: nature evolving.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. pp. 294, 295.

“… a number of examples are presented to demonstrate that successful efforts to constrain natural variability lead to self-simplification and so to fragility of the ecosystem. A variety of genetic, competitive, and behavioral processes maintain the values of parameters that define the system. If the natural variability changes, the values shift: the landscape of hills and valleys [stability multiple equilibria] begins to alter. Stability domains shrink, key variables become more homogeneous (e.g., species composition, age structure, spatial distribution), and perturbations that previously could be absorbed no longer can be….

“An example from biological evolution is the remarkably constant internal temperature maintained by endothermic (warm-blooded) animals in the presence of large changes in external temperature. A large metabolic load is required to maintain a constant temperature. As expected, the range of internal temperatures that sustains life becomes narrower than for (cold-blooded) ectotherms. Moreover, the typical endotherm body temperature of around 37̊ C is close to the upper lethal temperature for most living protoplasm. It does not represent a ‘policy’ of keeping well away from a dangerous threshold.

“The evolutionary significance of this internal temperature regulation is that maintenance of the highest body temperature, short of death, allows the greatest range of external activity for an animal. Speed and stamina increase and activity can be maintained at high and low external temperatures, rather than forcing aestivation or hibernation. There is hence an enhanced capability to explore environments and conditions that otherwise would preclude life. The evolutionary consequence of such temperature regulation was the suddenly available opportunity for dramatic organizational change and explosive radiation of adaptive life forms. hence the reduction of internal resilience as a consequence of effective self-regulation was more than offset by the opportunities offered by other external settings.

“Hence the study of evolution requires not only concepts of function, but also concepts of organization – of the way elements are connected within subsystems and the way subsystems are embedded in larger systems.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. pp. 295-6.

“Stability is the propensity of a system to attain or retain an equilibrium condition of steady state or stable oscillation. Systems of high stability resist any departure from that condition and, if perturbed, return rapidly to it with the least fluctuation. It is a classic equilibrium-centered definition.

“Resilience, on the other hand, is the ability of a system to maintain its structure and patterns of behavior in the face of disturbance. The size of the stability domain of residence, the strength of the repulsive forces at the boundary, and the resistance of the domain to contraction are all distinct measures of resilience.

“Stability, as here defined, emphasizes equilibrium, low variability, and resistance to and absorption of change. In sharp contrast, resilience emphasizes the boundary of a stability domain and events far from equilibrium, high variability, and adaption to change.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. pp. 296-7.

“The designations come from the terms of the logistic equation, where K defines the saturation density (stable equilibrium population) and r the instantaneous rate of increase. MacArthur pointed out the contrast between ‘opportunist’ species in unpredictable environments (r-strategists) and ‘equilibrium’ species in predictable ones (K-strategists).” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. p. 298; reference: MacArthur, R.H. 1960. “On the relative abundance of species.” American Naturalist. 94:25-36.

“The full dynamic behavior of ecosystems at an aggregate level can therefore be represented by the sequential interaction of four ecosystem functions: exploitation, conservation, creative destruction, and renewal. The progression of events is such that these functions dominate at different times: from exploitation, 1 [referring to a sequence on a horizontal figure eight with 1 being the lower left quadrant leading up to 2 at upper right and down to 3 at lower right …], slowly to conservation, 2, rapidly to creative destruction, 3, rapidly to renewal 4, and rapidly back to exploitation….

“The speed and amplitude of this cycle, as indicated earlier, are determined by whether the fast, intermediate, or slow variable dominates the timing.

“These patterns in time have consequences for patterns in space. rapidly cycling systems generate ecosystems that are patchy. Tropical ecosystems are an example. Slowly cycling systems produce higher amplitude, discontinuous change that tends to occur as a wave moving across space.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. p. 307.

“… the pattern of connectedness and the resultant balance between stability and resilience are a consequence of the pattern of external variability that the system has experienced. Systems such as those in the tropics, which have developed in conditions of constant temperature and precipitation, therefore demonstrate high stability but low resilience. They are very sensitive to disturbances induced by man. On the other hand, temperate systems exposed to high climatic variability typically show low stability and high resilience, and are robust to disturbance by man.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. p. 308.

“Man’s efforts to manage ecosystems can be viewed as weak experiments testing a general hypothesis of stability/resilience. In many of the examples discussed earlier, the management goal was to reduce the variability of a target variable by applying external controls. Crudely, it represented an equilibrium-centered view of constant nature. All the cases examined were successful in achieving their short-term objectives, but as a consequence of that success, each system evolved into a qualitatively different one.

“The evolution took place in three areas. First, the social and economic environment changed. More pulp mills were built to exploit the protected spruce-balsam forests; more recreational demand was developed in the parks protected from fire; more efficient and extensive fisheries were developed to exploit salmon; more land was used for cattle ranches on the savannas; and more development was possible in those areas protected from malaria.

“Second, the management agencies began to evolve. Effective agencies were formed to spray insects, fight fires, operate fish hatcheries, encourage cattle ranching, and reduce mosquito populations. And the objective of those agencies naturally shifted from the original socioeconomic objective to one that emphasized operational efficiency: better and better aircraft, navigation, and delivery systems to distribute insecticide; better and better ways to detect fires and control them promptly.

“These changes in the socioeconomic environments and in the management institutions were generally perceived and were rightly applauded. But evolution occurred in a third area – the biophysical – whose consequences were not generally perceived.

“Because of the initial success in reducing the variability of the target variable, features of the biophysical environment which were implicitly viewed as constants began to change to produce a system that was structurally different and more fragile. Reduction of budworm populations to sustained moderate levels led to accumulation and persistence of foliage over larger and larger areas. Any relaxation of vigilance, could then lead to an outbreak in a place where it could spread over enormous areas. Reduction of fire frequency led to accumulation of fuel and the closing of forest crowns so that what were once modest ground fires affecting limited areas and causing minor tree mortality became catastrophic fires covering large areas and causing massive tree mortality….

“In short, the biophysical environment became more fragile and more dependent on vigilance and error-free management at a time when greater dependencies had developed in the socioeconomic and institutional environment. The ecosystems simplified into less resilient ones as a consequence of man’s success in reducing variability.” Holling, C.S. 1986. The resilience of terrestrial ecosystems: local surprise and global change.” In: Clark, W.C. & R.E. Munn (Eds). pp. 292-320. Sustainable Development of the Biosphere. Cambridge UP. pp. 310-1.

“Convivial Conservation

“In its core, our conceptualization of conviviality is necessarily post-capitalist and non-dualist. Regarding dualisms, our understanding of ‘convivial’ is meant to build on its etymological roots of ‘con’ (with) and ‘vivire” (living) or ‘living with’. Hence, it is in line with our second theoretical principle, which fundamentally envisions a conservation that does not separate humans and nature ….” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 160.

“I consider conviviality to be individual freedom realized in personal interdependence and, as such, an intrinsic ethical value. I believe that, in any society, as conviviality is reduced below a certain level, no amount of industrial productivity can effectively satisfy the needs it creates among society’s members.” Illich, Ivan. 1973. Tools for Conviviality. Harper & Row. p. 11; subquote in: Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 161.

“Hence, the only solution to protecting nature’s value is to build an integrated (economic, social, political, ecological, cultural) value system that does not depend on the destruction of nature but on ‘living with’ nature.” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 165.

“In fact, we have long suspected that something must be terribly wrong if we have to put boundaries between ourselves and nonhuman nature; it means, essentially, that we have to protect ourselves from ourselves.” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 165.

“As Marshall Sahlins ‘modestly’ concluded: ‘Western civilization has been constructed on a perverse and mistaken idea of human nature’…. Sahlins refers to the idea of human nature as competitive, self-interested and rational, the stereotypical ‘homo economicus’ underlying neoliberal forms of governance that even ‘21st century economists’ do not believe in anymore.” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 166; subquote: Sahlins, Marshall. 2008. The Western Illusion of Human Nature. Chicago: Prickly Paradigm Press.

“As Kate Soper asserts, ‘Unless human beings are differentiated from other organic and inorganic forms of being, they can be made no more liable for the effects of their occupancy of the ecosystem than can any other species, and it would make no more sense to call upon them to desist from destroying nature than to call upon cats to stop killing birds.’” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 167; reference: Soper, Kate. What is Nature. p. 160.

“So, instead of asking how conservation can lead to more (necessarily monetized) ‘value’ in the future, we should start by asking how a (necessarily non-monetized) value is embedded in the here and now and in which contexts this value receives local and extra-local meaning. In short, we need to refocus from value in motion, or capital, to what we could call ‘embedded value’. The latter’s logic is not based in market-based commodity exchange whereby nature has to ‘provide services’ to humans to be protected, but receives its worth from and through humans and nonhumans ‘living with’, understanding, appreciating but also politically confronting and agonistically struggling with each other (through cultural, artistic, experiential, affective or other non-commodified or non-monetized forms).” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 173.

“The importance of nature – the web of life, the basis of all life – should never have to be ‘made’ visible. Living with nature means that it is visible by definition. ‘Money’ – the universal equivalent that is supposedly the tool to make nature ‘visible’ under capitalism – only renders nature visible on spreadsheets and through necessarily simplistic, technocratic decision-making models outside of relevant contexts. This renders nature unidimensional – solely what it is worth to humans-as-investors.” Buescher, Bram & R. Fletcher. 2020. The Conservation Revolution: Radical Ideas for Saving Nature Beyond the Anthropocene. NY: Verso. p. 175.

“Any protein structure exists in solution as a population of conformer families…. Moreover, the conformational landscape of the protein is not fixed. Binding of ligands, posttranslational modifications, temperature, pressure, solvent and other factors may drastically alter the conformational landscape by triggering a redistribution of conformers and changing heights of the energy barriers separating alternative conformers.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 3.

“Proteins performing multiple functions have come to be recognized as a phenomenon in itself under the cliche ‘moonlighting proteins’.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 4.

“The balance between order and disorder in protein structure, function, and interactions ensures that higher order macromolecular complexes and sub-cellular structures, and thus vital cellular functions, remain flexible and adaptive on relatively short timescales that are too fast to involve genetic mechanisms and that require rapid and efficient epigenetic adaptations.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 4.

“Steady-state macromolecular organizations are sustained by the flow of energy and matter passing through them, with their resident components entering and leaving organization with widely different recruitment probabilities, residence times, and turnover rates.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 5.

“… it appears that many, perhaps all, macromolecular complexes and sub-cellular structures are assembled and maintained as steady-state molecular organizations only when they perform their functions. They are dissolved or restructured when their functions are no longer needed or altered within the cell.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 5.

“Broadly defined, ‘compartmentalization of metabolism’ traditionally refers to an ordered physical association or clustering of metabolic enzymes performing sequential steps in a given metabolic pathway…. The more organized and coordinated are the individual enzymes in a complex or compartment, the less relevant diffusion becomes for the rate of metabolic production.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 7.

“… in contrast to conventional cellular compartments, which are relatively stable and are present in most cells most of the time under most conditions, metabolic compartments are often assembled on demand to satisfy changing or local needs of cellular economy that emerge in response to transitory environmental challenges and opportunities.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 7.

“An et al. have recently shown that all six enzymes of the de novo purine biosynthetic pathway reversibly co-cluster in human cultured cells under purine-depleted conditions, but remain disorganized within the cytoplasm in purine-rich medium…. In plant cells, glycolytic enzymes have been reported to reversibly partition from a soluble pool to a mitochondria-bound pool upon increased respiration and back into the soluble pool upon inhibition of respiration.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 7; reference: An, S., R. Kumar, ED Sheets, SJ Benkovic. 2008. “Reversible compartmentalization of de novo purine biosynthetic complexes in living cells.” Science. 320:103-106.

“Specifically, one can suggest that all the well-known relatively large and stable sub-cellular structures and macromolecular complexes constitute the relatively higher levels in the hierarchy of cellular metabolic organization. In other words, they represent the macromolecular organizations that operate and change on relatively large and slow spatiotemporal scales, akin to large-scale social and business organizations and institutions in a national economy…. In other words, all the larger-scale sub-cellular structures and macromolecular complexes are built on, and, at the same time, support productive activity of various dynamic metabolic compartments/sequences that transiently associate with them through mutually profitable exchanges of energy/matter…. Whatever molecule, complex, structure, or process we choose to consider, they all have some metabolic function within the hierarchically structured continuum of cellular economy, where they both define and are defined by metabolism.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 9.

“Importantly, what is preserved on the scales characteristic for such steady state macro-organizations are the spatio-temporal relationships between individual components, i.e. a certain organizational structure–a form–but not individual components passing through a given organization.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 10.

“The emergence of intertwined fluxes, gradients, and steady-state compartments in nonequilibrium systems such as the cell occurs not because some molecules were designed to pump other molecules across semi-permeable barriers with the purpose of creating and maintaining concentration gradients – that is the inevitable and faulty logic of equilibrium thermodynamics and classical mechanics – but rather because a steady-state system of interdependent fluxes and gradients is a normal state of an open physicochemical system operating in far-from-equilibrium conditions.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 12.

“Meanwhile, one of the critical parameters characterizing the structure and dynamics of nonequilibrium systems is not concentration but the rate of flow.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 13.

“Notice that, ironically, and hardly coincidentally, non-equilibrium thermodynamics of the West is in remarkable harmony with the traditional Eastern views on the organism and on life in general, which are based on such concepts as conflict of opposites (countervailing gradients), energy fluxes, and the disease state as a misbalance of energy flow, but not with the Western conceptualization of biology and life.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 13.

“… the cell can apparently preserve most of its structures and functions for extended periods of times, even when its plasma membrane is severely compromised. This implies that the plasma membrane is not a conventional membrane of the mechanistic world, but is a part of convection-like pattern of energy/matter exchanges that is relatively dispensable for the organization and dynamics of the remaining part of the pattern in a short run.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 15.

“The problem is that, instead of clarifying the hypothetical evolutionary design, ever-advancing technology and methods make it ever more confusing and elusive, by generating massive amounts of the experimental data that is manifestly inconsistent with and difficult or impossible to assimilate within the mechanistic/clockwork image of the cell. Hence, the accumulation of paradoxes, controversies, inconsistencies, and contradictions that persist unresolved over time; hence the rise of technology-driven ‘discovery’ science and a decline of hypothesis-driven research – a sure sign of the failure of the conventional paradigm to serve as a theoretical framework enabling understanding and prediction of experimental outcomes.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 20.

“The present work shows that the experimental reality in molecular and cell biology becomes largely devoid of paradoxes, inconsistencies, and contradictions, and is thus best understood, if the conventional interpretational framework of classical physics is replaced by an alternative paradigm of biological organization, which is based on the concepts and empirical laws of nonequilibrium thermodynamics.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 20.

“It is worth point out that the cell as a whole or any functional constituent of the cell is dynamic in two different senses. The cell or a functional part of the cell is dynamic in the sense that it represents a structured pattern of continuous energy/matter flow. At the same time, the cell or any functional part of the cell is dynamic in the sense that this structured flow pattern can adopt several, and potentially many, metastable organizational configurations that differ in the organization of energy/matter exchanges transiently maintained among the interacting components that make up (and flow through) the pattern. The latter type of dynamics, which may be called configurational dynamics, as opposed to flow dynamics, requires and relies on flexibility and adaptability of functional constituents comprising a given biological organization….

“In exactly the same way, various business, social, and political organizations compete and cooperate one with another in order to obtain and to ensure stable and accelerating flows of energy/matter passing through them, which they require for their maintenance and growth within the socio-politico-economic system they form. Those organizations that succeed in securing and accelerating the flow of energy/matter through their structures grow in size, order, complexity, and influence. Those organizations that fail to maintain achieved rates of energy/matter flow through their structures either diminish in their relative size, order, complexity, and influence or dissolve.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. pp.[numbering possibly not matching] 21, 22.

“Notice that, within the new paradigm of biological organization, economics explains nonequilibrium thermodynamics and, at the same time, nonequilibrium thermodynamics explains economics, making economics and nonequilibrium thermodynamics look like two different descriptions of one and the same phenomenon. I would like to suggest here, therefore, that economics holds keys to the understanding of nonequilibrium thermodynamics, while nonequilibrium thermodynamics holds keys to the understanding of economics, and that both of them hold keys to the understanding of biology. In other words, what appears to be three disparate sciences are, in fact, intimately interrelated aspects/dimensions of one and the same science.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 23.

“The cell as a well-mixed biochemical reactor becomes a ‘square’ fact, obvious to everyone. It becomes the reality. Once such a ‘reality’ has crystallized as a structure in the minds of researchers and educators, it becomes an unconscious theoretical framework, a paradigm, a conventional wisdom, which directs and filters the experience of the research community as a whole and defines which methods, questions, and interpretations are legitimate and which are not, which projects and ideas are valuable and which are dispensable…. It is of little surprise then that biochemical evidence indicating the existence of intracellular organization and circulation, direct microscopic visualization of elaborate cytoplasmic organization, experimental evidence suggesting compartmentalization of metabolism and substrate channeling, the flow theory of metabolism, alternative physical and physicochemical theories of the cell and intracellular organization and transport, and other related studies and theories are suppressed or ignored.” Kurakin, Alexei. 2009. “Scale-free flow of life: on the biology, economics, and physics of the cell.” Theoretical Biology and Medical Modelling. 6:6. doi: 10.1186/1742-4682-6-6. p.[numbering possibly not matching] 24.

“We define robustness as the ability of a living system to survive disturbances largely intact. In contrast, the resilience of a living system is the ability of that system to withstand stress and be restored after disturbance without losing its integral structure and function.” Davis, Jason, M.B. Kolozsvary, K.M. Pajerowska-Mukhtar & B. Zhang. 2021. “Toward a Universal Theoretical Framework to Understand Robustness and Resilience: From Cells to Systems.” Frontiers in Ecology and Evolution. 8:579098. doi: 10.3389/fevo.2020.579098. p. 1.

“At the molecular level [following stress from high heat], cellular signaling ensues that initiates stable changes in the genome (epigenetic memory) within the affected cell itself and/or adjacent cells/tissues; a phenomenon dubbed ‘epigenetic scarring’ that is now considered to be the molecular basis for cellular resilience.” Davis, Jason, M.B. Kolozsvary, K.M. Pajerowska-Mukhtar & B. Zhang. 2021. “Toward a Universal Theoretical Framework to Understand Robustness and Resilience: From Cells to Systems.” Frontiers in Ecology and Evolution. 8:579098. doi: 10.3389/fevo.2020.579098. p. 2.

“At the organismic level robustness and resilience are tightly connected to the concepts of stress, homeostasis, and allostasis.” Davis, Jason, M.B. Kolozsvary, K.M. Pajerowska-Mukhtar & B. Zhang. 2021. “Toward a Universal Theoretical Framework to Understand Robustness and Resilience: From Cells to Systems.” Frontiers in Ecology and Evolution. 8:579098. doi: 10.3389/fevo.2020.579098. p. 2.

“Some of the paradigms that have been proposed to be particularly useful for conceptually unifying the trans-scalar properties of systems are: (1) division of labor and spatiotemporal organization of production and exchange, such as the presence of cellular compartments, limb diversification in arthropods, or different tasks performed by different ant workers within the nest; (2) systemic homeostasis, achieved by balancing the economic efficiency and adaptability; while the former requires adequate and stable organization, the latter is best supported by flexibility and change; (3) ‘small-world’ network (SWN) propensity, where high local clustering of nodes is accompanied by short average path length between any two nodes. The emergence of SWN patterns has been described to occur within biochemical pathways in the cell, the brain neural network or ecological food webs; and (4) trade-off effects on growth and fitness at the cost of a heightened stress response.” Davis, Jason, M.B. Kolozsvary, K.M. Pajerowska-Mukhtar & B. Zhang. 2021. “Toward a Universal Theoretical Framework to Understand Robustness and Resilience: From Cells to Systems.” Frontiers in Ecology and Evolution. 8:579098. doi: 10.3389/fevo.2020.579098. p. 3.

“Biosphere is a specific envelope of the Earth, comprising totality of all living organisms and that part of planet matter which is in constant material exchange with these organisms. Biosphere includes geospheres i.e. lower part of the atmosphere, hydrosphere and upper levels of lithosphere. Virtually, it is a spherical layer 6-12 km thick. In the view of Vernadsky, life is the geological force. Indeed all geological features at Earth’s surface are bio-influenced. The planetary influence of living matter becomes more extensive with time. The number and rate of chemical elements transformed and the spectrum of chemical reactions engendered by living matter are increasing, so that more parts of Earth are incorporated into the biosphere.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 4.

“There is also another point of view concerning the origin of the life and its evolution on Earth. It is based on the assumption that all living organisms on the planet depend on one another i.e. any life outside biosphere is impossible. In this view, the biosphere (or – in western tradition – Gaia) is considered a separate system of the highest structural level of life-organization. This system controls and directs evolution of living organisms and earthly ecosystems. Such assertion is named the pan-biospheric paradigm.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 11.

“… one can argue that the pre-biosphere [early Earth] is a system, which is self-preserved, and which is similar to primitive organism without generative organs. In other words, the pre-biosphere in this view is weakly differentiated system, which develops as embryo by means of successive differentiations. The pre-biosphere with above particularities was named by us embryosphere.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 12.

“In our earlier works we discussed some regularities which characterize different stages of biospheric evolution: 1) gradual expansion of the life to new, before lifeless conditions and areas [sic]; 2) complication of the structure of the biosphere, the appearance of new circulations and ecosystems; as regular consequence of that – the gradual increasing of biodiversity up to some optimal level for the current conditions; 3) gradual inclusion of more and more matter of the planet into the living processes of the biosphere; 4) gradual increasing of energy flow through the biosphere during its evolution; 5) relative steadiness of all circulations of the biosphere; the disturbance of balance between circulations leads to a biospheric crisis; 6) auto-regulation (auto-canalization) of the biosphere evolution: every evolutionary step leads to the creation of new specific conditions on the planet which constrain the availability of directions for the subsequent steps.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 13.

“In our opinion the conception of the biosphere has to be included to any definition of contemporary life.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 16.

“The question ‘what is the origin of life: either origin of organisms or origin of biosphere?’ isn’t correct because only whole biosphere is independent unit of life among all known living forms.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 26.

“… we believe following Vernadsky that life without biosphere is impossible and doesn’t exist.” Levchenko, Vladimir, A.B. Kazansky, M. A. Sabirov & E. M. Semenova. 2012. “Early Biosphere: Origin and Evolution.” pp. 3-32. In: Ishwaran, Natarajan (Ed). The Biosphere. Rijeka, Croatia: InTech. p. 27.

“… the concept [adaptive cycle and nested adaptive cycles to form panarchy] has had uptake by researchers from a variety of fields despite the lack of empirical evidence demonstrating adaptive cycles in real data. However, work from a wide array of fields, focused on an even wider array of ideas–self-organized criticality, edge of chaos, regime shifts, sustainability, resilience, punctuated equilibrium, game theory, and thermodynamics–suggests that the adaptive cycle describes endogenously generated dynamics in complex adaptive systems as a result of the internal processes of self-organization and evolution over time.” Sundstrom, Shana & C.R. Allen. 2019. “The adaptive cycle: More than a metaphor.” Ecological Complexity. 39:100767. doi.org/10.1016/j.ecocom.2019.100767. p. 1.

“An adaptive cycle describes system movement through a 3-dimensional state space defined by system potential, connectedness, and resilience.

“System potential is concerned with the range of options available for future responses of the system; in ecosystems this can mean an accumulation of nutrients, resources, biomass, and diversity that provide a broad range of options for the future behavior of the system in response to change. Connectedness refers to the relationships between system elements and processes, and the degree to which elements are dominated by external variability, or by relationships that mediate the influence of external variability. Resilience refers to the degree of disturbance a system can buffer without moving into a new regime, or basin of attraction.” Sundstrom, Shana & C.R. Allen. 2019. “The adaptive cycle: More than a metaphor.” Ecological Complexity. 39:100767. doi.org/10.1016/j.ecocom.2019.100767. pp. 1-2.

“Nested adaptive cycles with bi-directional cross-scale feedbacks are called a panarchy. A core hypothesis of panarchy is that the key processes that structure ecosystems occur at different ranges of spatial and temporal scales, often separated by orders of magnitude.” Sundstrom, Shana & C.R. Allen. 2019. “The adaptive cycle: More than a metaphor.” Ecological Complexity. 39:100767. doi.org/10.1016/j.ecocom.2019.100767. p. 2.

“It has also been demonstrated that maximum entropy production occurs as a function of the stage of system development, and peaks during the early to mid-stages of successional development, which translates in the adaptive cycle to somewhere in the exploitation phase.” Sundstrom, Shana & C.R. Allen. 2019. “The adaptive cycle: More than a metaphor.” Ecological Complexity. 39:100767. doi.org/10.1016/j.ecocom.2019.100767. p. 6.

“Discontinuity theory argues that ecological processes, and therefore ecological structure, occur at discrete and limited ranges of scale.” Sundstrom, Shana & C.R. Allen. 2019. “The adaptive cycle: More than a metaphor.” Ecological Complexity. 39:100767. doi.org/10.1016/j.ecocom.2019.100767. p. 8.

“More’s attitude was that, notwithstanding the use to which mechanical or atomist physics had perennially been put in the name of a materialist atheism [for example, Lucretius], or at least of something very close to it, there was nothing truly inherent to such a physical system that should render it incompatible with a proper (i.e. Platonist) account of the spiritual realm. As we have seen, More felt that these theories had once been united in a single, all-encompassing system, divinely revealed to Moses himself. After so protracted a divorce [during Roman Catholicism], it was high time that they should be reunited.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 23.

“Indeed, and significantly, he [More] was even prepared to go so far as to suggest that Descartes’ knowledge of nature might itself have had its basis in a personal inspiration directly from God himself…. More viewed Descartes’ role as being one of reviving and rehabilitating the physical branch of the ancient Mosaic cabbala. And he viewed his own role as being one of reuniting this branch with its proper spiritual partner. In one extraordinary remark, More even drew a parallel between himself and Moses, as he indicated the conception he had of himself as the great restorer of the Mosaic philosophy to the world.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 24.

“More did not, of course, believe that innate ideas were explicitly conscious in the mind from birth. He compared them to the latent skill of a sleeping musician. There would be no actual representation of anything musical in his mind but, on his being prompted with only the most ‘slight and slender intimation’–the first two or three words of a song–he would spontaneously proceed to sing the remainder. Likewise, some kind of stimulus would be required to stir up the innate knowledge that had formerly been purely latent within a man’s mind. But, when it was thus roused into consciousness, this innate knowledge would provide his mind with ‘a more full and clear conception of what was but imperfectly hinted to her from external Occasions’. More described these innate ideas as the ‘natural Furniture of humans Understanding’, and he placed them at the foundation of our moral, mathematical and logical knowledge. Among these notions, he included such things as: ‘Cause, Effect, Whole and Part, Like and Unlike, and the rest. So Equality and Inequality, logos and analogia, Proportion and Analogy, Symmetry and Asymmetry, and such like: All which Relative Ideas I shall easily prove to be no material Impresses from without upon the Soul, but her own active Conception proceeding from her self whilst she takes notice of external Objects.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 29.

“In the first account [of Plato in the Timaeus of two stories of creation], he had focused on just two components, the intelligible pattern and its sensible imitation [matter]. But then he proposed to go back to the beginning, and to tell the story again, now adding a third component to these two. He described this new component in a variety of ways: as a certain ‘necessity’ that would work in conjunction with ‘mind’ to bring forth the creatures; as a ‘receptacle’ for the creatures that could be produced within it; as ‘in a manner the nurse, or all generation’; and as the ‘matter’ upon which various sensible forms were stamped. This third thing was a purely passive substrate upon which the eternal Ideas could work to produce temporal creatures, moulding it into various sensible imitations of their own intelligible forms. But, considered purely in itself, the receptacle was entirely formless.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 75.

“Although he [Aristotle] rejected the Platonic intelligible realm of independent Ideas, he was perfectly comfortable with a distinction between the sensible form of a created individual and the matter in which such a form inhered.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 76.

“Now, it would certainly be wrong simply to equate Aristotelian prime matter with the Platonic receptacle…. The important thing for us to draw from both of these two discussions is merely the notion of an ultimate limit of pure potentiality, however that notion might get theorised in detail. That is to say, the notion of a substrate, which could take on any form whatsoever and thereby make a (purely passive) contribution to the generation of creatures, but which, considered in its own right, was utterly formless.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. pp. 76-7.

“The existence of matter was purely a relative one, insofar as it served as the potentiality of, and the substratum for, those actual bodies that would result when form entered into it.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 77.

“‘Nullibism’, from the Latin for ‘nowhere’, signified the theory that spiritual substances were not present anywhere in the spatial world….. As for ‘holenmerianism’, from the Greek for ‘whole in parts’, this signified the theory that spirits were indeed substantially present in the extended world, but with the proviso that they were present therein in a manner very different from that of bodies. A body’s presence would amount to its being spread out through a certain region of space, with really distinct parts outside parts. When a spirit was spatially present in a region of space, according to the holenmerians, it would be ‘whole in the whole, and whole in each part’. When a human soul was united to a human body, for instance, the two substances really would both be in the same place. The whole of the soul would permeate the whole of the space that was simultaneously occupied by the whole of the body, and this was what set the holenmerians apart from the nullibists. However, as far as the individual parts of the body were concerned, the person’s foot would be in a different place from his head. In the case of the soul, by contrast, the holenmerians believed that its entire substance would be present in the place occupied by the person’s foot; but, thanks to its immateriality, it could also simultaneously be entirely present in the place occupied by his head.

“The roots of ths holenmerian doctrine can be traced at least as far back as Plato, with the account he sketched in Parmenides of how the spatial presence of a Form might be understood.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. pp. 141-2.

“As far as he [More, in comparison to Descartes] was concerned, the most fundamental difference between them was not to be understood in terms of either extension or thought, but rather in terms of life, i.e. the capacity that a spiritual substance had to initiate new motions spontaneously, either in itself or in other things. Indeed, it was precisely as More made the move towards declaring that spirits as well as bodies were extended, that he really began to insist upon a robust ontological distinction between the two kinds of substance.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 185.

“All in all, Morean space seems to have had an awful lot in common with God. Once More had removed the two final impediments to an association between the two things, promoting space from potentiality to actuality, and attributing to God the same kind of extension as pertained to space itself, the way was at last clear for him to draw the natural conclusion:

‘For this infinite and immobile extension will be seen to be not something merely real but something divine after we shall have enumerated those divine names or titles which suit it exactly, and with the greatest certainty make it not possible to be nothing, seeing that so many and such excellent attributes fit it. Of which kind are those which follow, which metaphysicians specifically attribute to First Being. Such as one, simple, immobile, eternal, complete, independent, existing from itself, subsisting by itself, incorruptible, necessary, immense, uncreated, uncircumscribed, incomprehensible, omnipresent, incorporeal, permeating and encompassing everything.’

“But the argument here hinged (albeit implicitly) on the incommunicability of several, at least, of the attributes to which More’s twenty titles referred…. As Anne Conway put it: ‘The divine attributes are commonly and correctly divided into those which are communicable and those which are not. The incommunicable are that God is a being subsisting by himself, independent, immutable, absolutely infinite, and most perfect. The communicable attributes are that God is spirit, light, life, that he is good, holy, just, wise, etc.’ Now, in More’s list of twenty attributes, a couple do seem to be communicable, such as simplicity and incorporeality…. But most of the others seem to fit the bill as incommunicable attributes….

“Instead of proposing an unqualified identification between space and the divine substance, he now [1671] preferred to treat it merely as one aspect thereof: ‘that inmost Extension or Amplitude which will necessarily remain after we have imagined all Matter, or whatever else is removeable, removed or exterminated out of the World is to be look’d upon as the permanent Expansion or Amplitude of the radical Essentiality of God.’” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. pp. 214-5; subquotes: More, Henry. 1995[1671] Enchiridion metaphysicum, vol. 1. p. 57; Conway, Anne. 1996. The Principles of the Most Ancient and Modern Philosophy. Cambridge UP. p. 45; More, Henry. 1688[1713]. Divine Dialogues. p. 289.

“For Descartes, as is well known, the principal attribute of body was extension, while the principal attribute of mind or soul was thought. For More, at least from 1659 onwards, extension as such was not going to help us to discriminate between bodies and souls at all, for it pertained equally to both. But, in addition, he did not accept that the essence of soul should be understood in terms of thought either. Rather, … he identified the defining attributes of the two species of substance as impenetrability, discerpibility and self-inactivity for bodies, and the opposites of these for spirits: penetrability, indiscerpibility [indivisibility] and self-activity.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 237.

“Descartes did more than merely define ‘mind’ in terms of thought: More actually would have been willing to accept that definition, just as long as it was restricted to that narrower term, ‘mind’. Indeed, this was the very reason why More preferred to frame things in terms of ‘soul’ or ‘spirit’, rather than ‘mind’, for his opinion was that thinking minds formed only a proper subset within a much larger and more general class of immaterial substances–and that the defining feature of that whole class, common to all of its members, was life or self-activity. More did accept that only spirits could possess thought and perception, but he expressly denied that all spirits did so. This was the really substantive difference between More and Descartes, for the latter believed that thinking minds were indeed the only immaterial substances around.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 238.

“The notion that ‘there is no life but what is Cogitative,’ he [More] wrote, ‘is a conceit taken up buy yesterday, and I believe will as soon expire.’” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 239; subquote: More, Henry. 1676. Remarks upon Two Late Ingenious Discourses. p. 23.

“For both More and Descartes, there was, at bottom, just one single essence common to all bodies, broadly indifferent between the various accidental forms and modifications that it could take on, rather than an array of fundamentally different essences corresponding to the different elements (fire, water, earth, etc.) according to the distinct substantial forms that defined these. However, unlike Descartes with his indefinitely divisible extended substance, More preferred to explicate this common essence in terms of a universal mist of indiscerpible [indivisible] atomic particles; and he explained in these poems that, when masses of such atoms came to be coagulated in a variety of different ways, they would manifest themselves sensible in the forms of these various different elements. The atoms, therefore, did still retain something of the flavour of Aristotelian prime matter, in that they had the potential to produce all manner of different compounds by coming together and congealing in a variety of different ways. And it was only when these atoms were thus ‘wakened’ into such compounds that the familiar world of bodies would arise.

“But such ‘supposed bodies’, and even their component atoms individually, would still possess at least some minimal form of intrinsic life. And they would thereby differ still further from the utterly dead matter of Descartes: For More’s matter, just as he observed in this passage, was form and life.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 244.

“So, all in all, the Cartesians were unmoved by the problem that More had identified, concerning the communication of motion [at impact More argued that a mode of bodies such as motion could not just jump to another body]. They agreed with his thesis, but they disagreed that there was anything problematic about it. Some of them might have been led by such considerations towards occasionalism; but others were content just to get on and do their physics. What none of them did was draw the vitalist conclusion that More (or Cevendish, or Leibniz) settled on.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 250.

“For More, this power to animate matter, by spontaneously applying motion to it, was nothing short of the central, defining attribute of a soul.” Reid, Jasper. 2012. The Metaphysics of Henry More. Springer. p. 329.

“There are three main facts, or classes of facts, that he [Lovelock] has advanced in support of the [Gaia] hypothesis. These three assertions are carefully examined in this book:

“Assertion No. 1: the environment is very well suited to the organisms that inhabit it.

“Assertion No. 2: the Earth’s atmosphere is a biological construct whose composition is far from expectations of (abiotic) chemical equilibrium.

“Assertion No. 3: the Earth has been a stable environment over time, despite variable external forcings.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 7.

“At the time that the Gaia hypothesis was first proposed, the dominant paradigm among geologists and others was that the nature of the earth’s environment is principally determined by a mixture of geological forces and astronomical processes.

“Geological processes affecting the environment include: (1) changing continental configuration due to plate tectonics (continental drift); (2) variations over time in the rates of volcanic activity, including occasional enormous outpourings of lava (the ‘flood basalts’ such as those making up the Deccan Traps in India and the Siberian Traps in Russia); and (3) fluctuations in mid-ocean ridge spreading rates.

“Astronomical processes of relevance to Earth habitability include: (1) changes in solar heating due to increasing luminosity of the Sun over time; (2) periodic changes in earth’s orbit around the Sun, known as Milankovitch cycles, and (3) collisions of extraterrestrial bodies with the earth….

“Throughout the rest of this book this hypothesis will be referred to as the geological hypothesis.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 8.

“The main difference between the coevolutionary hypothesis and Gaia is that the former makes no claims about the wider outcome of the interaction….

“Coevolution implies only that life and environment have both changed over time, and that changes in either have had effects on the other. There is no imputation that the result of the interaction should be beneficial for life.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 11.

“… neither true acidophiles nor true alkaliphiles can survive at a pH of 6 or 8. The extremophiles do not grow best at the optimum pH for life as a whole. In fact they are so specialized to their extreme pHs that they grow best at pHs that, while not quite at the outer bound of habitable pHs, are pretty near it….

“The most extreme prokaryotic thermophiles, on the other hand, grow most rapidly at about 105̊C. Although they can still multiply at temperatures up to 121̊C, temperatures below a scalding 85̊C are so cold, to them, as to be deadly.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 58.

“The last ice age lasted for about 100,000 years, from circa 110,000 years ago to circa 12,000 years ago. Taking this wider view, the ice age state is clearly the norm and the interglacial state the anomaly over Earth’s recent history.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 90.

“During the Cretaceous, green land stretched from pole to pole, with little or no snow covering the poles…. Although low-latitude land distant from the sea may have been too dry to support much life, nevertheless the Cretaceous planet was probably, on the whole, slightly more favorable for life….

“Of course it is true that a Cretaceous climate would not best suit the biota that resides on the planet today, adapted at it is to the present icehouse Earth. If today’s biota were to be instantaneously transplanted en masse to the Cretaceous, a big die-off would follow. However, if evolution were given time to produce a hotter-adapted biota, then life on the hotter Earth would, arguably, be more fertile, more verdant, more vigorous, and more diverse than on the present cold one. This need for time to adapt to climate change is an important reason why the ongoing global warming is likely to be so harmful for life on Earth, even though a warmer planet might, after thousands of years for biology to adapt, become more hospitable.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 112.

“The excessive coldness of our icehouse Earth, coupled with other features such as unnecessary nitrogen starvation, suggest strongly that the Earth is far from perfect for life. The data argue for rejection of this Gaian claim. The world as we see it does not correspond to any idea of optimality; it is not an uncannily good home for life. It is clearly adequate and suitable, but it is by no means perfect.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 112.

“The CO2 removal and climate cooling caused by plants invading the land was on balance overwhelmingly unfavorable for life.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 143.

“Where evolutionary developments have led to environmental impacts, then these have sometimes been beneficial and sometimes detrimental, with no obvious bias toward one or the other. But whatever the nature of the environmental modification, life has always changed to exploit and closely fit it, as it must because of evolution.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 143.

“The long-term temperature history of the Earth is not completely known. However, there is now reliable evidence of a long-term overall cooling over the last 100 million years or so….” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 157.

“New cores and techniques have led to climate and atmosphere reconstructions of much finer detail…. Whereas the early picture was one of rather smooth descents into glacials and then more rapid climbs out of them, as the frequency of sampling has increased so too has the ‘spikiness’ of the records. There is no ‘stately progression’ into and out of ice ages–instead, climate seems to jump about in a less controlled fashion.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 160.

“About 13,000 years ago the world was emerging from the severe cold of the last ice age. The biota in general, Mesolithic humans included, were enjoying the benefits of a move to warmer times. However, this warming was punctuated by the Younger Dryas period, at which time the Earth (certainly Europe and North America) was pitched back into full glacial cold for more than a thousand years, before climate once more resumed its warming trend…. At the beginning of the Younger Dryas, temperatures dropped precipitously, by as much as 10̊C within less than a century. At the end of the period, following about 1,300 years of extreme cold, temperatures suddenly shot up again by 10̊C or so within a few decades. As suddenly and surprisingly as it began, so too it ended. Climate then resumed its gradual trend toward the warmer world we enjoy today.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 161.

“There are good reasons to believe that the ends of snowball events were followed by extreme hothouses due to build-ups of volcanic carbon dioxide in the atmosphere. It is conjectured that once the snowball melted, average conditions jerked suddenly from about -15̊C to +40̊C in a matter of years.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 167.

“We can safely conclude that the assertion that Gaia has helped to keep the Earth environment stable is not supported, because the environment has not been all that stable.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 169.

“Silicate weathering could, it has often been suggested, act as a non-Gaian climate controller. In theory, it could control climate without any involvement of life, through purely inorganic processes, though life may strengthen the feedback. It has been put forward as an abiotic alternative to Gaia in accounting for the otherwise puzzling long persistence of life-friendly conditions.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 191.

“Ceding some ground to contrary evidence and the unarguable gradual decline in global temperatures over the last 50-100 million years (which silicate weathering, if a fully effective climate stabilizer, should have acted to oppose), Kump and co-workers concluded that ‘numerical models and interpretation of the geological record reveal that chemical weathering has played a substantial role in both maintaining climate stability over the eons as well as driving climatic swings in response to tectonic and paleogeographic factors.’” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 192; reference/subquote: Kump, L.R., S.L. Brantley & M.A. Arthur. 2000. “Chemical weathering, atmospheric CO2, and climate.” Annual Review of Earth and Planetary Sciences. 28:611-667.

“In light of what we know about the planet as it is today, and its history over time as revealed by various pieces of geological data, I consider that the only viable hypothesis is the coevolutionary one. There are no natural phenomena that either Gaia or the geological hypothesis is uniquely able to explain.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 206.

“… I believe that the ‘Gaia mindset’ unconsciously predisposes toward undue optimism.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. p. 211.

“During the last 800,000 years (the current limit of the ice core record), atmospheric CO2 has never made up more than about 0.03% (300 parts per million) of the atmosphere. In contrast, at the time of writing we have already caused it to rise to nearly 400 parts per million, and the rate of increase is still accelerating.” Tyrrell, Toby. 2013. On Gaia: A Critical Investigation of the Relationship Between Life and Earth. Princeton UP. pp. 212-3.

“Animists are people who recognise that the world is full of persons, only some of whom are human, and that life is always lived in relationship with others. Animism is lived out in various ways that are all about learning to act respectfully towards and among other persons.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. xi.

“The old usage of animism was entangled with Western worldviews that considered the myriad multiplicity evident everywhere to be problematic. Two solutions have been proffered. The first has been to insist on the underlying unity of all that exists. Such a unity may be located in a single creative God, a yet-to-be-discovered grand unifying theory, idealism, materialism or mysticism. The second has been to dichotomise everything and treat all that we encounter as a confrontation of dualities such as us/them, male/female, light/dark, spiritual/physical, mind/matter, truth/error, time/eternity, life/death, persons/objects, objectivity/subjectivity, human/non-human, self/other and good/evil…. Instead of crying ‘One!’ or ‘Two!’, animists celebrate plurality, multiplicity, the many and their entwined passionate entanglements. Instead of the hero who struggles against one or other side of things in an attempt to discern the underlying truth, animist stories present tricksters who multiply possibilities in increasingly amusing ways.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. pp. xiv-xv.

“Animisms are theories, discourses and practices of relationship, of living well, of realising more fully what it means to be a person, and a human person, in the company of other persons, not all of whom are human but all of whom are worthy of respect.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. xvii.

“The ubiquity of terms like respect and reciprocity in animist discourse demonstrates that the key identifier of a person is someone who responds to or initiates approaches to other persons.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. xvii.

“Religion … is, as Detwiler says about Oglala ritual, ‘a quest for ethical responsibility through communicative action’.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. 49; reference: Detwiler, Fritz. 1992. “‘All My Relatives”: Persons in Oglala Religion’. Religion. 22:235-46. p. 244.

“In Maori understanding pairs are related collaboratively rather than oppositionally, associatively rather than hierarchically. Rather than being placed over against one another they intertwine. Male and female, dark and light, war and peace, visible and invisible, sacred and profane, here and there, past and future, ancestors and descendants, front and behind, birth and death, above and below, creation and destruction, permission and restriction, revealed and secret, spoken and silent, friends and enemies–these and many other pairs are inseparably coupled. Without a partner neither member of a pair could exist. The existence of one in the other, and their participation in a wider community that includes all other pairs, unfolds towards all possibilities and potentials. Their procreative embrace engenders life (and all the deaths that life entails).” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. 52.

“I have brought up the subject of cannibalism because the kaupapa, design and active purpose, of the marae complex [space with some buildings where people meet] suggests that something akin to cannibalism takes place.

“Just as the cannibal eats the ancestor, so the whare nui [meeting house] as whare tipuna, ancestor/ancestral house, eats visitors. Just as the cannibal incorporates the ancestor and the anecestor’s mana [state of being efficacious or good], so the whare tipuna incorporates visitors. Just as the cannibal transforms the tapu-newness [cognate with tabu] of the ancestor’s death in the noa-normality of a meal, materiality and finally of excrement, so the marae and whare tipuna transform the tapu-newness of visitors into the noa-normality of guesthood or neighbourly friendship. Neither cannibalism nor guesthood become daily realities or needs. The cannibal does not rely on human flesh for protein. Guests do not become tangata whenua, locals or indigenous, they remain people from elsewhere. A warrior who offers a challenge–generously providing visitors with an opportunity to express their mana as aggressive ‘others’, skilled enemies–meets their potential hostility.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. 62.

“… Maori art is not principally the production of inanimate objects for prestigious display, but the transformation of living persons in and by new relationships. The forest tree is transformed into parts of the body of a living, acting ancestor in the form of whare nui. The whole ancestral person/structure acts to raise the mana, prestige, of the present generation. Strangers becoming guests, the dead becoming ancestors, the community deciding on actions to be taken, conflicts being resolved and so on, are precisely what these ancestor structures are about. Marae and whare nui and their constituent parts are not mere symbols that represent ancestors in order to provide a context for significant actions. They are participating persons. What animist humans do after they have transformed living tree–persons into living building-persons is to further unfold the actions such people have begun.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. 64.

“Everything begins and ends [for Australian aborigines] with land. More precisely, particular lands place everything, everyone and every happening in relation to and communion with one another…. The places where things happen are not mere scenery, backdrops or stages for the grand drama of life; they define, birth, contextualise and participate. Lands erupt into life and fully engage with the emergent and proliferating diversity.” Harvey, Graham. 2006. Animism: Respecting the Living World. Columbia UP. p. 66.

“In general, asking what a biological individual is means asking what constitutes a countable, relatively well-delineated, and cohesive unit in the living world….” Pradeu, Thomas. 2016. “The many faces of biological individuality.” Biology & Philosophy. 31:761-773. p. 762.

“Question-dependence: The answer to the question ‘what counts as a biological individual?’ will depend to a large extent on the scientific context in which the question is asked.

“”Anti-anthropocentrism: A scientifically fruitful approach to biological individuality should not be based on human intuition, common sense, or perception. It can be very unhelpful to use human beings (or other vertebrates) as the central model for biological individuals.

“Hierarchization: Biological individuality is nested and hierarchical: it can be realized at several different levels of the living world (for example the level of the cell and that of the organism).

“Continuity: Biological individuality comes in degrees; a biological entity can exemplify biological individuality to lesser and greater degrees.

“Transitions: There have been transitions in individuality: through evolution, new levels of individuality have emerged as a result of the coming together of previously distinct entities.” Pradeu, Thomas. 2016. “The many faces of biological individuality.” Biology & Philosophy. 31:761-773. p. 762.

“In their reflections about biological individuality, philosophers of biology have tended to focus on a single biological field–generally evolution. In so doing, they have left aside many biological fields where the problem of biological individuality has also played a central role, including physiology, developmental biology, immunology, ecology, the cognitive sciences, among others.” Pradeu, Thomas. 2016. “The many faces of biological individuality.” Biology & Philosophy. 31:761-773. pp. 763-4.

“Lidgard and Nyhart propose to divide the problem of biological individuality into four sub-problems: individuation (thresholds, boundaries, inside/outside, autonomy); hierarchy (levels of organization in complex systems); horizontality (interactions among parts in making a whole); and temporality (change through time, particularly in part-whole relations).” Pradeu, Thomas. 2016. “The many faces of biological individuality.” Biology & Philosophy. 31:761-773. p. 765; reference: Lidgard, S. & L.K. Nyhart (eds). 2017. Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. U of Chicago Press.

“Queller and Strassmann argue that complex holobionts are generally not organisms because, even when they show some cooperation, they still express levels of internal conflict that are too high to constitute organismic units. Skillings explores the holobiont debate from the point of view of the ‘founding’ example of corals. He holds that most holobionts share more affinities with communities than they do with individual wholes, and that, in general, holobionts do not meet the criteria for being evolutionary individuals, units of selection, or organisms. In contrast, Gilbert and Tauber consider that holobionts are unified communities, acting as units from physiological, developmental, immunological, and evolutionary viewpoints. Pradeu defends the vew that, from an immunological point of view, a biological individual is made of all the components that are immunologically tolerated, which include many (but not all) microbes found in or on a host. Chiu and Eberl assert that microorganims are constitutive of host immunity as external scaffolds, varying in degrees of reliability, specificity, and exclusivity. In their view, even if holobionts are not internally integrated enough to qualify as organisms or units of selection, they are still individuals in a different and more general way: the holobiont must be seen as the host plus the microorganisms that scaffold its immunity. Haber sees holobionts as nested individuals, with sometimes distinct, non-overlapping life cycles. Clarke interprets holobionts in light of reproductive synchrony and fitness alignment between the symbiotic partners.”” Pradeu, Thomas. 2016. “The many faces of biological individuality.” Biology & Philosophy. 31:761-773. p. 768; references: All are from Biology & Philosophy 2016. V. 31. Queller, D.C. & J.E. Strassmann. “Beyond society: the evolution of organismality.” Skillings, D. “Holobionts and the ecology of organisms: Multi-species communities or integrated individuals?” Gilbert, S.F. & A.I. Tauber. “Rethinking individuality: the dialectics of the holobiont.” Pradeu, Thomas; this article. Chiu, L. & G. Eberl. “Microorganisms as scaffolds of host individuality: an eco-immunity account of the holobiont.” Haber, M.H. “The individuality thesis (3 ways).” Clarke, E. “A levels-of-selection approach to evolutionary individuality.”

“The fundamental features shared by all three periods [Axial Age, Modernity, Anthropocene] include the following six-part sequence: 1. Political fragmentation; 2. Social experiments grounded in foundational stories–a vision of cultural success based on its society’s old world story; 3. Intensification of warfare; 4. Appearance of a new world story; 5. Developing commentary of that story, so that the society can amend its approach to unexpected challenges, and; 6. Emergence of empire.” Kelly, Sean. 2021. Becoming Gaia: On the Threshold of Planetary Initiation. Olympia, WA: Integral Imprint. p. 24.

“… Swimme and Berry’s proposal for a threefold ‘cosmogenetic principle … differentiation, autopoiesis (or self-organization), and communion…. In fact, as they say, if [there] were no differentiation, ‘the universe would collapse into a homogeneous smudge; were there no subjectivity [which Swimme and Berry associate with autopoiesis], the universe would collapse into inert, dead extension; were there no communion, the universe would collapse into isolated singularities of being.” Kelly, Sean. 2021. Becoming Gaia: On the Threshold of Planetary Initiation. Olympia, WA: Integral Imprint. pp. 50-1; reference: Swimme, B. & T. Berry. 1992. The Universe Story: From the Primordial Flaring Forth to the Ecozoic Era–A Celebration of the Unfolding of the Cosmos. HarperCollins. p. 71.

“The great Neo-Confucian Zhu Xi, for instance,

“discerned a tripartite patterning or principle of the emergence of the person, and by extension, all the other objects or events of the world in terms of form or principle [li], dynamics or vital force [qi] and their unification via the mind-heart [xin]; the mature schematic is form, dynamics and unification. Moreover, once this unification of the principle and vital force was achieved and perfected, the outcome, at least for the human person, was a state of harmony or balance.” Kelly, Sean. 2021. Becoming Gaia: On the Threshold of Planetary Initiation. Olympia, WA: Integral Imprint. p. 52; subquote: Berthrong, J.J. “Neo-Confucian Philosophy.” Internet Encyclopedia of Philosophy. www.iep.utm.edu/neo-conf/#5H5a.

“… I am also just as committed to enacting the three dimensions of the Great Turning that Joanna has identified: holding actions to slow, if not halt, the unraveling; promotion of Gaia structures as life-affirming alternatives to the ways of business as usual; and the shift in consciousness associated with the growing awareness of our deeper Gaian identity and our inter-being with all that is.” Kelly, Sean. 2021. Becoming Gaia: On the Threshold of Planetary Initiation. Olympia, WA: Integral Imprint. pp. 158-9.

“Zhiwa asks what a ‘good death’ might look like as we accelerate into what are sure to be ever more chaotic times. Here he draws from both palliative care and hospice work, suggesting how we might adapt them to the growing awareness of the Great Dying [planet-wide die-off]. As with assisting individuals to accept and prepare for their individual deaths, Zhiwa imagines the emergence of planetary hospice workers as spiritual midwives who will help ‘transform the planetary death/ rebirth process from a painful dislocation rife with suffering and regret into a healing process for both the human race and the Earth itself–even into a Great Awakening.’” Kelly, Sean. 2021. Becoming Gaia: On the Threshold of Planetary Initiation. Olympia, WA: Integral Imprint. pp. 166-7; reference: Woodbury, Zhiwa. “PLanetary Hospice: Rebirthing Planet Earth.” www.guymcpherson.com/wp-content/uploads/2014/03;planetary-hospice.pdf.

“The notion that cells, and therefore living organisms, are astoundingly complicated, but ultimately comprehensible, chemical and physical machines is now the accepted way to think about life.” Nurse, Paul. 2020. What is Life? W.W. Norton & Co. p. 78.

“[Answer to what is life] The answer I got at school was something like the MRS GREN list, which states that living organisms exhibit Movement, Respiration, Sensitivity, Growth, Reproduction, Excretion and Nutrition.” Nurse, Paul. 2020. What is Life? W.W. Norton & Co. p. 127.

“[J.B.S. Haldane in his book What is Life?] ‘I am not going to answer this question. In fact, I doubt if it will every be possible to give a full answer.’” Nurse, Paul. 2020. What is Life? W.W. Norton & Co. p. 128.

“I cannot imagine a more elegant solution; different configurations of linear carbon polymers [nucleic acids and proteins] generate both chemically stable information storage devices and highly diverse chemical activities. I find this aspect of life’s chemistry both utterly simple and completely extraordinary.” Nurse, Paul. 2020. What is Life? W.W. Norton & Co. p. 130.

“During the period 2000-1400 Ma there were 4 biological innovations (Eukarya, organelles, multicellularity, sex) discussed below. We can calculate the probability of the 4 events occurring in this period by assuming that these 4 events could occur independently and with uniform probability anytime between 2000 and 800 Ma. Since the periods 2000-1400 Ma and 1400-800 Ma are equal length intervals and, by our assumption, the events could occur with the same probability in each, then the probability of them co-occurring only between 2000-1400 Ma would be (1/2)4=0.0625.” Mukherjee, Indrani, Ross Large, Ross Corkrey & Leonid Danyushevsky. 2018. “The Boring Billion, a slingshot for Complex Life on Earth.” Scientific Reports. 8:4432. doi:10.1038/s41598-018-22695-x. p. 3.

“Interestingly, most of the key biological innovations took place in a period where bio-essential trace element concentrations are consistently low between 2000 to 1400 Ma.” Mukherjee, Indrani, Ross Large, Ross Corkrey & Leonid Danyushevsky. 2018. “The Boring Billion, a slingshot for Complex Life on Earth.” Scientific Reports. 8:4432. doi:10.1038/s41598-018-22695-x. p. 3.

“We observe an increase in trace element concentrations at around 1400 Ma which also coincides with an oxygenation event recognized using independent geochemical proxies. Interestingly, this event is coeval with a major diversification of eukaryotes. Complex cellular morphological capacities (cytoskeletal architecture) were observed and eukaryote habitation spread to a wider range of environments…. This was followed by the diversification of crown group eukaryotes between 1200-1100 Ma and the emergence of a gene (1000-800 Ma), recently identified, that is linked with protein and choline kinases responsible for cell adhesion and transfer of signals within cells efficiently. The period ended with the appearance of metazoans at ~750 Ma and the origin of fungi between 760 and 1000 Ma.” Mukherjee, Indrani, Ross Large, Ross Corkrey & Leonid Danyushevsky. 2018. “The Boring Billion, a slingshot for Complex Life on Earth.” Scientific Reports. 8:4432. doi:10.1038/s41598-018-22695-x. p. 4.

“In summary, key biological innovations in eukaryotes seemed to have co-occurred during the low trace element period, followed by a broad-scale diversification of eukaryotes, in the relatively high trace element period. We attribute this trend from a prokaryotic community (> 1800 Ma) to the formation of the first eukaryotes (1800-1500 Ma) and their diversification (1400-800 Ma) to nutrient trace element availability….” Mukherjee, Indrani, Ross Large, Ross Corkrey & Leonid Danyushevsky. 2018. “The Boring Billion, a slingshot for Complex Life on Earth.” Scientific Reports. 8:4432. doi:10.1038/s41598-018-22695-x. p. 4.

“Our primary conclusions lead to a paradigm shift in understanding evolution during the Proterozoic. First, the Proterozoic ocean witnessed periods of both low and high trace element availability; trace element trends are not flat and uniform as previously assumed. Second, we emphasize that the low nutrient trace element periods were possibly essential triggers in the course of evolution. Previous studies claim low concentrations of trace element may have stalled evolution. However, we argue that these periods of trace element crisis forced organisms to explore their options to adapt to stressful conditions and promoted mechanisms to cope and evolve. On the upside of nutrient trace element cycles, when conditions improved in terms of high trace element availability from 1400 Ma to 800 Ma, organisms diversified. Thus, the need for both unfavorable and favorable nutrient conditions may have been required to generate the necessary evolutionary pressure and diversification respectively through time. Third, we propose that the high and low trace element periods in the ‘Boring Billion’ may have played a critical role in establishing the prerequisites for metazoan evolution.” Mukherjee, Indrani, Ross Large, Ross Corkrey & Leonid Danyushevsky. 2018. “The Boring Billion, a slingshot for Complex Life on Earth.” Scientific Reports. 8:4432. doi:10.1038/s41598-018-22695-x. p. 5.

“Life and the chemical environment are united in an inescapable feedback cycle. The periodic table of the elements essential for life [subset of the full periodic table] has transformed over Earth’s history, but, as today, evolved in tune with the elements available in abundance in the environment.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. p. 1.

“By contrast to the major ions that, today and always, have the highest concentration in the oceans and life, the transition (and trace) metals have the potential for an extraordinarily flexible redox state, owing to their partially filled d-orbitals in the ground state. This flexibility has two important implications for life. First, the transition metals are unique in providing life with unparalleled opportunities for performing electron transfer, redox and acid-base chemistry. Second, their availability is highly sensitive to the average redox state of Earth’s surface.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. p. 3.

“The increasing redox potential of the environment affects elemental availability via the simple chemistry of three equilibria. The general restrictions on the availability of elements as free cations, M+ and M2+ in the sea are insolubility and complex ion formation [ligands] with redox chemistry controlling the redox state of the ions.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. p. 4.

“Within the framework of the advancing oxidation potential of the Earth’s surface, the three chemical equilibria prescribe the evolving transition metal availability: declining Fe, Mn and Co and increasing Cu, Zn and Cd across each step of oxygen rise.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. p. 5.

“Of note is the step change in use of zinc-finger containing proteins and zinc hydrolytic enzymes, the copper chaperones, homeostatic proteins and redox enzymes within eukaryotic and multicellular organisms. There appears a clear trend of novel and multiple copies of the genetic code for these metal proteins as the metal availability rises in the environment due to oxidation. It is thought that the availability of these key d-block metals acted as a handbrake on the evolution of life, only permitting the functions necessary for eukaryotic cells and multicellularity to arise as and when the metals such as Zn and Cu, best suited to the metallo-centres of enzymes responsible for, e.g. cellular communication, splitting and cohesion between cells, were sufficiently available.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. pp. 6-7.

“From consideration of the evolution of the new chemistry of the elements, it transpires that it is not only the concentration of an element which dictates its degree of toxicity (Paracelsus ‘[a]ll things are poison and nothing is without poison, only the dose permits something not to be poisonous’) but also its availability within evolutionary history. The evolutionary cycle of invention and unwitting poisoning of life predicts a systematic temporal evolution to the dose-response curve of increasingly complex life as the concentration of a new chemical increased in the environment, e.g. O2, Cu and Zn. Across each step in elevated concentration of newly introduced elements in the environment, increasingly complex life would have gained an increase in the toxic threshold, as the initial metal toxicity management systems (recognition, binding and accumulation and/or expulsion) transitioned towards biological use.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. p. 7.

“Subsequent to the introduction of oxygen as a waste product into the environment as an inevitable consequence of the emergence of photosynthesis, the periodic table of the elements essential to life evolved systematically according to element availability in the environment, directly controlled by the three inorganic equilibria [solubility, complexation such as by ligands, environmental redox]. These equilibria enabled the advancement of life towards complexity via phased release of key elements into the environment, initially toxic to life but ultimately employed for use.” Rickaby, R.E.M. 2015. “Goldilocks and the three inorganic equilibria: how Earth’s chemistry and life coevolve to be nearly in tune.” Philosophical Transactions of the Royal Society: A. 373:20140188. dx.doi.org/10.1098/rsta.2014.0188. p. 8.

“An increasing νe [electron flux density in photosynthesis] coinciding with a decreasing νn [flux density of key nutrients] over the course of Prochlorococcus [most abundant photosynthetic cell on Earth] evolution can be expressed as a single variable: the electron-to-nutrient flux ratio, νe /νn.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3094.

“If selection to lower [n]* [concentration of limiting nutrients] drives the maximization of νe /νn, why should it lead to an increased excretion of organic carbon? We argue this ultimately emerges from mass and energy conservation. That is, in the presence of kinetic bottlenecks, cells can drive up their ATP/ADP ratio by increasing their ATP supply rate, but to maintain steady state, they must also increase ATP consumption rates. [The same argument applies to the NAD(P)H/NAD(P) ratio.]” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3094.

“…the layered population structure observed in stable water columns reflects the sequential evolution of new ecotypes near the surface, each with increasing metabolic rates, drawing down limiting nutrients and restricting ancestral ecotypes to ever deeper waters. … an increase in electron flux could have produced ecological feedbacks that drove further differentiation within Prochlorococcus ecotypes and in those with which it interacts. Lastly, this framework suggests that by promoting the fixation and excretion of increasing amounts of organic carbon as a by-product of increasing the nutrient affinity, the evolution of Prochlorococcus increased the long-term steady-state concentrations of dissolved organic carbon (DOC) in the oligotrophic oceans, which are much higher (by a factor of up to ~2) than elsewhere in the ocean. Because several compounds that Prochlorococcus may be excreting are known non-binding ligands, including polysaccharides and carboxylic acids like citrate, it may, in turn, also play a key role in buffering trace metal bioavailability in these environments.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3095.

“Unlike in the classic ‘Red Queen hypothesis,’ in which evolution is a zero-sum game, here, the evolutionary dynamic increases resource capture, and thereby biomass, of the ecosystem. The imprint of this collective dynamic can be seen in the broadly convergent features of all oceanic microbes. Slow growth, small cell size, streamlined genomes and proteomes, and use of nonphospholipid membranes–signature features of Proochlorococcus–are observed across both autotrophic and heterotrophic microbes in the oligotrophic oceans.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3095.

“Thus, oceanic SAR11 populations [heterotrophs] have evolved a dependency on exactly the compounds (pyruvate and glycolate) that our metabolic reconstructions suggest emerged as excretion pathways in Prochlorococcus.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3095.

“These observations [changed metabolic pathways in SAR11] are consistent with selection acting to maximize νe /νn in both systems and thereby producing pathways that transfer pyruvate and glycolate from Prochlorococcus to SAR11 and malate from SAR11 to Prochlorococcus. Oligotrophic waters have nanomolar concentrations of pyruvate and glycolate, with midday maxima for the latter, consistent with biological cross-feeding synchronized with the input of sunlight, although abiotic photochemistry may also contribute….

“”These observations suggest that metabolic mutualisms are self-amplifying feedback loops that maximize the collective νe /νn, and thus total productivity, of ecosystems.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3096.

“We have proposed that maximizing the metabolic rate of cells lowers their minimal subsistence nutrient requirements and that this is achieved by maximizing the cellular electron-to-nutrient flux ratio (νe /νn), while increasing the excretion of organic carbon. This leads to an evolutionary dynamic that increased total ecosystem biomass and paves the way for self-amplifying feedback loops that recycle organic carbon and reinforce the maximization of cellular metabolic rate at the ecosystem level.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3096.

“Our framework … is consistent with the theorem that the flow of energy through the biosphere promotes its self-organization into chemical cycles [referring to early work from H. Morowitz, Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics].” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3096.

“We suggest an additional negative feedback involving iron, the most widely used metal cofactor for biological electron transfer. The free O2 produced during the rise of oxygenic photosynthesis transformed iron from its soluble Fe2+ form into its insoluble Fe3+ form, effectively causing early oxygenic photosynthesizers to self-limit their expansion in the global oceans by locally extinguishing available iron. Extant oceanic microbes surmount this negative feedback on photosynthetic electron transfer through reduced cellular Fe demands, and through Fe- ligation by DOC, including polysaccharides, citrate, and other carboxylic acids, all of which may be excreted by marine picocyanobacteria. Polysaccharides and small carboxylic acids also enhance the dissolution of minerals, and minerals in wind-blown dust are a major source of Fe and P to the surface oceans. Thus, we hypothesize that the evolution of marine picocyanobacteria increased both the bioavailability and the overall supply of iron under aerobic conditions and helped transform the oceans from an anoxic state rich in free iron to an oxygenated state with DOC-bound iron. This positive iron-DOC feedback, strengthened by an increased metabolic rate, was critical in pushing the marine biosphere past a major evolutionary bottleneck and paved the way for an expansion of oceanic oxygenic photosynthesis and a rise in atmospheric O2.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3097.

“… one could argue that the emergence of modern human societies is a variant of the general framework we propose. As our populations expanded and extracted ever more electrons from fossil fuels, we have increased global CO2, while drawing down natural resources and global O2. In the process, we have become increasingly socially, technologically, and economically interconnected, analogous to what we have observed in the evolution of oceanic microbial ecosystems and plant cells. As in those systems, this has increased our collective ability to harvest more difficult-to-access natural resources.” Braakman, Rogier, Michael Follows & Sallie Chisholm. 2017. “Metabolic evolution and the self-organization of ecosystems.” PNAS. www.pnas.org.cgi.doi/10.1073/pnas.1619573114. E3091-E3100. p. E3098.

“There are three alternative scenarios to be tested relating network structure across individuals, ecosystems, and the entire biosphere…. In the first, biochemistry does not have shared network structure across levels, and different scaling behaviors emerge at different levels. In the second scenario, biochemistry has shared network structure across levels, but this shared structure can be fully explained by the structure of random, chemical networks…. In a third scenario, biochemistry has shared structure across levels, which is different from that of random reaction networks. We find the third scenario the be consistent with our analysis, suggesting the presence of universal organizing principles unique to biology that recur across biological levels of organization. We show that these can be explained as an emergent property of the topological structure of the most common reactions participating in living processes.” Kim, Hyunju, Harrison Smith, Cole Mathis, Jason Raymond & Sara Walker. 2019. “Universal scaling across biochemical networks on Earth.” Science Advances. 5:eaau0149. p. 2.

“Our results establish that Earth’s biochemistry exhibits universal scaling behavior across levels of organization not explainable by the organizational patterns of randomly sampled chemistry alone.” Kim, Hyunju, Harrison Smith, Cole Mathis, Jason Raymond & Sara Walker. 2019. “Universal scaling across biochemical networks on Earth.” Science Advances. 5:eaau0149. p. 5.

“… the existence of individuals sharing a common set of biochemical reactions is a sufficient condition for networks of all sizes (from small individuals to large ecosystems) to exhibit the scaling behavior observed in real living systems. Together with the results of the previous section, we can conclude that the particular form of the scaling relations observed across life on Earth emerges due to the structure of interactions among compounds common across all life, which is not in general characteristic of nonbiological chemical reaction networks.” Kim, Hyunju, Harrison Smith, Cole Mathis, Jason Raymond & Sara Walker. 2019. “Universal scaling across biochemical networks on Earth.” Science Advances. 5:eaau0149. p. 7.

“Our analyses reveal that biochemical networks display common scaling laws governing their topology and biochemical diversity that are independent of the level of organization they are sampled from. These scaling laws cannot be fully explained by the structure of random reaction networks that do not account for the structure of the subset of reactions shared across life on Earth.” Kim, Hyunju, Harrison Smith, Cole Mathis, Jason Raymond & Sara Walker. 2019. “Universal scaling across biochemical networks on Earth.” Science Advances. 5:eaau0149. p. 7.

“A key implication of our analysis is the importance of individuals sharing a common set of biochemical reactions in shaping the universal scaling laws observed across hierarchical levels.” Kim, Hyunju, Harrison Smith, Cole Mathis, Jason Raymond & Sara Walker. 2019. “Universal scaling across biochemical networks on Earth.” Science Advances. 5:eaau0149. p. 8.

“Here we have shown the relevant scaling parameter for biochemical organization is the number of biochemical compounds (in a network representation this is the size of the network). Individuals, ecosystems, and the biosphere obey much the same scaling behavior for biochemical network structure, indicating that the same universal mechanisms could operate across all three levels of organization.” Kim, Hyunju, Harrison Smith, Cole Mathis, Jason Raymond & Sara Walker. 2019. “Universal scaling across biochemical networks on Earth.” Science Advances. 5:eaau0149. p. 8.

“… the new world-views … brought forth by the revolution of the seventeenth century. They seemed to be to be reducible to two fundamental and closely connected actions that I characterised as the destruction of the cosmos and the geometrization of space, that is, the substitution for the conception of the world as a finite and well-ordered whole, in which the spatial structure embodied a hierarchy of perfection and value, that of an indefinite or even infinite universe no longer united by natural subordination, but unified only by the identity of its ultimate and basic components and laws; and the replacement of the Aristotelian conception of space – a differentiated set of innerworldly places – by that of Euclidean geometry – an essentially infinite and homogenous extension – from now on considered as identical with the real space of the world.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. vi.

“… barely a hundred years separate the De revolutionibus orbium coelestium of Copernicus (1543) from the Principia philosophiae of Descartes (1644); barely forty years these Principia from the Philosophia naturalis principia mathematica (1687).” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. vii.

“Yet it was Nicholas of Cusa, the last great philosopher of the dying Middle Ages [his book Learned Ignorance appeared in 1440], who first rejected the mediaeval cosmos-conception and to whom, as often as not, is ascribed the merit, or the crime, of having asserted the infinity of the universe.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 6.

“His [Nicholas of Cusa’s] universe is not infinite but ‘interminate’, which means not only that it is boundless and is not terminated by an outside shell, but also that is it not ‘terminated’ in its constituents, that is, that it utterly lacks precision and strict determination. It never reaches the ‘limit’; it is, in the full sense of the word, indetermined.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 8.

“No one, not even Lefevre d’Etaples who edited his [Nicholas of Cusa’s] works, seems to have paid much attention to them, and it was only after Copernicus – who knew the works of Nicholas of Cusa, at least his treatise on the quadrature of the circle, but does not seem to have been influenced by him – and even after Giordano Bruno, who drew his chief inspiration from him, that Nicholas of Cusa achieved fame as a forerunner of Copernicus, and even of Kepler, and could be quoted by Descartes as an advocate of the infinity of the world.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp. 18-9.

“Indeed, in the infinitely rich and infinitely diversified and organically linked-together universe of Nicholas of Cusa, there is no center of perfection in respect to which the rest of the universe would play a subservient part….” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 21.

“… [Copernican astronomy] undermined the very foundations of the traditional cosmic world-order with its hierarchical structure and qualitative opposition of the celestial realm of immutable being to the terrestrial or sublunar region of change and decay.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 29.

“… nevertheless, the world of Copernicus would remain a finite one, encompassed by a material sphere or orb, the sphere of the fixed stars – a sphere that has a centrum, a centrum occupied by the sun….

“We have to admit the evidence: the world of Copernicus is finite. Moreover, it seems to be psychologically quite normal that the man who took the first step, that of arresting the motion of the sphere of the fixed stars, hesitated before taking the second, that of dissolving it in boundless space….” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp. 32, 34.

“Where Nicholas of Cusa simply states the impossibility of assigning limits to the world, Giordano Bruno asserts, and rejoices in, its infinity….” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 41.

“The importance for Bruno’s thought … two other features … They are: (a) the use of a principle that a century later Leibniz … was to call the principle of sufficient reason … and (b) the decisive shift from sensual to intellectual cognition in its relation to thought (intellect)…. Bruno asserts that sense-perception, as such, is confused and erroneous and cannot be made the basis of scientific and philosophical knowledge.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp. 44-5.

“As a matter of fact, Bruno’s world-view is vitalistic, magical; his planets are animated beings that move freely through space of their own accord like those of Plato or of Pattrizzi. Bruno’s is not a modern mind by any means. Yet his conception is so powerful and so prophetic, so reasonable and so poetic that we cannot but admire it and him.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 54.

“Indeed, Kepler … sees in the world… embodying in its structure a mathematical order and harmony. Order and harmony that cannot be found in the infinite and therefore perfectly formless – or uniform – universe of Bruno.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 58.

“Now Descartes’ God, in contradistinction to most previous Gods, is not symbolized by the things He created; He does not express Himself in them. There is no analogy between God and the world; no imagines and vestigia Dei in mundo; the only exception is our soul, that is, a pure mind, a being, a substance of which all essence consists in thought, a mind endowed with an intelligence able to grasp the idea of God, that is, of the infinite (which is even innate to it), and with will, that is, with infinite freedom.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 100.

“… the world created by the Cartesian God, that is, the world of Descartes, is by no means the colorful, multiform and qualitatively determined world of the Aristotelian, the world of our daily life and experience – that world is only a subjective world of unstable and inconsistent opinion based upon the untruthful testimony of confused and erroneous sense-perception – but a strictly uniform mathematical world, a world of geometry made real about which our clear and distinct ideas give us a certain and evident knowledge.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp. 100-1.

“Thus Descartes does not content himself with stating, as did Giordano Bruno and Kepler, that there is no really void space in the world and that the world-space is everywhere filled with ‘ether.’ He goes much farther and denies that there is such a thing at all as ‘space,’ an entity distinct from ‘matter’ that ‘fills’ it.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 102.

“It is exactly the same concerning the problem of the constitution of the stars. This, too, becomes a purely scientific, factual question. The old opposition of the earthly world of change and decay to the changeless world of the skies which, as we have seen, was not abolished by the Copernican revolution, but persisted as the opposition of the moving world of the sun and the planets to the motionless, fixed stars, disappears without trace. The unification and the uniformization of the universe in its contents and laws becomes a self-evident fact ….” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 105.

“Thus, it seems to him difficult to understand or to admit the radical opposition established by Descartes between body and soul. How indeed can a purely spiritual soul, that is, something which, according to Descartes, has no extension whatever, be joined to a purely material body, that is, to something which is only and solely extension? Is it not better to assume that the soul, though immaterial, is also extended; that everything, even God, is extended [to go in the direction of Henry More]?” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp. 110-1.

“Indeed, without the action of a non-mechanical principle [e.g. something like the role later identified as gravity, cures] all matter in the universe would divide and disperse; there would not even be bodies, because there would be nothing to hold together the ultimate particles composing them. And, of course, there would be no trace of that purposeful organization which manifests itself not only in plants, animals and so on, but even in the very arrangement of our solar system.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 134.

“Henry More, it is clear, cannot transform the concept of motion into that of a pure relation. He feels that when bodies move, even if we consider them as moving in respect to each other, something happens, at least to one of them, that is unilateral and not reciprocal: it really moves, that is, changes its place, its internal locus. It is in respect to this ‘place’ that motion has to be conceived and not in respect to any other, and therefore:

“‘the supposition of the Cartesians that local motion is relative to the place where the body is not, and not where it is, is absurd.’

In other terms, relative motion implies absolute motion and can only be understood on the basis of absolute motion and thus of absolute space.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 144; subquote: More, Henry. 1671. Enchiridium metaphysicum. C. VII, 6, p. 55.

“To sum up [for Henry More]: Descartes was right in looking for substance to support extension. He was wrong in finding it in matter. The infinite, extended entity that embraces and pervades everything is indeed a substance. But it is not matter. It is Spirit; not a spirit, but the Spirit, that is, God.

“Space, indeed, is not only real, it is something divine.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 147.

“When we shall have enumerated those names and titles appropriate to it [space], this infinite, immobile, extended [entity] will appear to be not only something real but even something Divine…. Of this kind are the following, which metaphysicians attribute particularly to the First Being, such as: One, Simple, Immobile, Eternal, Complete, Independent, Existing in itself, Subsisting by itself, Incorruptible, Necessary, Immense, Uncreated, Uncircumscribed, Incomprehensible, Omnipresent, Incorporeal, All-penetrating, All-embracing, Being by its essence, Actual Being, Pure Act.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 148.

“Absolute space is infinite, immovable, homogeneous, indivisible and unique. These are very important properties which Spinoza and Malebranche discovered almost at the same time as More, and which enabled them to put extension – an intelligible extension, different from that which is given to our imagination and senses – into their respective Gods; properties that Kant – who, however, with Descartes, missed the indivisibility – was to rediscover a hundred years later, and who, accordingly was unable to connect space with God and had to put it into ourselves.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp.149-150.

“An indeterminately vast but finite world merged in an infinite space is the only conception, Henry More sees it now, that enables us to maintain the distinction between the contingent created world and the eternal and a se and per se existing God.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 154.

“Newton’s physics, or, it would be better to say, Newton’s natural philosophy, stands or falls with the concepts of absolute time and absolute space, the selfsame concepts for which Henry More fought his long-drawn-out and relentless battle against Descartes. Curiously enough, the Cartesian conception of the only relative, or relational, character of these and connected notions is branded by Newton as being ‘vulgar’ and as based upon ‘prejudices.’” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 160.

“Place – locus – is thus something which is in the bodies, and in which bodies are in their turn. And as motion is a process in which bodies change their places, not taking them along with them but relinquishing them for others, the distinction between absolute and relative spaces implies necessarily that of absolute and relative motion, and vice versa, is implied by it….” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 163.

“It is … a well-known fact that Newton did not believe in attraction as a real, physical force. No more than Descartes, Huygens or Henry More could he admit that matter is able to act at a distance, or be animated by a spontaneous tendency.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 176.

“… More’s distinction between the infinite, immovable, immaterial extension and the material, mobile and therefore finite one is, according to him, the sole and only means of avoiding the Spinozistic identification of God with the world.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 191.

“Leibniz wrote:… ‘Sir Isaac Newton, and his Followers, have also a very odd Opinion concerning the Work of God. According to their Doctrine, God Almighty wants to wind up his Watch from Time to Time: Otherwise it would cease to move. He had not, it seems, sufficient Foresight to make it a perpetual Motion…. According to My Opinion, the same Force and Vigour remains always in the World, and only passes from one part of Matter to another, agreeably to the Laws of Nature, and the beautiful pre-established Order.’” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 236; quote from Leibniz letter written November 1715. A Collection of papers, which passed beteen the late learned Mr. Leibnitz and Dr. Clarke. In the years 1715 and 1716 Relating to the Principles of Natural philosophy and Religion. Also available from Alexander, G.H. 1956. The Leibniz-Clarke correspondence. Manchester UP.

“… Leibniz does not understand the difference between his own conception of space – a lattice of quantitative relations – and that of Newton, for whom space is a unity which precedes and makes possible all relations that can be discovered in it.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 252.

“Indeed, it is only from the point of view of the Cartesio-Leibnizian rigid dualism of mind and body, with its negation of all intermediate entities and consequent reduction of material nature to a pure, self-sustaining and self-perpetuating mechanism, that the intervention in nature of non-mechanical and therefore non-material agencies becomes a miracle. For Clarke [metaphysical correspondent for Newton in Leibniz correspondence], as for Henry More before him, this dualism is, of course, unacceptable. Matter does not constitute the whole of nature, but is only a part of it. Nature, therefore, includes both mechanical and non-mechanical forces and agencies, just as ‘natural’ as the purely mechanical ones, material as well as immaterial entities which ‘fill’ and pervade space and without which there would be no unity or structure in the world, or better to say, there would not be a world.

“The world, of course, is not an organism, like the animal, and possesses no ‘soul.’ Yet it can no more be reduced to pure mechanism than the animal, in spite of Descartes.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. pp. 258-9.

“Leibniz, who was much more interested in morals than in physics and in man than in the cosmos, could have answered [to Clarke’s question of Leibniz of why the world is perfectly prepared by God so that it requires no more of God’s intervention] that it was the only means to avoid making God responsible for the actual management, or mismanagement, of this our world. God just did not do what He wanted, or would like to do. There were laws, and rules, that He could neither change nor tamper with. Things had natures that He could not modify.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 273.

“Yet it can be argued that this victory [Newton’s over Leibnizians and Cartesians in the decades following their dispute] was a Pyrrhic one, and that the price paid for it was disastrously high. Thus, for instance, the force of attraction which, for Newton, was a proof of the insufficiency of pure mechanism, a demonstration of the existence of higher, non-mechanical powers, the manifestation of God’s presence and action in the world, ceased to play this role, and became a purely natural force, a property of matter, that enriched mechanism instead of supplanting it.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 274.

“God, even the Newtonian one, could obviously not limit His creative action and treat a certain part of infinite homogeneous space – though able to distinguish it from the rest – in a way so utterly different from the others. Thus the material universe, in spite of filling only an exceedingly small part of the infinite void, became just as infinite as this….

“Space, consequently, lost progressively its attributive or substantial character; from the ultimate stuff which the world was made of (the substantial space of Descartes) or the attribute of God, the frame of his presence and action (the space of Newton [and More]), it became more and more the void of the atomists, neither substance nor accident, the infinite, uncreated nothingness, the frame of the absence of all being; consequently also of God’s.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 275.

“Last but not least, the world-clock made by the Divine Artifex was much better than Newton had thought it to be. Every progress of Newtonian science brought new proofs for Leibniz’s contention: the moving force of the universe, its via viva, did not decrease; the world-clock needed neither rewinding, nor mending.

“The Divine Artifex had therefore less and less to do in the world. He did not even need to conserve it, as the world, more and more, became able to dispense with this service.” Koyré, Alexandre. 1957[2016]. From the Closed World to the Infinite Universe. Kettering, OH: Angelico Press. p. 276.

“We are familiar with the very odd habit in Western painting, starting in the fifteenth century, of organizing the viewer’s gaze so that it can serve as a counterpart to a spectacle of objects or landscapes. Viewers must not only remain at a certain distance from what they are looking at, but what they see must be arranged, prepared, aligned so as to be rendered perfectly visible. Between the two, there is the plane of the painting, which occupies the midpoint between the object and the subject….

“What has been invented by Western painting is a pair whose two members are equally bizarre, not to say exotic, a pairing that has not been observed in any other civilization: the object for this subject, the subject for this object. Here, then, is proof that there is an operator, an operation, that distributes object and subject, exactly as there is a common concept that distributes the respective roles of Nature/Culture by occupying the same place ‘human’ occupies with respect to the marked categories man/woman….

“This schema makes it easier, I hope, to understand why it would be pointless to seek to ‘reconcile’ or ‘go beyond’ the subject and the object without taking into account the operator – represented here by the architect-manipulator – who has distributed the roles to these strange characters, some of whom are going to play the role of nature – for a subject – and others the role of consciousness – of this object….

“Emphasizing this work of distribution makes it clearer that the expression ‘belonging to nature’ is almost meaningless, since nature is only one element in a complex consisting of at least three terms, the second serving as its counterpart, culture, and the third being the one that distributes features between the first two.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 16, 17, 18, 19.

“What moralists tend to ignore is something engineers know: on the side of the subject, there is no mastery; on the side of the object, no possible deanimation. As one of the engineers says, ‘It is not a question of whether or not the Atchafalaya [closed off river bed leading from the Mississippi] will end up capturing the entire river, but a question of when.’” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 54.

“When we claim that there is, on one side, a natural world and, on the other, a human world, we are simply proposing to say, after the fact, that an arbitrary portion of the actors will be stripped of all action and that another portion, equally arbitrary, will be endowed with souls (or consciousness). But these two secondary operations leave perfectly intact the only interesting phenomenon: the exchange of forms of action through the transactions between agencies of multiple origins and forms…. This may appear paradoxical, but, to gain in realism, we have to leave aside the pseudo-realism that purports to be drawing the portrait of humans parading against a background of things.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 58.

“Galileo’s Earth could revolve, but it had no ‘tipping point,’ no ‘planetary frontiers,’ no ‘critical zones.’ It had a movement, but not a behavior. In other words, it was not yet the Earth of the Anthropocene.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 60.

“Being a subject does not mean acting in an autonomous fashion in relation to an objective context; rather, it means sharing agency with other subjects that have also lost their autonomy.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 62.

“… Newton had to discover an agent capable of instantly transporting action at a distance from one body to another. At the time, there was no character available to him who could transport an instantaneous movement without any obstacle – except angels. Through several hundred pages of angelology, Newton gradually managed to trim their wings and transform this new agent into a ‘force.’ A ‘purely objective’ force? Of course, because it had answered the objections, but it was still charged, upstream, by millennia of meditations on an ‘angelic system of instant messaging.’ As we know quite well, purity would sterilize the sciences: behind the force, the wings of angels are always beating invisibly.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 66.

“It is the material world that we have rendered mute in order to avoid answering the questions ‘Who or what is speaking” Who or what is acting?’” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 67.

“It takes just a few moments’ reflection, however, to notice that the idea of an inert world is itself an effect of style, a particular genre, a certain way of muting the agencies that we cannot prevent ourselves from proliferating as soon as we begin to describe any situation whatsoever…. Similarly, the idea of a deanimated world is only a way of linking animations as if nothing were happening there. But agency is always there, whatever we may do. The idea of a Nature/Culture distinction, like that of human/nonhuman, is nothing like a great philosophical concept, a profound ontology; it is a secondary stylistic effect, posterior, derived, through which we purport to simplify the distribution of actors by proceeding to designate some as animate and others as inanimate. This second operation succeeds only in deanimating certain protagonists, called ‘material,’ by depriving them of their activity, and in overanimating certain others, called ‘human’….” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 67-8.

“How can one possibly produce the impression that nothing is happening in a narrative in which events, adventures, exchanges of properties, transactions among agencies are multiplied from one moment to the next?… How is this possible? By transforming the concatenation of causes and consequences in such a way that all the action is – or at least appears to be – in the cause, and that there is no more agency left in the consequences. Obviously this is impossible; the consequences are always surprising and, in practice, in the history of discovery, as in the narrative of discovery, and even in the teaching of the most solidly established facts, the cause arrives a long time after the consequences.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 68.

“One of the great enigmas of Western history is not that ‘there are still people naive enough to believe in animism,’ but that many people still hold the rather naive belief in a supposedly deanimated ‘material world.’ And this is the case at the very moment when scientists are multiplying the agencies in which they – and we – are more and more implicated every day.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 70; subquote: no attribution.

“Strangely, and I shall come back to the point, this form of causalist narrative closely resembles the creationist stories through which one attributes to a first cause, to a creation deemed ex nihilo, the whole series of what follows…. Nothing, literally, happens any longer, since the agent is taken to be the ‘simple cause’ of its predecessor. All the action has been placed in the antecedent. It hardly matters, then, whether the antecedent is called an omnipotent Creator or omnipotent Causality. The consequence might as well not be there at all; as we might say colloquially, it is there only ‘as an extra.’ We can go on stringing episodes one after another; the quality that made them ‘events’ has disappeared.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 71-2.

“Through a complete reversal of the favorite trope of Western philosophy, human societies seem to be resigning themselves to playing the role of witless object, while it is nature that is unexpectedly taking on the role of active subject! Have you noticed that we are now attributing to natural history the terms of human history – tipping points, acceleration, crisis, revolution – and that to speak of human history we are using the words inertia, hysteresis, path dependency, as if humans had taken on the aspect of a passive and immutable nature in order to explain why they are doing nothing against the threat?” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 74.

“When, on the basis of the shaky, haloed, and distorted images of the Moon captured by his telescope, Galileo decided, thanks to his extensive knowledge of perspective drawing, to see shadows projected by the Sun on lunar hills, mountain chains, and valleys, he quickly established a new type of continuity, not to say a new fraternity, between the Earth and its satellite. They were both planets; they were both bodies made of the same homogeneous matter; they both had the same dignity; and they both revolved around another center…. The Earth was no longer relegated to the lower depths of a sublunary world surrounded by circles of dignity each more elevated than the one before …. The Earth henceforth had the same importance as all the other celestial bodies, without any hierarchy among them; as for God, he could be encountered anywhere in the vast immensities of the world.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 76-7.

“If there is no frame, no goal, no direction, we have to consider Gaia as the name of the process by which variable and contingent occurrences have made later events more probable. In this sense, Gaia is a creature no more of chance than of necessity. Which means that it closely resembles what we have come to regard as history itself.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 107.

“… he who looks at the Earth as a Globe always sees himself as a God. If the Sphere is what one wishes to contemplate passively when one is tired of history, how can one manage to trace the connections of the Earth without depicting a sphere? By a movement that turns back on itself, in the form of a loop. This is the only way to draw a path between agents without resorting to the notions of parts and a Whole that only the presence of an all-powerful Engineer – Providence, evolution, or Thermostat – could have set up.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 136-7.

“… it is only when humans see pollution falling back on them that they begin really to feel that the Earth is in fact round. Or, rather, the roundness of the Earth … takes on more and more verisimilitude as the number of circles with which it can be surrounded gradually increases.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 139.

“The learned say that the word religion could have two sources or origins. According to the first, it would come from the Latin verb religare, to attach…. According to the second origin, which is more probable, though not certain, and related to the first one, it would mean to assemble, gather, lift up, traverse, or reread. But they never say what sublime word our language opposes to the religious, in order to deny it: negligence. Whoever has no religion should not be called an atheist or unbeliever, but negligent. The notion of negligence makes it possible to understand our time and our weather [notre temps].” Serres, Michel. 1995. The Natural Contract. pp. 47-8; subquote in Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 152.

“To address a collective is first to find a way of naming what it respects the most, what it recognizes as its supreme authority.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 153.

“Jan Assmann, the great Egyptologist and historian of mythic memory, has reminded us that there was a venerable tradition in the various city-states of the Mediterranean and the Middle East, before the advent of Judaism and Christianity, in which translation tables were drawn up for the names of the gods that were worshipped….

“According to Assmann, these translation tables worked by shifting attention from the proper names of the divinities to a series of characteristics that the names summed up in the mind of their worshippers. If, for example, the name ‘Zeus’ was incomprehensible to a listener, the speaker would reel off the list of his attributes: ‘Guide of destinies’, ‘Protector of the suppliants’, or ‘God of the favorable winds’, and of course, ‘Bearer of thunder’, until the foreigner found a corresponding divinity in his own language….

“[But after Akhenaten’s god, the ‘Mosaic division,’ and the monotheistic movement] Whatever these tables may have allowed in the past, the ‘one, unique God’ could no longer be synonymous with any other deity whatsoever. Translating the name of the one into the name of the Other became not only unfeasible but scandalous and even impious. ‘True’ divinity became untranslatable by any other name; no cult but its own could be tolerated on pain of idolatry…. This is why Assmann proposes, for this new association between religion and truth, the apparently counter-intuitive term counter-religion,….” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 154, 155, 156; reference: Assmann, Jan. 1998. Moses the Egyptian: The Memory of Egypt in Western Monotheism.

“To declare oneself without any divinity at all does not suffice to cast into oblivion the voice of the supreme authority that, for its part, fulminates just as violently as the previous one: ‘You shall under no circumstances make knowledge of the laws of nature commensurable with any cult [as purist scientists might exhort].’” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 157.

“These are two ways, as we now understand, of seeing nothing about the world, either by depriving it of all action, and thus deanimating it, or by adding to it a soul for which it has no use, and thus overanimating it.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 174.

“The intuition of the counter-religion [regular Western monotheism], such as it can be reconstituted through multiple metamorphoses, is that, despite the passage of time, the world has an end,….

“The problem with such an intuition is that it is fundamentally unstable, for the excellent reason that the end times have come, but that time is lasting! There is no way to escape from this tension. The end has been reached, and it is unreachable. We are saved, and we are not. Enough to drive us mad.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 174, 175.

“‘By 1620, people in positions of political power and theological authority in Europe no longer saw Montaigne’s pluralism as a viable intellectual option, any more than Henry’s [King assasinated in 1610] tolerance was for them a practical option. The humanists’ readiness to live with uncertainty, ambiguity, and differences of opinion had done nothing to prevent religious conflict from getting out of hand: ergo, it had helped cause the worsening state of affairs. If skepticism let one down, certainty was more urgent. It might not be obvious what one was supposed to be certain about, but uncertainty had become unacceptable.’” Toulmin, Stephen. 1990. Cosmopolis: The Hidden Agenda of Modernity. U of Chicago Press. p. 55: subquote in: Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 187.

“‘[English] Commonwealth sectarians [the radical challengers of the period] read any proposal [by the naturalists] to deprive physical mass (i.e. Matter) of a spontaneous capacity for action or motion, as going hand in hand with proposals to deprive the human mass (i.e. the ‘lower orders’) of the population of an autonomous capacity for action, and so for social independence. What strikes us as a matter of basic physics was, in their eyes, all of a piece with attempts to reimpose the inequitable order of society from which they had escaped in the 1540s. After 1660, conversely English intellectuals stopped questioning the inertness of matter, for fear of being tarred with the same brush as the Commonwealth regicides.

“Doesn’t that sound familiar? That the earth may react to our actions bothers today’s intellectual elites as the autonomy of matter once bothered the supports of the established order!” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 188; subquote: Toulmin, Stephen. 1990. Cosmopolis: The Hidden Agenda of Modernity. U of Chicago Press. p. 80.

“Joachim [de Flore (1130 – 1202)] in fact adds to the traditional Christian division between the epoch of the Father and that of the Son – and thus between the Old and the New Testament – a new epoch, which he called the Kingdom of the Spirit….

“… waiting for the Kingdom of the Spirit seems to be a perfect interpretation of the dogma of the Incarnation, which is after all defined by eternity in time. With this nuance: Joachim makes the waiting period, by definition impossible to control, the realization within history of the end of history…. The relations between the end of times and the finitude of time have been reversed. History begins to bear, in its very movement, the transcendence that puts an end to it!” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 197; refers to an argument made by Voegelin, Eric. 2000. “Ersatz Religion: The Gnostic Mass Movements of Our Time.” pp. 295-313. In: The Collected Works of Eric Voegelin, vol. 5: Modernity without Constraint: The Political Religions, The New Science of Politics, and Science, Politics and Gnosticism. Henningsen, Manfred (ed.) U of Missouri Press.

“But to realize here below [from heaven to take up Joachim’s call for a Kingdom of Spirit] the promise of the beyond inevitably means passing from a definition that could be called spiritual to a form of politics. One then abandons St Augustine’s wise and precarious solution, which consisted in expecting nothing from the earthly City but everything from the heavenly city. The monks of subsequent generations, enthusiastic readers of Joachim, dreamed for their part of actually realizing the heavenly City right here, by radically transforming the earthly one…. From that moment on, poor politics, so impotent, so modest, so concrete, always to disappointing, was charged with the crushing weight of making the kingdom of the Spirit realistic!…

“… you have before your eyes the terrifying prospect of entrusting to militants, inspired by the certainty of truths from on high, the achievement of Paradise on Earth.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 198.

“If the history of the Moderns had consisted in moving from the abandonment of illusions about the beyond to the solid resources of the here below, it would have become wholly attentive to the terrestrial. But for those who have immanentized Heaven, there is no longer any accessible Earth. The whole paradox of modernization is that it has lost sight, more and more, of any contact with the down-to-earth, with materiality….” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 200.

“According to him [Eric Voegelin; see above], the Moderns have not been secularized – and this is the object of a vast dispute – but, conversely, immanentized. The inevitable result: they have no sort of possible contact with the terrestrial, since they can see in it only the transcendent, which would be trying awkwardly to fold itself into the immanent. And necessarily failing! Fundamentalism was born, and has never stopped metastasizing.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 204.

“… the West has landed on all other civilizations like an Apocalypse that has put an end to their existence. By believing oneself to be a bearer of salvation, one becomes the apocalypse for others.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 205-6.

“Telling Westerners – or those who have recently become Westernized, more or less violently – that the time has come, that their world has ended, that they have to change their way of life, can only produce a feeling of total incomprehension, because, for them, the Apocalypse has already taken place. They have already gone over to the other side. The world of the beyond has been achieved – in any case for those who have become wealthy. They have already crossed the threshold that puts an end to historicity.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 206.

“What doesn’t manage to get through to people bombarded by bad news about the ecological mutation is the activity, the autonomy, the sensitivity to our actions, of the materials that make up the critical zones in which we all reside.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 207.

“Now we can grasp the religious – and, more precisely, apocalyptic – origin of such deanimation. It results from the narratives of causality that attribute all action to the cause – going back step by step to the First Cause – and all passivity to the consequences. A strange competition between Nature and Creation, between the blind Watchmaker and the all-seeing God, in order to try to empty the world, as much as possible, of any activity.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 208.

“… the Moderns believe that they are in a post-apocalyptic epoch – it hardly matters whether it is the Enlightenment of Revelation, the Enlightenment of Science, or the glare of Revolution. In the most profound sense of the term, history for them is always over. Without any way to regain the present, there will be no exit, since they will hear every call to come back to Earth as a return to the archaic or the barbarous.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 212.

“In the great repertory of the history of religions, it is hard to find a divinity whose authority has been less contested than Nature and the laws through which She could compel all things to obey Her.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 214.

“… the Old [climatic or Modernist] Regime did not really make it possible to do politics, since it never encountered real opponents; it was enough to struggle against irrational people or infidels, who needed to be educated or converted, but never fought. In any case, they didn’t need to be combated in the radical sense that they might, in turn, put us in danger of losing our own values. These values remained protected, in Nature, in inevitable Progress, in the Meaning of History, in indisputable Science.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. pp. 223-4.

“‘Nature’ immunizes against the risks of politics. It was conceived for the purpose. This is why, in the proper sense, there has never really been a political ecology…. Even if you claim to be ‘at war’ against such adversaries, this war won’t be a real one, since it will remain pedagogical. You will remain basically convinced that, if only you could have explained things clearly to them, they would have been convinced of the rightness of your struggle.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 225.

“Today, what is strange is that this state of nature [all against all] is not situated, as it was for Hobbes, in the past; it is coming toward us, it is our present.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 227.

“As Schmitt writes: ‘A world in which the possibility of war is utterly eliminated, a completely pacified globe, would be a world without the distinction of friend and enemy and hence a world without politics.’” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 240; subquote: Schmitt, Carl. [1932]1976. The Concept of the Political. Ed. and trans. George Schwab. Rutgers UP.

“The choice Schmitt sets before us is terribly clear: either you agree to distinguish the enemy from the friend, and then you are engaging in politics, strictly defining the boundaries of very real wars, ‘wars over what the world is made of,’ or else you scrupulously avoid waging wars and having enemies, but then you are renouncing politics, which means that you are giving yourselves over to the protection of a State of Nature that encompasses everything and that has already unified the world in a single whole, in a Globe that is supposed to be capable of solving all conflicts from its own disinterested, neutral, all-encompassing point of view.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 240.

“Because of the phenomenon that Voegelin calls immanentization, the Moderns are never of their time but always on the other side of the Apocalypse, suspended between senseless hope and senseless despair.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 242.

“… if we want to have a political ecology, we have to begin by acknowledging the division of a human species that has been prematurely unified.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 247.

“Naturalist scientists – those who proudly assert that they are ‘of Nature’ – are unfortunate figures, bound to disappear, disembodied, behind their Knowledge, or to have souls, voices, and places, but at the risk of losing their authority. In contrast, earthbound scientists are embodied creatures. They form a people. They have enemies. They belong to the territory outlined by their instruments. Their knowledge extends as far as their ability to finance, to control, to maintain the sensors that make the consequences of their actions visible. They have no scruples about acknowledging the existential drama in which they are engaged…. If their territory knows no national boundaries, this is not because they have access to the universal, but because they keep on bringing in new agents to be full participants in the subsistence of the other agents.” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 252.

“… act in such a way that a loop is traceable and publicly visible….” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 276.

“One can address Gaia, not as one addressed Nature, as an impersonal but nonetheless personalized entity, but rather directly, naming it as a configuration of new political entities. To live in the epoch of the Anthropocene is to acknowledge a strange and difficult limitation of powers in favor of Gaia, considered as the secular aggregation of all the agents that can be recognized thanks to the tracing of feedback loops. Here, just as with the earlier invention of the political personification of the State, both thought and practice need fiction: ‘Gaia, I name you as that which I am addressing and that which I am prepared to face’” Latour, Bruno. 2017. Facing Gaia; Eight Lectures on the New Climatic Regime. Medford, MA: Polity. p. 283.

“… it must be emphasized that biology is an experimental discipline to a much larger extent than physics and chemistry….” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 6.

“The fact that reproducibility can be enhanced by modifying experimental setups demonstrates that data are not categorically ‘clean’ or ‘noisy’, reproducible or irreproducible, but rather come in degrees of noisiness and reproducibility, depending on the experimental setup used to generate them. This does not mean, however, that degrees of reproducibility are subjective constructs. Unlike McAllister’s thresholds of statistical significance, which are imposed by convention, degrees of reproducibility are discovered a posteriori, by trial and error, and are objective, in the sense that they are determined by the physical structure of experimental setups.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 13; reference: McAllister, James. 1997. “Phenomena and Patterns in Data Sets.” Erkenntnis. 47:217-28

“Historical case studies reveal that research is typically driven by a reciprocal feedback between attempts at explanation and experimental fiddling aimed at increasing reproducibility…. Once some measurable degree of reproducibility is secured, the control labels on the basis of which experimental setups are replicated provide a preliminary list of causally relevant factors marking the first step in the elucidation of mechanisms.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 14.

“Inasmuch as researchers typically characterize explananda in the absence of any putative explanans, I think it is correct to assume that most phenomena begin their epistemic career as data reproduced when experiments are replicated.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 19.

“The fact that a mechanism produces a certain phenomenon in one biological system offers no firm guarantees that similar mechanisms produce similar phenomena in other biological systems. Even in the same biological system, the same phenomenon may be simultaneously generated by more than one mechanism, with some mechanisms having a higher biological relevance in one situation, but not another.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 20.

“… despite a much-argued-for distinction between data and phenomena, the two are intimately linked to a much greater extent than most philosophers are willing to admit. The fact that phenomena are described as less noisy, reliable, reproducible, and recurrent explananda does not preclude them from being data. Conversely, noisiness does not automatically disqualify data from fulfilling the epistemic role of explananda typically attributed to phenomena. None of these descriptions apply exclusively to phenomena or data. The situation is further complicated by the fact that phenomena are a dynamic category. In the early stages of research, any data generated by a controlled experiment is a potential phenomenon. In the most fruitful phase of experimental research, phenomena typically amount to data reproduced across one or, more commonly, a series of experimental setups, although experimental research neither excludes the investigation of irreproducible and noisy data nor is incompatible with the possibility that such data may be phenomena amenable to systematic explanation. In later stages, the identification of causal factors and the eventual elucidation of mechanisms prompts more-or-less dramatic recharacterizations of phenomena. Finally, a small number of phenomena are predicted top-down, from theories and explanatory accounts already enjoying substantial empirical support.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. pp. 21-2.

“A mechanism is said to be responsible for a phenomenon in the sense that it produces or underlies that phenomenon. Two metaphysical accounts are standardly offered. An etiological account captures the intuition that mechanisms should be causally relevant to phenomena given that the discovery of mechanisms relies on experiments demonstrating causal relevance. The implication, however, that phenomena are end-point outcomes of causal chains is at odds with experimental characterizations of phenomena. Alternatively, a constitutive account captures the notion that phenomena are behaviors of systems explained by referring to the behavior of their parts. Yet this account raises a profound puzzle about how evidence for causal relevance can justify a metaphysical interpretation postulating noncausal relationships between mechanisms and phenomena. I reject both accounts in favor of a third one, stating that a phenomenon is nothing else but the data generated by measuring a mechanism. Conversely, a mechanism is a causal structure linking the variables probed by the measurements involved in the description of a phenomenon in relationships of correlation and causal dependency.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. pp. 22-3.

“… Carl Craver and William Bechtel argue that the phenomenon of light transduction in the eye consists of, as opposed to being caused by, a hierarchical structure of mechanisms involving parts behaving in certain ways, much in the same way the temperature off a gas consists of, and is not caused by, the mean kinetic energy of gas molecules.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 27; reference: Craver, Carl & William Bechtel. 2007. “Top-Down Causation without Top-Down Causes.” Biology and Philosophy. 22:547-63.

“The mutual manipulability account presupposes a system or whole exhibiting a specific behavior, along with a decomposition strategy yielding parts exhibiting their own specific behaviors… In the examples discussed in the literature, a system is typically an organism, a part of an organism (cell, organ), or a population of organisms. This conception, relying on tacit intuitions about what counts as a biological individual, is rather restrictive, since it entails that mechanisms cannot extend beyond the spatiotemporal boundaries of a given biological system. For example, Earth’s magnetic field cannot be part of the biological mechanism of bird navigation. As a result, a somewhat arbitrary distinction is drawn between triggering conditions located outside a biological system and relegated to various etiological mechanisms, and the constitutive mechanism, which is strictly confined within the boundaries of the system.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 28.

“Although a behavior is tacitly assumed to be the behavior of a biological system, the implication here being that one first chooses a system and then describes its behavior, an equally legitimate approach is to first choose a behavior and then define the system as a collection of variables or factors relevant to that behavior. For instance, two associated factors often constitute a system worthy of further investigation. The main advantage of this approach is that the boundaries of wholes and mechanisms are determined a posteriori, thus avoiding the need to rely on prior intuitions.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. pp. 28-9.

“It may therefore be concluded that a mechanism includes only a subset of the parts of a system, namely those involved in a mutual manipulability relationship with the system.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 29.

“Nevertheless, Craver and Bechtel insist that the requirement for part-whole relationships has unpalatable consequences for a causal interpretation, chief among which is the fact that cause and effect are no longer distinct events…. If lower levels supervene on higher ones, as implied by the part-whole constituency requirement, then top-down interventions invariably have an effect on the behaviors of both wholes and their parts…. This argument further highlights the fact that talk about interventions on and measurement of parts and wholes is remarkably vague. If I push a cup of coffee over the edge of the desk, do I intervene on the cup? Or do I intervene on the room, Earth, the solar system, the whole universe, and all those many other things of which the cup is a part?” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 31; reference: Craver, Carl & William Bechtel. 2007. “Top-Down Causation without Top-Down Causes.” Biology and Philosophy. 22:547-63.

“In summary, a phenomenon is analogous to an incomplete or low-resolution measurement-mediated representation of a mechanism.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 35.

“In contrast, the causal mediation account [author’s account] neither assumes nor entails that reality is systematically structured as hierarchies of ontologically distinct macro-state phenomena consisting of micro-level mechanistic components. On this account, one and the same causal structure is probed by an increasing number of measurements and interventions gradually revealing additional causal intermediaries.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. pp. 35-6.

“The account of phenomena and the causal mediation account of the relationship between mechanisms and phenomena defended in the previous sections assume a minimalist ontology, which best describes experimental research conducted outside any discipline-specific theoretical framework….

“The minimal experimental ontology consists of variables and relationships between variables. It would be misleading to think of variables as physical entities or structures and of relationships between variables as activities, interactions, or functions. Inasmuch as nothing else is known or assumed by hypothesis, variables are defined in operational terms, according to the techniques used to measure and manipulate them. This leaves unanswered questions about the physical nature of variables, as well as about potential identities, part-whole composition, and other physical relationships between variables.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 39.

“The fact that the terms ‘function’ and ‘activity’ are used to describe both data and physical structures, processes, and interactions suggests that they are umbrella terms indicative of a pluralist stance about physical interpretation and not genuine ontological categories.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 56.

“Considerations pertaining to part-whole composition, interactions, identity, and structure add novel elements to the minimal experimental interpretation, extending it into the full-blown mechanistic ontology representative of most research in cell and molecular biology.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 60.

“The notion that mechanisms are, ontologically speaking, organized systems of interacting parts doesn’t please everybody.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 60.

“A pluralist stance has the notable advantage of providing a means for accommodating ontological complexity by introducing placeholder terms, such as ‘function’ and ‘activity’, where individual instances of the placeholder can be filled by whatever turns out to correspond to it in terms of physical reality. For as long as the placeholders themselves are not reified, the presupposition of a monolithic mechanistic ontology is avoided, allowing for the true nature of biological mechanisms to be discovered and reconstructed from bits and pieces of interpreted experimental results.” Baetu, Tudor. 2019. Mechanisms in Molecular Biology. Cambridge UP. p. 61.

“In the words of one of the most prominent of anti-reductionists, reductionism’s ‘mistake consists in the loss of understanding through immersion in detail, with concomitant failure to represent generalities that are important to ‘growth and form.’” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 2; subquote: Kitcher, P. 1999. “The hegemony of molecular biology.” Biology and Philosophy. 14:195-210.

“If the aim of science is explanation and many explanations in functional biology are adequate, complete, and correct, then the methodological prescription that we must search for molecular completions or corrections of these functional explanations in molecular processes will be unwarranted. Consequently, molecular biology will not be the inevitable foundation for every compartment of functional biology. But if the aim of science is explanation and functional explanations are either incorrect or incomplete and molecular explanations are either (more) correct or (more) complete, then biology must act on the methodological prescription that we should seek macromolecular explanations of all functional biological phenomena. All biologists who seek complete and correct explanations will have eventually to be molecular biologists.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 4.

“Reduction was initially introduced as an inter-theoretical relation between theories. Broader or deeper theories explained narrower theories in special cases or approximations. Post-positivists held that explanation in general was deemed to be a matter of deductive derivation from laws (whence the label ‘deductive-nomological [D-N] model of explanation’)….

“However, as exponents of reduction noted, the most difficult and creative part of a reduction is establishing these connections of meaning (i.e., formulating ‘bridge principles,’ ‘bilateral reduction sentences,’ or ‘coordinating definitions’). The ideal gas law, PV = nRT, was reductively explained by the kinetic theory of gases only after Kelvin realized that heat can be defined in terms of the mean kinetic energy of the constituent particles comprising gases…. Similarly, in biology, Watson and Crick’s achievement consisted in telling the world what genes really are by showing how polynucleotide sequences can do the work of replication and phenotypic regulation required of genes as units of heredity.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. pp. 9-10.

“The suggestion that the history of scientific ‘progress’ is a matter not of reduction but of replacement emerged with Kuhn’s hugely influential work…. … as Kuhn claimed to document, the institutional discipline that science imposes requires that its history be regularly rewritten after each replacement – each paradigm shift – in order to make these replacements easy to mistake for mere corrections and smooth reductions. This mythic self-deception was required, according to Kuhn, by the institutional imposition of disciplinary norms in each of the sciences.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 12.

“Soon after the philosophy of biology ‘took off’ as a distinctive domain of research in the philosophy of science [1970s], two facts about the domain of biology became evident that completely undermined reduction as derivation: First, as philosophy of science then understood the term ‘law,’ there are no laws in functional biology to derive from molecular biology, nor laws in molecular biology to derive from biochemistry, organic chemistry, or any other kind of chemistry; and second, the proprietary (presumptive natural) kinds of biology – its vocabulary of functional properties – couldn’t be defined in the terms of molecular biology, and so it couldn’t be reduced to chemistry. And these two obstacles to reduction by derivation had the same biological sources. Consequently, either reductionism about biology had to be surrendered or it had to be radically reconfigured.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. pp. 13-4.

“But, as Hull first noted in 1974, the required ‘bridge principles’ between the concept of gene as it figures in functional biology (population biology, evolutionary biology, developmental biology) and as it figures in molecular biology could not be constructed. Any attempt to define, say, the gene for hemoglobin in terms of a nucleic acid sequence is bound to be incomplete. To begin with, as Hull noted, the genetic code is redundant, so that three different DNA nucleotides can constitute the same RNA sequence and same amino acid…. Moreover, if the genetic code is a frozen accident, in Crick’s words, there will be sequences never actually realized that could code for the same RNA sequences and the same functional protein….

“Once introns and exons were discovered, the question arose as to whether the latter were parts of the genes from which they were removed during or after transcription… The molecular biologists’ identification of promoters and suppressors – cis- and trans-acting regulatory sequences operating on structural sequences – further increased the obstacles to finding any manageable systematic link between what the molecular geneticists’ were discovering about nucleotide mechanisms and the functional biologists’ explanatory concept of the gene….

“Two problems arise for metaphysical reductionism (i.e., physicalism), the thesis everyone thought was safely beyond dispute. First, if physical facts fix all of the facts, then facts about genes need to be fixed by facts about nucleic acids…. Second, if possible, this account should be combined with a nondeductive conception of reduction, one that still shows how molecular biology can and does explain functional biological phenomena. And finally, these explanations are going to have to be improvements on nonmolecular explanations in functional biology if the research program of reductionism is to be vindicated.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. pp. 14-5; reference: Hull, D. 1974. The Philosophy of Biological Science. Englewood Cliffs, NJ: Prentice Hall.

“The second problem facing reductionism in biology was the almost complete absence of strict laws at the level of either the reducing theory or the reduced theory. If there aren’t any laws in either theory, there is no scope for derivational reduction at all.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 15.

“That there are no strict laws in biology, only relatively restricted ceteris paribus [all else being equal] regularities, is no widely recognized among philosophers of biology.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 16.

“… many of its [biology’s] explanatory concepts – its proprietary kinds – and almost all of its descriptive concepts appeal to functions. For instance, to call something a wing, a fin, or a gene is to identify it in terms of its function.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 17.

“On Cummins’s account, a function is a causal capacity that is nested in a broader system. This broader system engages in the programmed manifestation’ of some more complex capacity. The original component’s function is the causal contribution it makes to the manifestation of this more complex capacity, relative to some ‘analytical account.’” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 17; reference and subquote: Cummins, R. 1975. “Functional analysis.” Journal of Philosophy. 72:741-764.

“It is the nature of any mechanism that selects for effects that it cannot discriminate between differing structures with identical effects. And functional equivalence combined with structural difference will always increase as physical combinations become larger and more physically differentiated from one another…. Since selection for function is blind to differences in structure, there will be no laws in any science that, like biology, individuates kinds by selected effects – that is, by functions.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 18.

“It is worth reiterating that, as many philosophers of biology will argue, biological explanation does not require strict laws. Non-strict ceteris paribus laws will suffice for biological explanation. Models, for example, apply to systems only ceteris paribus. But the issue here is not explanation – it is the metaphysical thesis of reduction and the methodological dictum to seek reductions. Without strict laws, the derivational demands of metaphysical and methodological reductionism are impossible to act upon. Without recourse to laws of either kind, reductionism must be rejected or reformulated.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 21.

“Fifty years of work in the philosophy of biology established the broad consensus that there are no strict laws in biology of the sort familiar to physics or even chemistry. Ergo, neither reductionism nor antireductionism about laws is tenable in biology. The entire character of biology as a discipline reflects the considerations that make laws impossible. All of the kinds of biology are functional and therefore have etiologies that reflect natural selection operating on local conditions, and natural selection is constantly changing local conditions….

“The principles of the theory of natural selection are the only universally invariant laws in biology.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 27.

“Reductionism must be a thesis about both sorts of explanation. Even to endorse proximate explanations, reductionism needs to hold that ultimate explanations at the level of functional biology are completed, corrected, improved, deepened, and otherwise underwritten by proximate explanations at the molecular level.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 31.

“Only a molecular account of the process of selection for eyespots [on wings of butterflies] could provide the details that turn a how-possible explanation into a why-necessary one. Such an account would itself also be an adaptational explanation: It would identify strategies that were historically available for adaptation by identifying the genes that determine the characteristics of the evolutionary ancestors of lepidopterans and that provide the only stock of phenotypes on which selection can operate to move along pathways to alternative predation-avoiding outcomes – leaf color camouflage, spot camouflage, or other forms of Batesian mimicry, repellant taste to predators, Muellerian mimicry of bad-tasting species, etc. The reductionist’s ‘why-necessary explanation’ would show how the extended phenotypes of these genes competed and how the genes that generated the eyespot eventually became predominant. In other words, the reductionist holds that: (1) Every functional ultimate explanation is a how-possibly explanation; and (2) there is a genic and biochemical selection process underlying the functional how-possibly explanation. Once completed, reduction turns the merely how–possible scenario of the functional ultimate explanation into a why-necessary proximate explanation of a historical pattern.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 33.

“We have to understand why, in a universe made only by physics, the process that Darwin discovered is the only game in town.

“There are three things we need to keep in mind to show this. First, and as already noted, if we are out to explain how any adaptation at all could ever happen, we can’t help ourselves to some prior adaptation, no matter how slight, puny, or insignificant. Second, the second law requires that the emergence and persistence of orderliness of any kind be energetically expensive. An explanation of adaptation’s emergence and persistence is going to have to show that the process is wasteful. The more wasteful the better, so far as the second law is concerned. Third, physics is going to have to drive the asymmetry of evolutionary change.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 48.

“In fact, the right way to look at the emergence of adaptation on Earth is to recognize that it is the most wasteful, most energetically expensive, and most entropy-producing process that occurs on the planet. The evolution and maintenance of adaptations by natural selection wins the prize for greatest efficiency in carrying out the second law’s mandate to create disorder. Forget design – evolution is a mess.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 49.

“No matter what brings it about, the process of adaptation is different from the more basic physical and chemical processes in nature. The latter are all ‘time symmetrical’ – adaptation is not.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 53.

“There is only one physical process available to drive asymmetrical adaptational evolution: the entropy increase required by the second law of thermodynamics. Therefore, the second law must be the driving force in adaptational evolution.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 53.

“Any adaptation-creating process has to produce suboptimal alternatives all of the time. It has to do this not just to ensure entropy increase, but also to honor the one-way direction that the second law insists on.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 55.

“But ‘reduction’ and ‘reductionism’ have never really been able to shake this association with a clearly unwarrantable approach to explanation and theorizing. As a result, by the beginning of the twenty-first century, the terms had begun to be supplanted as labels by the term ‘mechanism’, which is employed to describe the demand that biology uncover mechanisms, and ultimately molecular, physical mechanisms, and that biological systems and processes be explained by identifying the mechanisms that compose them….

“Mechanism, as we will see, is very close to reductionism, perhaps even being an old wine in a newer bottle.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. pp. 56, 57.

“Mathematical models, even when empirically adequate to phenomena, lack the asymmetry that causal explanations must report.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 59.

“All too often in the life sciences, nonmechanistic explanations trade in completely different forces and factors [e.g., functions], not merely in more abstract versions of the ones mechanists countenance.

“This is the point of those who contrast ultimate evolutionary explanations with proximate mechanistic ones.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 59.

“Once distinct higher-level causes are acknowledged, some philosophers and opponents of reductionism throughout the sciences may argue that these causes can operate in downward directions, exercising effects on lower levels of organization, something no mechanist, reductionist, or physicalist should want to countenance.

“Writing with Bechtel, another strong advocate of mechanism, Craver has advanced such an argument seeking to show that mechanism is compatible with higher-level causation, but not downward (or upward) causation….

“Assuming that higher-level causation obtains, they have claimed that mechanism rules out both downward causation from wholes to parts and upward causation from parts to wholes. Instead, what appears to be ‘inter-level’ (upward or downward) causation is always just a combination of ‘constitution’ plus intra-level (same level) causation. Thus, high-level causation is preserved independent of lower-level causation and provides a basis for autonomous higher-level explanations. Demands such as MDBr [more details are better] are preserved since the higher-level causation, although independent of lower-level causation, consists in lower-level causation plus constitution of higher-level objects and processes by their mechanical components suitably arranged, and such explanations can be improved by greater detail. Craver and Bechtel write: ‘We assume that there are higher-level causes and, further, that all higher-level causes are fully explained by constitutive mechanisms’.

“Craver and Bechtel’s proposal raises a question about in exactly what ‘constitution’ consists in terms of how it differs from causation and what special contribution it makes, a contribution that makes higher-level causation real without being mysteriously ‘emergent’ – distinct, autonomous, and capable of downward effects. Elsewhere, Craver seeks to deliver a conception of ‘constitution’ that does these things. Mechanism requires that particular mechanisms constitute the phenomena they explain.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. pp. 60-62; references: Craver, Carl & W. Bechtel. 2007. “Top-down causation without top-down causes.” Biology and Philosophy. 22:547-563; Craver, Carl. 2007. Explaining the Brain. Oxford UP.

“Consider, for example, Fisher’s well-known model of the 50:50 sex ratio in sexually reproducing species. Fisher’s model explains this ratio without any reference to the mechanism of reproduction shared by all of these species. Fisher wrote down a proof from some harmless idealizations that when one sex or the other exceeds 50 percent of the population, natural selection confers higher fitness on females that disproportionately bear offspring of the minority sex. This process will shift the population back to 50:50, and when it overshoots, it will enhance the fitness of females that disproportionately give birth to offspring of the minority sex so that, other things being equal, ceteris paribus, the sex ratio always remains close to 50:50….

“One challenge to the agenda of mechanism, then, is to show that natural selection is a mechanism, one that can be described at various levels of abstraction – that models such as Fisher’s are at the higher levels and that the causal mechanisms that underwrite them fill out the concrete details of particular cases in ways that vindicate MDBr and the original abstractions that later details improve.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 64.

“One upshot for demands such as MDBr is obvious. MDBr can’t tolerate much convergent evolution: convergent evolution produces functional kinds that are instantiated by radically different realizations, with quite different details of implementation that are so different from one another that they may not share even an abstract mechanism in common. When an environment begins to channel a variety of preexisting mechanisms into a narrow range of functions, it may result in unmanageable multiple realizability, the barrier to mechanistic and reductionist lower-level explanations that antireductionists have long insisted upon.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 66.

“Many mechanists recognize that in their analysis mechanisms take the place of laws as the drivers of explanation in the life sciences. Since there are no laws in these disciplines, there is nothing in the life sciences for classical reductionists to demand (further) explanation of. But if there are no laws, then something else has to do the work laws were supposed to do: explain, test, and predict.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 67.

“Several mechanists have addressed the matter of what the causal relation that obtains within mechanisms and between components and the phenomena they produce consists in. Almost the full range of alternative analyses of the causal relation – the ‘cement of the universe’ in Hume’s words – are formally compatible with mechanism. But the attractions of a ‘quantity conserved in transmission’ analysis are obvious. This is an approach that takes causation to consist in the transfer of a conserved quantity – momentum, for example, transmitted by physical contact or physical fields. Mechanisms must ‘bottom out’ into relations between physical objects and systems that preserve such quantities as they are transferred. There is only one way in which this can happen: the operation of physical law.” Rosenberg, Alex. 2020. Reduction and Mechanism. Cambridge UP. p. 69.

“Rosen was especially concerned with the implications of closure to efficient causation for the possibility of making a model of a living organism; Eigen with the need for specific proteins to catalyse production of molecules for storing information efficiently; Ganti with the need to relate life chemistry to accepted principles of chemistry and chemical engineering; Maturana and Varela with the need for an organism to be separated from its environment by a membrane or other barrier; and Dyson and (independently) Kauffman with the possibility for life to arise naturally in mixtures of large numbers of components….

“The authors we have mentioned had very different backgrounds and training, and none of them were biochemists.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2020. “Contrasting Theories of Life: Historical Context, Current Theories: In search of an ideal theory.” Biosystems. 188. doi.org/10.1016/j.biosystems.2019.104063. p. 20.

“Robert Rosen’s theory of life tries to explain how a living organism could avoid infinite regress…. How can the organism avoid piling up catalysts ad infinitum? He resolved this question in terms of closure to efficient causation, whereby there is a circular organization of effects with no beginning and no end, and that final cause was not an appeal to an external creator but a reference to the way in which an organism continuously recreates itself.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2020. “Contrasting Theories of Life: Historical Context, Current Theories: In search of an ideal theory.” Biosystems. 188. doi.org/10.1016/j.biosystems.2019.104063. p. 21.

“… all giants in their different ways [Dyson, Eigen, Ganti, Herrera, Kacser, Kauffman, Maturana, Mettrie, Leduc, Pasteur, Rosen, Schroedinger, Schuster, Wentworth Thompson, Varela], but even when they lived through the same period they barely communicated with one another (with the obvious exceptions of those who worked together…) or considered one another’s ideas; moreover, none of them attempted a synthesis of the different theories of life.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2020. “Contrasting Theories of Life: Historical Context, Current Theories: In search of an ideal theory.” Biosystems. 188. doi.org/10.1016/j.biosystems.2019.104063. p. 60.

“All of the theories we have considered contain some useful features that need to be included in a definitive theory of life, but all lack some that are important. In particular, none of them incorporate any mechanism of regulation, or any other mechanism to prevent a self-organizing system from growing until it forms a tar.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2020. “Contrasting Theories of Life: Historical Context, Current Theories: In search of an ideal theory.” Biosystems. 188. doi.org/10.1016/j.biosystems.2019.104063. p. 61.

“The main points that we see are the following:

“(a) Construction of a membrane needs to be described explicitly, not just left for future development.
“(b) Thermodynamic requirements need to be satisfied explicitly. For a system at the origin of life it may be sufficient to suppose a supply of energy-rich nutrients, but a more long-term system certainly needs to harness gradients across boundaries.
“(c) It is not enough to have a cycle labelled ‘information cycle’: there must be a clear mechanism for collecting, storing and using the information.
“(d) Any living system must be closed to efficient causation: the catalysts must be produced by the organism in such a way that infinite regress is avoided.
“(e) There must be regulation of the metabolism, so that organisms cannot grow indefinitely, and metabolites are produced only as needed.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2020. “Contrasting Theories of Life: Historical Context, Current Theories: In search of an ideal theory.” Biosystems. 188. doi.org/10.1016/j.biosystems.2019.104063. p. 61.

“The golden era of the organism lasted only a relatively short period of time. In the course of the 1940s and 1950s, it came to an abrupt halt.” Baedke, Jan. 2018. “O Organism, Where Are Thou? Old and New Challenges for Organism-Centered Biology.” Journal of the History of Biology. doi.org/10.1007/s10739-018-9549-4. p. 23[?].

“A novel, so-called ‘Extended Evolutionary Synthesis’ (EES) is currently being developed, at the heart of which lies the concept of the organism….

“The new kind of OCB–a new ‘Organism-centred perspective’–arises as an opposite standpoint against theoretical positions that are different from those in the early twentieth century. For example, it opposes not reductionist biochemistry and cell theory or vitalism but gene-centrism…. The EES is more and more challenged by anti-individualistic tendencies that provide an indication of unsolved conceptual problems. In fact, these fundamental problems are very similar to the ones the earlier version of OCB faced a century earlier. Again, the organism seems to be (1) inextricably interwoven with and (2) indistinguishable from its environment. In addition, (3) the boundaries between organisms become blurred.” Baedke, Jan. 2018. “O Organism, Where Are Thou? Old and New Challenges for Organism-Centered Biology.” Journal of the History of Biology. doi.org/10.1007/s10739-018-9549-4. p. 25[?].

“In the early twentieth century, and especially in the interwar period, a number of theoretical approaches tried to establish organisms as the central unit in biological theorizing. This OCB–different from both vitalism and mechanism–arose from new insights into the various causal roles organisms play in nature. This includes studies on the plasticity and robustness of organisms as well as their collective and symbiotic activities in the environment. However, as it turned out, the attempt to develop a consistent concept of the organism struggled with a number of cases in which the biological individual seems to be dissolved.” Baedke, Jan. 2018. “O Organism, Where Are Thou? Old and New Challenges for Organism-Centered Biology.” Journal of the History of Biology. doi.org/10.1007/s10739-018-9549-4. p. 27[?].

“As a novel OCB–EES–appears on the horizon, we should not forget that an emphasis on the organism is easily associated with the organism’s disappearance. In fact, organisms are ambiguous units. Often, once we approach them, they vanish away, merging with the environment and with each other. As new anti-individualistic tendencies show, the EES has not yet developed a satisfying conceptual solution to these problems.” Baedke, Jan. 2018. “O Organism, Where Are Thou? Old and New Challenges for Organism-Centered Biology.” Journal of the History of Biology. doi.org/10.1007/s10739-018-9549-4. p. 28[?].

“… this concept [organism is machine] was developed by Charles Darwin as a response to another metaphor of the natural theology of his time: that of the organic world as being the product of design. Whereas the natural theologians considered the world to be an artifact in a literal sense, as God’s creation, Darwin thought of it as if it were designed, that is, strictly in the metaphorical sense. However, Darwin – and many Darwinians and neo-Darwinians ever since – never rejected the design metaphor. This metaphor fit very well with another metaphor first proposed by Rene Descartes: that of the world as a machine.” Kampourakis, Kostas. 2020. “Why Does It Matter That Many Biology Concepts Are Metaphors?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 102-22. Cambridge UP. p. 110.

“It was hard for Darwin’s early supporters to miss the core of his theory of evolution by natural selection, but, undervaluing as they did his comparison to the art of breeding, miss it they indeed did [the statistical power of little modifications to create novel features, species]…. But as his extended correspondence with his botanical American friend Asa Gray demonstrates, Darwin never tackled the interpretive problem head on because as long as he lived he toiled as much as his friends, including Gray, within the bounds of scientific assumptions in which quasi-Newtonian dynamical models and intelligent design seemed the only available alternatives. All he could come up with, he told Gray, was that God created the laws by which natural selection evolved well-designed ‘contrivances,’ but in doing so necessarily left much to chance. ‘Not that this notion at all satisfies me,’ he continued.’” Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 123-45. Cambridge UP. p. 130.

“It took until 1918 for R. A. Fisher, who was simultaneously the most important figure in the development of advanced statistical science and an ardent Darwinian, to demonstrate that the probability that genetic mutations of the sort postulated by the new Mendelians will take hold in populations is exceedingly small…. On the other hand, genetic mutations of small effect, if any happen to be available that lead a population to reproduce more effectively in a specific environment, can readily be amplified by natural selection across many generations to gradually evolve adaptations. Suddenly the fortunes of Darwinism, or rather of genetic neo-Darwinism, began to shine more brightly.

“This happened because Fisher used models of system dynamics taken from statistical rather than classical physics. The distribution of gases in statistical mechanics and thermodynamics is measured by looking at ensembles of molecules whose trajectories are probabilistic rather than deterministic.” Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 123-45. Cambridge UP. p. 131.

“But the new models of evolutionary dynamics taken from statistical physics made it a matter of definition that organisms develop but don’t evolve, while populations evolve but don’t develop.” Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 123-45. Cambridge UP. p. 132.

“Applied to evolutionary theory, fitness is a not [sic] a single characteristic like physical robustness, but a macroscopic propensity to reproduce more effectively that supervenes on myriad changing and interacting properties of organisms.” Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 123-45. Cambridge UP. p. 133.

“… population thinking allowed species to be reconceived as geographically distributed populations within which reproduction occurs freely, but between which genetic barriers evolve to prevent it. This meant that species are recast as historical particulars, not abstract classes defined by essential, that is, necessary and sufficient, properties.” Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 123-45. Cambridge UP. p. 134.

“I have been arguing that concepts play at least three key roles in scientific discovery as metaphors, as models, and as conceptual frameworks that figure in controversies about the scope and limits of research programs.” Depew, David. 2020. “How Do Concepts Contribute to Scientific Advancement?” In: Philosophy of Science for Biologists. Kampourakis, Kostas & Tobias Uller (eds). pp. 123-45. Cambridge UP. p. 141.

“A rapid survey of the 1.5 million of the living species described to date reveals that about one-fourth of them match this definition of soil animals [by Decaens et al. 2006] at least for one stage of their life cycle. Soil and leaf litter arthropod richness alone has been estimated to be about five times that in the canopy.” Decaens, Thibaud, Patrick Lavelle & Juan-Jose Jimenez. 2008. “Priorities for conservation of soil animals.” CAN Reviews: Perspective in Agriculture, Veterinary Science, Nutrition and Natural Resources. 3(014). p. 2[?]; reference: Decaens, T., JJ Jimenez, C. Gioia, GJ Measey & P. Lavelle. 2006. “The values of soil animals for conservation biology.” European Journal of Soil Biology. 42:S23-38.

“The reasons why biotic mechanisms that normally reduce diversity have allowed such a large number of species to coexist in soils have been referred to as the ‘enigma of soil diversity’. A number of factors have been proposed to explain this pattern. First, the three-dimensional structure of the edaphic environment is responsible for a high micro-habitat heterogeneity and a considerable spatial and temporal resource partitioning, which may promote greater species coexistence, since a wide range of pores, surface types and microclimates may reduce competitive exclusion. On the other hand, the amount of dead organic matter needed to support decomposers or detritivores is known to be lower on average than what would be required to support herbivores, and the resident time of energy within detritus-based systems is also longer than in grazer systems. This enhances the efficiency of detrital versus grazer-dominated food webs and explains why the former support longer food chains and greater food-web complexity. Finally, complex species interactions also participate in soil biodiversity enhancement. At the most local scale, soil biodiversity is affected by interactions within trophic levels, direct inter-trophic interactions or by soil engineers that influence the diversity of smaller-sized organisms by promoting dispersal and by enhancing habitat complexity in soil. At larger scales, soil biodiversity is driven by the diversity, composition and dynamics of vegetation as well as by above-ground trophic interactions.” Decaens, Thibaud, Patrick Lavelle & Juan-Jose Jimenez. 2008. “Priorities for conservation of soil animals.” CAN Reviews: Perspective in Agriculture, Veterinary Science, Nutrition and Natural Resources. 3(014). p. 2[?].

“The amount of C stored in soils is estimated to be 2344 Pg, which is the third largest global C pool after the lithosphere and the deep oceans and also the third largest regarding accumulation rate (1.4 Pg/year), right after oceanic net uptake (1.7) and atmospheric uptake (3.2).” Decaens, Thibaud, Patrick Lavelle & Juan-Jose Jimenez. 2008. “Priorities for conservation of soil animals.” CAN Reviews: Perspective in Agriculture, Veterinary Science, Nutrition and Natural Resources. 3(014). p. 6[?].

“A set of concepts and ecological theories have been proposed to explain the extremely rich diversity in soils with the advent of soil ecology that is progressively becoming a truly interdisciplinary field of scientific innovation. For example, one of the theories explaining how soil macrofauna selectively triggers micro-organism activities uses the ‘sleeping beauty paradox’, which states that micro-organisms are inactive most of the time in soil due to their inability to move significantly and find new feeding resources. Invertebrates and roots are the ‘Prince Charming’ that awaken micro-organisms by bringing them into contact with organic particles through bioturbation.” Decaens, Thibaud, Patrick Lavelle & Juan-Jose Jimenez. 2008. “Priorities for conservation of soil animals.” CAN Reviews: Perspective in Agriculture, Veterinary Science, Nutrition and Natural Resources. 3(014). p. 7[?].

“The World Resources Institute estimates that over 66% of cultivated soils suffer degradation, of which a third are severely degraded.” Decaens, Thibaud, Patrick Lavelle & Juan-Jose Jimenez. 2008. “Priorities for conservation of soil animals.” CAN Reviews: Perspective in Agriculture, Veterinary Science, Nutrition and Natural Resources. 3(014). p. 12[?]; reference World Resources Institute at wri.org.

“As pointed out half a century ago (Schroedinger, 1944), the second law of thermodynamics imposes the requirement that life, and a fortiori its emergence, is possible only as a subset of a larger system featuring strong thermodynamic disequilibria.” Russell, Michael & Wolfgang Nitschke. 2017. “Methane: Fuel or Exhaust at the Emergence of Life?” Astrobiology. 12(10):1053-1066. p. 1059.

“These [the fields of rheology, atmospheric sciences, or networked chemical reactions] feature many of the defining properties of living systems, and the emergence of a dissipative structure, ‘life,’ under appropriate conditions of high disequilibria appears as a quasi-necessity in the theoretical framework of far-from-equilibrium thermodynamics. In addition to strong free energy gradients characterizing the system, far-from-equilibrium thermodynamics has worked out further important parameters that favor the emergence of dissipative structures: (a) nonlinear equations of motion in reaction phase space and (b) reaction feedback loops (note that mathematically (a) and (b) are often intimately correlated with the high ΔG criterion).” Russell, Michael & Wolfgang Nitschke. 2017. “Methane: Fuel or Exhaust at the Emergence of Life?” Astrobiology. 12(10):1053-1066. p. 1059.

“From the already described observations, we conclude that a reaction producing methane as an exhaust does not only appear geochemically compromised but also comparatively poorly suited for kick-starting life’s emergence in the form of a dissipative structure. By contrast, the oxidation of the ‘fuel’ methane by high potential electron acceptors, such as, for example, nitrogen oxides and oxyanions, fulfills several of the criteria laid out by far-from-equilibrium thermodynamics for the emergence of self-organizing systems.” Russell, Michael & Wolfgang Nitschke. 2017. “Methane: Fuel or Exhaust at the Emergence of Life?” Astrobiology. 12(10):1053-1066. pp. 1059-60.

“Our general conclusion is that what drove life’s emergence was not merely speeding up of chemistry or geochemistry (toward biochemistry) as sometimes assumed. Key to the emergence and the maintenance of all life are specific enzymes, many of which are effectively disequilibria-converting engines. These are turnstile-like engines, often hosed in membranes that, for example, couple strong redox and pH gradients to drive endergonic reactions.” Russell, Michael & Wolfgang Nitschke. 2017. “Methane: Fuel or Exhaust at the Emergence of Life?” Astrobiology. 12(10):1053-1066. p. 1060.

“… life and chemistry are fundamentally incompatible. To function life has to take its transformations out of the hands of chemistry and operate them itself, using macromolecular ‘mechano-chemical- machines, requiring one machine (roughly) for each transformation life must, in Nick Lane’s evocative phrasing, ‘transcend chemistry.’

“A principal reason for this is that purely ‘chemical’ processes run thermodynamically ‘downhill,’ whereas life has to run its most essential transformations ‘uphill’–transformations that go thermodynamically ‘backwards’….” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 1

“… all ideas of how life arose that are predicated on a ‘chemistry in a bag’ view of living systems, and/or on the notion of life arising from an ‘energized assemblage of building blocks,’ cannot in principle be correct.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 1.

“Here we argue that such ‘cooking-the-soup’ notions are uniformly untenable. In our opposition, we contend that hardly anything could be less compatible with the general inner workings of life, much less its emergence, than the results of exposing any mix of molecules to any sort of chemically non-specific ‘energy,’ whether stably or episodically. That one can find, among the inevitable myriad of organic products of such experiments and processes some ‘building blocks of life’ is utterly irrelevant and misleading.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 2.

“… they are in addition [requirement issues for life beyond organization], and more essentially, three characteristics of the chemistry of life that distinguish it fundamentally from that of ‘non-life,’ all three of which have the form of constraints on its molecular transformations including at its emergence. In brief, they are i) that they all must achieve high and quite ‘unnatural,’ performance in terms of chemical specificity; ii) they in general must be dynamically and conditionally controllable; and iii) that a specific subset of them must be constantly driven, and maintained thermodynamically, uphill into more-or-less far-from-equilibrium states.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. pp. 2-3.

“Only very specific sources of free energy can be made use of: all of the basic, task-specific conversion engines must be in place and working to convert those externally supplied disequilibria into the ones needed internally. And all of the parts must be functionally and spatially organized and wired-together with high specificity.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 3.

“Merely having access to a source of free energy is very far from sufficient to power life–for the same reason that access to wind or to water behind a damn [sic] is by itself insufficient for getting electrically powered work done. Instead i) the ‘negentropy’ needed to power life must be embodied in one of a very restricted list of disequilibria; ii) the system it is to drive must be capable of ‘converting’ that disequilibrium into a specific cascade of usable internal disequilibria in conformity to an elaborate organizational design; and iii) the myriad of unwanted reactions that the resulting chemistry would, if permitted, produce, must be suppressed.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 3.

“The main ‘power source’ for driving the high wire act called ‘life’ is not ATP, but a disequilibrium in the ATP hydrolysis reaction.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 3.

“ATP’s richly deserved reputation as life’s main power source generally doesn’t credit the frantic industry of its production and use. We turn over our body’s weight in ATP daily; each molecule lasting, between synthesis and hydrolysis, scarcely more than a minute.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 3.

“And, of course, we mammals die in minutes when deprived of our oxygen ‘ground wire’ for the electrons flowing through the electron transport chain.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 4.

“… what the Ox/Phos ATP-synthase system is principally up to is not the synthesis of ATP molecules, but is instead acting as a thermodynamic pump, forcing the ratio of ATP to its hydrolysis products–[ATP]/([ADP][Pi])–out of what it would be at equilibrium, and by the astounding factor of ~1010!” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 4.

“… life needs what is mistakenly thought to be ‘energy’; instead it is usable disequilibria.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 4.

“… the second law dictates that all of the disequilibria that living systems must constantly be creating and maintaining are products of specific processes of ‘disequilibria conversion’–dissipating one to create another. And in life, all such conversions are mediated by purpose-built macromolecular ‘engines,’ acting as escapement mechanisms, each managing the conversion of a specific reaction pair…” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 4.

“… contrary to general belief, ATP does not drive endergonic processes by transferring energy derived from the hydrolysis of one of its phosphoanhydride bonds to the reaction being driven–supposedly providing the energy needed to make that reaction happen. Rather, energy transfer (not even the ‘free part’ of a literal energy) is just not how ‘coupling’ happens, not, therefore, how endergonic processes are driven.

“Instead, a macromolecular conversion engine is a stochastic device that uses probable ‘forward’ thermal fluctuations in one process to ‘rectify’ those in another (that is, to select improbable, ‘reverse’ fluctuations in that process). In this it exploits the fact that in chemical reactions both forward and reverse events are inevitably occurring, with a statistical directional bias given by how much more frequently the system experiences a thermal fluctuation moving ‘reagents’ rather than ‘products’ into the reaction’s transition state. On that basis a conversion engine, managing two reactions in parallel, operates by making a successful forward fluctuation in either reaction contingent on the ‘quasi-simultaneous’ occurrence (by pure ‘Brownian’ chance) of a backward (‘anti-entropic’) fluctuation in the other. This then causes the statistically stronger of the two reactions to proceed forward (downhill)–in the net–and weaker to be driven backward (uphill), thereby generating a disequilibrium in the latter process. No (literal energy passes between the two processes.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 4.

“We have implied that the driven output of a biological conversion process is always the creation or maintenance of a thermodynamic disequilibrium. We take note here that, somewhat counterintuitively, this is true even when that output is ‘mechanical work.’ In that case the work always involves ‘rectifying’ thermal fluctuations in the position of some molecular structure (e.g., the position on a microtubule of a kinesin molecule and its cargo). The motor arranges to have positional fluctuations in a specific direction trigger the hydrolysis of a bound ATP. The relative irreversibility of that hydrolysis has the consequence of ‘trapping,’ i.e., ‘selecting,’ that particular fluctuation motion, while allowing those in all other directions to be ignored.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 4.

“In their molecular hearts living systems are conspiracies of rejection–everywhere and constantly rejecting the probable in favor of the improbable…. And it underlies the fact, invoked above, that a living system is, inherently, a state of extreme improbability–in both process and organization.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 5.

“Importantly, this state of extreme improbability is marked by two further properties unique to life, and both present ‘of necessity.’ First, it is composed of a multitude of specific, separate, dynamically maintained ‘substrates of improbability’ (e.g., the ATP, and Proton Motive Force disequilibria we discussed above, but very many others). Second, these improbable substates are ‘plumbed’ together, via disequilibria conversions (e.g., the specific coupling between the ATP and PMF disequilibria), in a specific architecture that is itself a state of extreme improbability.

“Also, ‘of necessity’ is the fact that each of the component disequilibrium substates is the product of specific macromolecular ‘improbability generator’ (aka ‘disequilibrium converter’) whose operation inherently ‘transcends chemistry’….” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 5.

“In this light, all else about the devices of life, those of ‘information,’ containment, replication, etc., are just that–‘devices’: ‘inventions’ that came along in due evolutionary course as incremental improvements on the overall efficiency with which the living forms dissipate the disequilibria driving them.” Branscomb, Elbert & Michael Russell. 2018. “Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?” BioEssays. 1700179. doi:10.1002/bies.201700179. p. 5.

“Ecological scaffolding underpinned a recent (and ongoing) experimental exploration of the evolution of multicellularity. Discrete lineages established from the bacterium Pseudomonas fluorescens were propagated under conditions that required, for long-term persistence, repeated completion of a two-phase life cycle involving soma- and germ-like states. In the experiment, variation was discretized using glass microcosms but the design is loosely analogous with an environment such as a pond in which reeds extend from the water. Each reed allows establishment of a single microbial mat (the soma-like phase), with the spacing of reeds ensuring variation at the level of mats. Mats that collapse, for example, through physical disturbance, allow the possibility that an extant mat might, via production of a dispersing (germline-like) phase, increase its representation among the population of mats. The possibility of a selective process thus unfolds at the level of mats. After ten life-cycle generations, the fitness of derived mats significantly improved, with the most successful lineage having evolved a simple genetic switch that ensured quasi-reliable developmental change between soma- and germline-like phases.” Black, Andrew, Pierrick Bourrat & Paul Rainey. 2020. “Ecological scaffolding and the evolution of individuality.” Nature Ecology & Evolution. 4:426-36. pp. 426-7.

“If Darwinian properties do not pre-exist or cannot arise by co-option of pre-existing lower-level traits, then their earliest manifestation necessarily lies in some exogenous factor(s). The solution we have advocated involves recognizing the continuity between organisms and their environments; the idea that Darwinian-like properties can be scaffolded by the environment in much the same way that reproduction in viruses is scaffolded by the host cell or that development can be scaffolded by overlap of parts between parents and offspring.” Black, Andrew, Pierrick Bourrat & Paul Rainey. 2020. “Ecological scaffolding and the evolution of individuality.” Nature Ecology & Evolution. 4:426-36. pp. 431-2.

“There is no doubt that cooperation and integration are basic features of multicellular organisms but the scaffolding perspective does not presuppose cooperation among cells as a necessary first step. Nonetheless behaviours (interactions) that are clearly cooperative stand to evolve given appropriate ecological scaffolds. For example, the slow-growing cells favoured when dispersal time is long could be labelled cooperating types because they show restraint in the face of plentiful resources, whereas the fast-growing mutants arising within patches might be termed selfish types, but there is no need to use such labels.” Black, Andrew, Pierrick Bourrat & Paul Rainey. 2020. “Ecological scaffolding and the evolution of individuality.” Nature Ecology & Evolution. 4:426-36. p. 433.

“The discussion at the workshop identified an urgent need for a better, comprehensive theory of life to better define the aims of OoL investigations, that is, to define the phenomena whose spontaneous onset is being studied. It was recognized that arguments or controversy over definitions, while not always helpful, may continue while we lack such a theory. It was also noted that a compatible, substrate-neutral, quantitative theory of evolution is highly desirable.” Scharf, Caleb, Nathaniel Virgo, H. James Cleaves, Masashi Aono, Nathanael Aubert-Kato, Arsev Aydinoglu, Ana Barahona, Laura Barge, Steven Benner, Martin Biehi, Ramon Brasser, Christopher Butch, Kuhan Chandru, Leroy Cronin, Sebastian Danielache, Jakob Fischer, John Hernlund, Piet Hut, Takashi Ikegami, Jun Kimura, Kensei Kobayashi, Carlos Mariscal, Shawn McGlynn, Brice Menard, Normal Packard, Robert Pascal, Juli Pereto, Sudha Rajamani, Lana Sinapayen, Eric Smith, Christopher Switzer, Ken Takai, Feng Tian, Yuichiro Ueno, Mary Voytek, Olaf Witkowski & Hikaru Yabuta. 2015. “A Strategy for Origins of Life Research.” Astrobiology. 15(12):1031-42. p. 1035.

“Although it has presently evaded us, it is clear that there is a critical need for a quantitative (even if incomplete) continuous scale or measurement that can be used as a practical tool to evaluate the ‘aliveness’ of any given system.

“There are a number of traits that typify life, such as complexity, adaptiveness, and thermodynamic disequilibrium. To develop a scale of ‘aliveness’ will require a proper study of these and perhaps other variables, as well as the concept of ‘continuity’ within these scales as they may apply to life.” Scharf, Caleb et al [see complete list above]. 2015. “A Strategy for Origins of Life Research.” Astrobiology. 15(12):1031-42. p. 1036.

“[The OoL research community should consider the following practices:] Effective exploration of OoL scenarios will likely require the use of high-throughput chemical laboratory automation (e.g., robotics, microfluidics), so-called ‘cyber chemistry.’

“‘Cyber-chemistry’ offers new opportunities for exploring OoL landscapes and may strengthen ties between the wet and dry A-Life communities through the study of system dynamics and processes.

“There is a need for experiments designed to identify the prebiotic selection of efficient self-reproducing systems instead of individual biomolecules. Cyber-chemistry may offer a method for accomplishing this….

“We should consider the application of these interactive technologies to mimic living systems. This may represent a unique opportunity to identify signposts toward the abstraction of organisms.

“The community should identify existing long-term experiments or potential experiments (e.g., those spanning decades, centuries, or longer that are intentional or unintentional) and actively encourage the performance of new ones….

“Competitions, along the lines of competitions already held for artificial intelligence research, autonomous vehicles, space exploration, and the like, could be useful for making progress in understanding the OoL–both in terms of channeling science activities and in terms of building community.” Scharf, Caleb et al [see complete list above]. 2015. “A Strategy for Origins of Life Research.” Astrobiology. 15(12):1031-42. p. 1037.

“Today, three mechanisms of energy conservation are recognized, which allow coupling of chemical reactions to metabolic ‘work.’ They are (1) substrate-level phosphorylation, (2) charge separation across a membrane with ion pumps (aka, chemiosmosis), and (3) electron pair bifurcation.” Scharf, Caleb et al [see complete list above]. 2015. “A Strategy for Origins of Life Research.” Astrobiology. 15(12):1031-42. p. 1038.

“Looking at microbes only, recent estimates point to 1 trillion different species on Earth and orders of magnitude more bacterial cells on the planet than the number of stars in the known universe. A single one of those cells can have at any given moment 2-4 million expressed proteins.” Preiner, Martina, Silke Asche, Sidney Becker, Holly Betts, Adrien Boniface, Eloi Camprubi, Kuhan Chandru, Velntina Erastova, Sriram Garg, Nozair Khawaja, Gladys Kostyrka, Rainer Machne, Giacomo Moggioli, Kamila Muchowska, Sinje Neukirchen, Benedikt Peter, Edith Pichlhofer, Adam Radvanyi, Daniele Rossetto, Annalena Salditt, Nicolas Schmelling, Fliipa Sousa, Fernando Tria, Daniel Voros & Joana Xavier. 2020. “The Future of Origin of Life Research: Bridging Decades-Old Divisions.” Life. 10, 20. doi:10.3390/life10030020. p. 3.

“Neither world alone [RNA or protein worlds] can provide a clear explanation for the interlacing of the two, though, and there are relatively few endeavours to try out ‘messy emergence’, where some initial cooperation between non-coded proteins and RNAs was vital.” Preiner, Martina et al [see complete list above]. 2020. “The Future of Origin of Life Research: Bridging Decades-Old Divisions.” Life. 10, 20. doi:10.3390/life10030020. p. 3.

“It is now clear that the building blocks for RNA and DNA are intermediates of metabolic networks; they are never directly uptaken from the environment in their ready-for-polymerization forms (i.e. as phosphorylated nucleosides), but as unphosphorylated biogenic nucleosides, and are also in fact moieties of several essential cofactors. The idea of the simultaneous and interdependent origins for RNA and DNA’s building blocks has been given experimental evidence.” Preiner, Martina et al [see complete list above]. 2020. “The Future of Origin of Life Research: Bridging Decades-Old Divisions.” Life. 10, 20. doi:10.3390/life10030020. p. 8; “experimental evidence” refers to: Bhowmik, S. & R. Krishnamurthy. 2019. “The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA.” Nat. Chem. 11:1009-1018.

“A historically important division … if the carbon source for organosynthesis was eminently inorganic (usually CO2), this represented an autotrophic origin, whereas if the carbon source were reduced organic compounds, a heterotrophic one. This division usually links to whether the earliest cells are considered autotrophic or heterotrophic…. For the origin of the first biochemical networks, potentially acellular IDAs [initial Darwinian ancestors], we propose referring instead to whether all or some of the reactions leading to organic molecules occurred in situ (i.e. within, or physically contiguous to the nascent proto-biochemistry) or ex situ (i.e. physically separated from it). Note that this is not just a geographical distinction. Instead, it aims to find out whether the nascent chemical network (eventually leading to living cells) could affect the chemical reactions feeding it. This, we believe, is a meaningful change in language aiming to mend the limitations associated with the autotrophic vs heterotrophic dilemma.” Preiner, Martina et al [see complete list above]. 2020. “The Future of Origin of Life Research: Bridging Decades-Old Divisions.” Life. 10, 20. doi:10.3390/life10030020. p. 12.

“Still, there is a ‘cooperation barrier’ in the transition of non-life to life, caused by (i) molecules that could cooperatively contribute to the success of an ensemble but which are often not supported by the ensemble, and (ii) side reactions or processes that undermine cooperation. To overcome this barrier, the management of those otherwise unconstrained ensembles is required. This hypothesis is particularly interesting because it exposes the necessity of a digitally-coded (genetic, on/off) management of the analog (continuous) reactions of metabolism in order to overcome the cooperation barrier efficiently, reflecting the two-tiered structure of all known living cells.” Preiner, Martina et al [see complete list above]. 2020. “The Future of Origin of Life Research: Bridging Decades-Old Divisions.” Life. 10, 20. doi:10.3390/life10030020. p. 13.

“In fact, nature offers numerous examples of ‘reductive evolution,’ where simple organisms derive from more complex ancestors. This phenomenon is typified by macro- and microscopic parasites and symbionts, particularly those that reside inside their hosts. Such organisms tend to lose the capacity to synthesize metabolites provided by their hosts. For example, tapeworms lack digestive tracts, absorbing all their required nutrients transdermally from their host’s gut. Similarly, many host-associated bacteria are no longer able to synthesize certain essential metabolites, such as amino acids.” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. p. 1.

“… sterile filtered seawater exposed to sunlight accumulates enough HOOH in a few hours to kill axenic Prochlorococcus cultures. But fortunately for Prochlorococcus, other members of its natural community act as a sink for HOOH and keep concentrations low enough for Prochlorococcus to thrive. The sink effect occurs because HOOH is roughly as membrane permeative as water, so the cells that protect their interiors by detoxifying intracellular HOOH eventually also reduce the level of extracellular HOOH and thus protect neighboring cells. In this way, some marine microbes act as ‘helpers’ that protect the vulnerable majority–the ‘beneficiaries’–from HOOH as a side effect of protecting themselves.

“Placing this ecological interaction into an evolutionary context, the loss of HOOH resistance can be described as a community-dependent adaptive event. It is adaptive because resources may be shunted from HOOH defense to growth, but only because other members of the community condition the environment such that a robust oxidative-stress response becomes dispensable to the beneficiaries.” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. p. 2.

“To better understand the proposed evolutionary process, we can separate it into several underlying components. First, there is a selective advantage of becoming a beneficiary, which drives the loss of genes from some organisms and, by default, turns other community members into helpers. The helpers are thus passive players in this process–perhaps the unlucky ones that were the slowest to change. Second, the fitness advantage of losing the gene and its encoded function must be frequency dependent, such that when the helpers become sufficiently rare the benefit of any further loss is negated by its cost, preventing the extinction of the function from the community. Last, we emphasize that HOOH removal differs from many other functions by being ‘leaky,’ so that its detoxification by some members of the community inevitably benefits other cells in their vicinity.” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. p. 2.

“In contrast, the evolution of functional dependency on helpers by definition generates commensalistic or even mutualistic interactions. We present here an alternative theory of coevolution that we name the ‘Black Queen Hypothesis’ (BQH). Similar to the red queen the black queen refers to a playing card, in this case the queen of spades in the game Hearts. In Hearts the goal is to score as few points as possible. The queen of spades, however, is worth as many points as all other cards combined, and therefore a central goal of the game is to not be the player that ends up with that card. In the context of evolution, the BQH posits that certain genes, or more broadly, biological functions, are analogous to the queen of spades. Such functions are costly and therefore undesirable, leading to a selective advantage for organisms that stop performing them. At the same time, the function must provide an indispensable public good, necessitating its retention by at least a subset of the individuals in the community–after all, one cannot play Hearts without a queen of spades….

“Treated formally, the BQH specifies the conditions under which it is advantageous for an organism to stop performing a function. Any loss of a functional gene comes with a potential cost in fitness; therefore, in order to invade a population, a loss-of-function (LOF) mutation must also provide a gain in fitness that outweighs this cost.” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. p. 3.

“In the special case of a mutant expanding in an environment occupied only by itself and its ancestor, the mutant will expand until the ancestors reach a concentration that provides exactly enough of the public good to facilitate an equal growth rate for the ancestor and the mutant….

“However, in a mixed community with unrelated organisms that provide the public good at a sufficient level but are not in direct competition with the mutant and its ancestor, we would expect the LOF mutant to drive its ancestor to extinction.” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. p. 3.

“Any function that is both costly to perform and leaky is a potential target for loss. … we suggest that nitrogen fixation, inorganic nutrient acquisition, and biofilm matrix deposition meet these criteria and thus may be analyzed ecologically and evolutionarily in the framework of the BQH….

“All these examples involve the following: (i) products that are energetically or nutritionally expensive; (ii) functions that are performed and products produced by only a fraction of the community; (iii) functions that are leaky enough for the resulting public goods to be used by other species; and (iv) products that are vital to the community, not just the producer.” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. p. 4.

“The BQH also provides a new framework for looking at several classic problems in microbial ecology. How are microbial communities organized? Why do many organisms fail to grow in pure cultures? Are there unknown niches, even in relatively homogenous environments, that allow the persistence of many species competing for a few limiting resources? And what forces lead to the dependence of communities on rare keystone organisms, whose extinction can lead to instability and potential catastrophe?” Morris, J. Jeffrey, Richard Lenski & Erik Zinser. 2012. “The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss.” mBio. 3(2):e00036-12. doi:10.1128/mBio.00036-12. pp. 5-6.

“Broadly speaking, the Neoproterozoic is when photosynthetic eukaryotes began to take over from cyanobacteria as Earth’s dominant primary producers, eventually driving a major increase in global primary production.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 173.

“… the modern oceans are largely oxygenated. The exact time course of ocean oxygenation is actively debated – recent evidence suggests the oceans may not have become permanently oxygenated until the early Ordovician (ca. 400 Mya) or even the Triassic (ca. 200 Mya) – but evidence for the initiation of this process reaches back to the Neoproterozoic.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 173.

“… an additional negative feedback preventing ocean oxygenation was built into the machinery of photosynthesis itself. That is, oxygenic photosynthesis depends on substantial amounts of iron, but iron is highly insoluble under aerobic conditions, especially at the pH of ambient seawater. Thus, as ocean oxygenation proceeded, iron would become increasingly scarce….

“This hypothesized feedback is fundamentally different than those involving phosphorus and nitrogen as it is strengthened rather than weakened as oxygenation proceeds. As a result, transient perturbations to the ocean redox state alone are ultimately insufficient to explain persistent oxygenation. An important clue to understanding how the biosphere nevertheless overcame this evolutionary bottleneck lies in observations that in the extant oceans iron is not dissolved as free ions but instead is bound to a vas pool of dissolved organic carbon.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 174.

“Similarly, changes in the photosynthetic machinery and core metabolic pathways decrease the iron requirements of cells, helping explain how photosynthesis was able to begin extending its reach in the face of declining iron levels as the ocean became oxygenated. In addition, the classes of organic carbon compounds excreted by marine picocyanobacteria (carboxylic acids, polysaccharides) are known to chelate iron and enhance its bioavailability. Thus, the evolution of marine picocyanobacteria added a positive feedback that counteracted the negative feedbacks built-in to ancestral cyanobacterial photosynthesis and paved the way for ocean oxygenation.

“The identified positive feedback is linked to metabolic rate, and so is strengthened with each innovation that enhances the harvesting of solar energy.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 177.

“There are a wide range of parallels between the rise of marine picocyanobacteria and the rise of land plants. Key observations at the level of cellular metabolism come from analyses of the alphaproteobacterial group SAR11, Prochlorococcus’ most abundant sympatric heterotroph and globally the most abundant microbe. Like marine picocyanobacteria, SAR11 is estimated to have emerged during the Neoproteriozoic, suggesting these lineages have co-evolved over hundreds of millions of years. We reconstructed evolution of the metabolic core of SAR11 and found it underwent a major remodeling that was complementary to that of Prochlorococcus, resulting in compatible pathways for the exchange of organic carbon between the two groups. This is consistent with previous experiments that showed that SAR11 requires several of the compounds identified as excretion pathways in Prochlorococcus. The pathways involved in these exchanges are highly similar to those mediating metabolic interactions between chloroplasts and mitochondria in green plant cells.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 179.

“Collected paleontological and geological observations have led to the argument that the rise of land plants enhanced continental weathering and organic carbon burial as the productivity of the terrestrial biosphere increased, driving an increase in atmospheric oxygen. The proposal outlined above extends those arguments to the water column and highlights the convergent biogeochemical evolution of eukaryotic photosynthesis on land and in the sea.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 180.

“In addition to being linked to major biosphereic expansions, the periods of Earth history around the Great and Neoproterozoic Oxidation Events share a number of other general similarities. Sediment records indicate that both periods had a turbulent climate with major carbon cycle perturbations and global glaciations.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 180.

“The oxygen penetration depth of sediments in turn depends on their composition and on the oxygen concentration of bottom waters. As a consequence, Earth oxygenation effectively acts to stymy itself by decreasing the fractional burial of sedimentary organic carbon, unless increases in oxygen levels are coupled to increases in sedimentation rates and/or changes in the composition of sediment that make them less penetrable to oxygen. Evidence for the latter around the Proterozoic-Phanerozoic boundary comes from analyses that suggest biologically-driven increases in the production of fine-grained clays and muds by the early Phanerozoic. Sedimentary clay minerals have recently been shown to trap organic carbon and prevent its breakdown even in the presence of oxygen through a combination of physical and chemical effects, significantly contributing to the global sequestration of organic carbon. It thus appears that increases in overall weathering/sedimentation rates and in the production of less-penetrable sediments worked in tandem to counteract the negative effect of oxygenation on organic carbon burial, allowing oxygen to rise.

“The existence of a positive feedback between biospheric productivity and continental weathering leads to two possible endmembers for interpreting the drivers of global change around the Great and Neoproterotezoic Oxidation Events. One possibility is that the solid Earth is the ultimate pacemaker of change – biospheric expansions occur when the cooling of the mantle and crust passes through tipping points that trigger changes in the nature of plate tectonics and/or continental exposure, thereby increasing the weathering supply of rock-derived nutrients. This is consistent with observations that transient periods of enhanced weathering of mafic rocks during the assembly and break-up of super continents is associated with transient cycles of enhanced productivity, biodiversity and atmospheric oxygen during both the Proterozoic and Phanerozoic. In this scenario, the biosphere still plays a key role in unlocking the nutrient supply that fuels it, but this feedback is driven from the bottom up by changes in the nature of plate tectonics.

“The other possibility is that life plays a more active role in driving change. Indeed, it has been argued that, by coupling an increasing flux of solar energy into Earth’s geochemical cycles and increasing overall weathering rates, the evolution of photosynthesis accelerated the formation of lighter granites from heavier basalts, thereby increasing crustal buoyancy, promoting the rise of stable continents and directly influencing the mode of plate tectonics. These arguments were subsequently extended to say that by modulating the production of sediments available to subduction, life directly influences the flow of water and other volatiles into the mantle and promotes greater continental exposure.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 181.

“A range of genomic and geochemical evidence nevertheless suggests that the roots of cyanobacteria and the initiation of atmospheric oxygenation pre-date the Great Oxidation Event by several hundred million years. Similarly, paleontological evidence and molecular clock estimates generally agree the roots of eukaryotic photosynthesis pre-date the Neoproterozoic Oxidation Event by at least several hundred million years. This has led to major debates, because if oxygenic photosynthesizers are ultimately responsible for both stages of oxygenation, what explains the long delays between their evolutionary roots and major increases in atmospheric oxygen?

“Considering the role of continental weathering provides insights to this question. If biospheric expansions require long-term increases in the weathering supply of rock-bound nutrients, then changes in the mode of plate tectonics and resulting increases in continental weathering place central constraints on when major expansions can happen, even if the classes of metabolism ultimately driving those expansion already previously existed. Alternatively, if evolutionary increases in the coupling of solar energy into Earth’s geochemical cycles played a central role in driving changes in solid Earth dynamics, then the long delays between photosynthetic innovations and their ecological expansions that ultimately triggered increases in atmospheric oxygen levels may simply reflect the inertia of changes in solid Earth dynamics in response to driving by the biosphere.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 181.

“It has become increasingly clear that the biosphere is intimately intertwined with the rest of the Earth system and that evolution of the energy flows it mediates have far-reaching consequences for the planet.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 182.

“The two main repositories of Earth history are the planetary inventory of rocks and the DNA inside living cells, each of which have their own unique advantages and difficulties…. Despite these challenges, the geologic and genomic records are highly complementary and metabolism provides a key lens for helping us align them and achieve a more integrated view of how Earth and the biosphere have changed together over time.” Braakman, Rogier. 2019. “Evolution of cellular metabolism and the rise of a globally productive biosphere.” Free Radical Biology and Medicine. 140:172-187. p. 182.

“Systems ecology builds on the four columns of (1) hierarchy, (2) thermodynamics, (3) networks, and (4) biogeochemistry.” Jorgensen, Sven, Soren N. Nielsen & Brian Fath. 2015. “Recent progress in systems ecology.” Ecological Modelling. dx.doi.org/10.1016/ j.ecolmodel.2015.08.007. p. 1.

“The various biological networks are not operating in isolation, but are connected and interact with the networks on other levels of the entire ecological hierarchy. This implies that both vertical and horizontal connections and interactions come into play and should be considered. The vertical effects and their integration with the horizontal networks are, however, a new challenge, as network theory has largely only considered the horizontal connections and dominantly on the ecosystem level. The key question is how two or more networks in two or more different levels of the hierarchy can interact and function together. The hierarchical levels in biology and ecology – molecules, cells, organs, organisms, populations, ecosystems, landscapes and the ecosphere – appear at first sight to be working two-by-two molecules/cells, cells/organs, organs/organism, organisms/population, populations/ecosystems, and landscapes/eco-sphere), with levels like molecules, organs, populations and landscapes forming competing horizontal more firmly linked networks, which are driven by an energy input which takes place on the cell, organism, ecosystem and ecosphere level, respectively. This hierarchical image is obviously dependent on how the networks are described. However, all the levels have networks but the levels of molecules, organs, populations, and landscape have generally a more complex network than the four other levels.” Jorgensen, Sven, Soren N. Nielsen & Brian Fath. 2015. “Recent progress in systems ecology.” Ecological Modelling. dx.doi.org/10.1016/ j.ecolmodel.2015.08.007. p. 2.

“… the number of discovered prokaryotic protein-coding genes is orders of magnitude greater than those of all plants and animals combined. Metabolic pathways encoded in microorganisms drive the bulk of elemental cycles in most ecosystems, shaping Earth’s surface chemistry over billions of years. yet, our mechanistic understanding of microbial systems (microbial communities and coupled abiotic physicochemcial processes) remains in its infancy.” Louca, Stilianos, Martin Polz, Florent Mazel, Michaeline Albright, Julie Huber, Mary O’Connor, Martin Ackermann, Aria Hahn, Diane Srivastava, Sean Crowe, Michael Doebeli & Laura Wegener Parfrey. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 936.

“Functional community profiling – describing communities in terms of metabolic functions of interest – can simplify microbial systems to a level permissible to mathematical modeling and can reveal patterns of community structuring across environmental gradients. A wave of recent studies in a multitude of environments, ranging from soil to the ocean and to the human gut, suggest that certain metabolic functions are strongly coupled to certain environmental factors and can, in many cases, appear decoupled from the species assemblages associated with them at a given place and time.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 936.

“In one of the first comparative metagenomic surveys of microbial communities, Tringe et al. showed that functional profiles (in terms of the genes found in communities) were highly correlated with the type of sampled environment (seawater vs soil, etc), suggesting that the environment selected for specific functions. A subsequent comparison of gut microbiota between different human hosts revealed that the taxonomic composition of microbiomes varied strongly across hosts while their community gene content was strongly conserved. Similarly, in a survey of bacterial communities on the macroalgae Ulva australis, communities appeared to be assembled on the basis of functional genes rather than species. These finding suggest that alternative microbial assemblages can exhibit similar community gene profiles selected by their environment. In line with this perspective, a recent study of bacterial and archaeal communities inside the foliage ‘tanks’ of bromeliad plants found that the functional composition of communities (in terms of genes involved in various energy-transducing functions…) was highly conserved across bromeliads. In contrast, the taxa associated with each functional group (i.e., capable of performing a specific metabolic function) varied strongly between bromeliads, regardless of the taxonomic resolution used. Hence, the taxonomic composition within functional groups must have been shaped by additional factors that are distinct from the factors shaping the functional structure of communities, that is, taxonomic composition and functional composition (genetic potential) appeared ‘decoupled’.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. pp. 936-7; reference: Tringe, S.G. et al. 2005. “Comparative metagenomics of microbial communities.” Science. 308:554-557.

“Thus, while the phylogenetic placement of an organism in principle determines its metabolic potential, the reverse need not be true, i.e. metabolic potential is not necessarily indicative of a specific clade. Adaptive loss of function or genome streamlining, convergent evolution, and horizontal gene transfer all erode the phylogenetic signal of many traits.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 937.

In experiments, broadly distributed functions such as respiration, overall carbon catabolism and biomass production often appear more resistant to changes in taxonomic community composition or diversity, than narrow functions such as the degradation of specific compounds. A possible reason for this pattern is that broad functions may be more functionally redundant and thus better buffered against taxonomic shifts caused by biotic or abiotic disturbance. Thermodynamically favored endpoints of linear catabolic pathways may be less sensitive to taxonomic variation than individual intermediate steps that can be performed in alternative ways. For example, models for methanogenic bioreactors fed continuously with glucose suggest that the relative flux rates through ‘alternative’ catabolic pathways may be less stable in the face of taxonomic shifts, than the overall methane production rate.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 937.

“A high functional redundancy with respect to energy-transducing metabolic pathways has long been observed in macrobial communities. Almost all plants, for example, share a common metabolic niche – they are oxygenic photoautotrophs. In microbes and macrobes alike, functional redundancy indicates that additional factors beyond the mere availability of different energy sources must be controlling diversity.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 937.

“… Tilman’s classical competition theory asserts that at steady state and in a well-mixed system any given resource – such as an electron donor or acceptor – can only be limiting to at most a single persisting population. This population will be the one that can maintain a steady size at the lowest possible resource level, since all other populations are either outcompeted or limited by a different resource.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 937; reference: Tilman, D. 1982. Resource Competition and Community Structure. Princeton UP.

“Similarly to macroorganisms, functional redundancy in microbial communities may be promoted by differentiation along other niche axes than just metabolic resources, including differences in their response to environmental perturbations, differences in attachment strategies to particles, differences in chemotactic strategies for exploring nutrient gradients and finding food particles, differences in the number and types of lyase genes for specific polysaccharides, fluctuating nutrient concentrations combined with different growth kinetics, limitation by different trace nutrients and predation by phages and protist grazers.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 938.

“Functional redundancy is an inevitable emergent property of open microbial systems that become visible when a high-dimensional trait space is projected to a lower-dimensional function space of interest.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 939.

“… macrobial ecology … has had a long history of describing community structure in terms of guilds, lifeforms and strategies, all of which may be considered analogous to metabolic functional groups in microbes. More recently, there have been calls to entirely abandon modeling macroscopic communities in terms of species, but instead to focus on functional traits. Reducing microbial communities to energy-transducing metabolic functions, and investigating functional redundancy with respect to these functions, may thus also be a fruitful approach for microbial ecology.” Louca, Stilianos et al [see full list above]. 2018. “Function and functional redundancy in microbial systems.” Nature Ecology & Evolution. 2:936-943. p. 939.

“… one may define a ‘function’ as pertaining to the movement or storage of energy or material. An ‘ecosystem function’ therefore, refers to the movement or storage of energy or material within an ecosystem. Following this definition, the terms ‘ecosystem function’ and ‘ecosystem process’ are effectively the same and can be used interchangeably. Working within this new definition, the defining characteristic of a functional group (from an ecosystem perspective) is the extent to which it modifies or facilitates the transfer or storage of energy or material within the system. In this respect, a scraping parrotfish, a sand-winnowing goby and a sticky-tentacled sea cucumber would all be classified as particulate removers. They are, in this context, a discrete functional group defined by what they do regardless of how they do it.

“This highlights both differences in, and interdependence between, the two types of FGs [functional groups]; phenotype-based ‘how’ definitions and the ecosystem-based ‘what’ definitions.” Bellwood, David, Robert Streit, Simon Brandl & Sterling Tebbett. 2018. “The meaning of the term ‘function’ in ecology: A coral reef perspective.” Functional Ecology. 33:948-961. doi:10.1111/1365-2435.13265. p. 950.

“… there has recently been a rapid increase in the use of ‘functional traits’. For plants, these functional traits have been defined as ‘any biological attribute of an individual that impacts organism performance and thus fitness’. Such traits, as proxies for functions, have been widely used in the terrestrial plant literature, using attributes that are easy to measure and thought to be tightly linked to ecological performance….

“Despite limitations, traits and their presumed functions offer a potential avenue to overcome the complexity that is inevitable in high-diversity systems such as coral reefs. Furthermore, they can operate in the absence of functional knowledge, avoiding the need to empirically measure each species’ contribution to a variety of ecological processes. Such correlations offer fertile ground for further investigation of causality. Traits therefore off a first step in the evaluation of broad-scale trends that may be functionally relevant.” Bellwood, David, Robert Streit, Simon Brandl & Sterling Tebbett. 2018. “The meaning of the term ‘function’ in ecology: A coral reef perspective.” Functional Ecology. 33:948-961. doi:10.1111/1365-2435.13265. p. 953.

“From the beginning, there has been some confusion over the identification of critical ecosystem functions versus the critical FGs that mediate them. The most important step is to recognize that the ecosystem function is paramount, not the providers. We posit that there are four essential steps, in the order of decreasing importance: (a) identify the critical ecosystem function(s), e.g. removal of sediment) at the appropriate spatial and temporal scale for the system of interest, (b) at a matching scale, identify the traits that are important for mediating this function (e.g. scraping teeth to remove sediments from turfs), (c) identify the species that possess the requisite traits and deliver the required functions. Finally, (d) identify and quantify critical FGs, that is collections of species with appropriate traits that deliver the required ecosystem function.” Bellwood, David, Robert Streit, Simon Brandl & Sterling Tebbett. 2018. “The meaning of the term ‘function’ in ecology: A coral reef perspective.” Functional Ecology. 33:948-961. doi:10.1111/1365-2435.13265. p. 956.

“How do we identify individuals without relying on features like cell membranes that may be solutions to challenges faced by particular systems for maintaining integrity rather than foundational properties? We want to allow for the possibility that microbes and loosely bound ecological assemblages such as microbial mats and cultural and technological systems, when viewed with a mathematical lens, qualify as individuals even though their boundaries are more fluid than the organisms we typically allow.” Krakauer, David, Nils Bertschinger, Eckehard Olbrich, Jessica Flack & Nihat Ay. 2020. “The information theory of individuality.” Theory in Biosciences. 139:209-223. doi.org/10.1007/s12064-020-00313-7. p. 210.

“… almost all definitions of individuality assume a set members [sic] (individual) and a set complement (environment). These are articulated in different ways including: (1) as an immunological concept pertaining to the idea of self and non-self, (2) as a temporal aggregate encoding a common past separable or independent from the past of other aggregates (ontogenetic or phylogenetic), (3) as a spatially bounded collection of metabolic reactions insulated by a membrane from reactions in the environment, and more abstractly, (4) as a unit of selection and evolutionary change.” Krakauer, David, Nils Bertschinger, Eckehard Olbrich, Jessica Flack & Nihat Ay. 2020. “The information theory of individuality.” Theory in Biosciences. 139:209-223. doi.org/10.1007/s12064-020-00313-7. p. 210.

“We propose:

“• Individuality can be continuous, with the possible surprising result that some processes possess greater individuality than others.
“• Individuality can emerge at any level of organization. This requires we dispense with privileging a single level or object–for example, replicating cells or organisms–and then defining individuality based on features of these objects, such as sequestered germ cells, vertical transmission of genetic material, a common pool of metabolic free energy, or coordinated immune responses. Although these features may indeed be effective proxies when we have significant prior knowledge of a system, our goal should be to find fundamental, rather that derivative, properties of individuality. Defining individuality around derived properties risks precluding the possibility of individuality in at super-organismal levels and in distributed systems.
“• Individuality can be nested. Given that life is hierarchically organized into trophic and functional levels, we allow the possibility of multiple, parallel levels of individuality.”
Krakauer, David, Nils Bertschinger, Eckehard Olbrich, Jessica Flack & Nihat Ay. 2020. “The information theory of individuality.” Theory in Biosciences. 139:209-223. doi.org/10.1007/s12064-020-00313-7. p. 211.

“Increasing entropy for a phone-call corresponds to the loss or disruption of light-pulses, whereas increasing entropy during inheritance corresponds to mutation or developmental noise. The same scheme can be applied to development, in which case the signaler is an organism in the past and the receiver the same organism in the future. One way in which we might identify individuals is to check to see whether we are dealing with the same aggregation at time t and t + 1. If the information transmitted forward in time is close to maximal, we take that as evidence for individuality.” Krakauer, David, Nils Bertschinger, Eckehard Olbrich, Jessica Flack & Nihat Ay. 2020. “The information theory of individuality.” Theory in Biosciences. 139:209-223. doi.org/10.1007/s12064-020-00313-7. p. 212.

“What is fundamental in our view is the idea that information can be propagated forward through time, meaning that uncertainty is reduced over time…. … we suggest individuality is a natural extension of the ideas of Boltzmann and Von Neumann, and as such has foundations in statistical mechanics and thermodynamics, which consider the conditions required for a persistently ordered states.” Krakauer, David, Nils Bertschinger, Eckehard Olbrich, Jessica Flack & Nihat Ay. 2020. “The information theory of individuality.” Theory in Biosciences. 139:209-223. doi.org/10.1007/s12064-020-00313-7. p. 214.

“Further to identifying nested or hierarchical partitions, we also require some specification of the machine itself–the generator of the time series. This will be equated with parts of the individual and needs to possess some level of robustness or an error-correcting property. This is because individuality in adaptive systems often seems to be associated with adaptive mechanisms of homeostasis–mechanisms that monitor internal states and ensure that deviations are minimized. It is this self-preserving quality of the individual that allows us to make some useful discrimination between physical phenomena and biological ones, without exaggerating the dynamical differences.” Krakauer, David, Nils Bertschinger, Eckehard Olbrich, Jessica Flack & Nihat Ay. 2020. “The information theory of individuality.” Theory in Biosciences. 139:209-223. doi.org/10.1007/s12064-020-00313-7. p. 220.

“The reefs are at least biological individuals. And taking seriously their life, growth and death leads to the question of whether they too might be organisms. The dependence of the reefs on polyps does not rule this out, since such dependence is common in organisms. For example, we depend on internal bacteria that outnumber our own cells by about ten to one, and yet we are organisms. And the polyps that reefs depend on are themselves dependent on single-celled algae, zooanthellae, for the glucose that provides the energy necessary for polyp photosynthesis, which in turn drives the process of calcification….

“Further reflection along these lines may suggest that an integrated network of dependence relations is itself a mark of being an organism. If that were so, then we may come to view the coral reef as a better example of an organism than either the polyps or zooanthellae, as the reef enjoys a kind or degree of complex, functional integrity that polyps and zooanthellae arguably lack.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 2.

“… addressing the Problem of Biological Individuality does not require an essentialist answer according to which biological individuals form a kind individuated by a set of singly necessary and jointly sufficient properties. Indeed, biological essentialism is a view with little credibility… among philosophers of biology.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 3.

“When philosophers of biology discuss individuality they understand individuals to be distinct from other entities such as properties, processes, and events, even if certain (say) properties and processes are constitutive of some forms of individuality. Biological individuals have three -dimensional spatial boundaries, endure for some period of time, are composed of physical matter, bear properties, and participate in processes and events. Biological processes (such as photosynthesis) and biological events (such as speciation) lack such a suite of features.

“A further feature often associated with individuals is agency: a typical individual is a locus of causation, as are electrons in physics and molecules in chemistry. The sense in which biological individuals are agents is compatible with their also playing a more passive role in biological processes, or with their functioning as products rather than as causes of the evolutionary processes they are involved in.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). pp. 3-4.

“In fact, the conception of agency that we draw on is compatible with recognizing that the vast majority of biological agents are not psychological agents at all. It remains an interesting question as to why the use of cognitive metaphors in describing biological agency is widespread.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 4.

“While we break with traditional views that simply equate organisms with biological individuals, or with living agents, we do think a sort of organism-centred view is a good start on the Problem of Biological Individuality. On this view biological individuals include exactly:

“• organisms (such as wasps and whales, and perhaps endosymbionts and slime molds)
“• some parts of organisms (such as hearts, placentas and plasmids) and
“• some groups made up of organisms (such as zebra populations and aggregates of bacteria).

“We call this an organism-centred view because each of its three parts reference organisms. It allows that many biological individuals–for example, hearts and populations–are not themselves organisms. And it allows us to recognize a thing as a biological individual even when we are not sure whether it is an organism, or a part of an organism (e.g., an endosymbiont) or a group of organisms (e.g., a colony of eusocial insects). Organism-centered views of biological individuality seems widely, if implicitly, endorsed, though confusing choices of terminology can conceal this.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). pp. 4-5.

“… in the physical sciences and in pre-Darwinian biology, variation was understood as deviation from a natural or normal state, whereas in the post-Darwinian era, and especially through the Evolutionary Synthesis, variation came to be viewed as prodigious and itself crucial to the underlying causal mechanisms at the heart of biological stasis and change. Rather than being explained away, variation goes all the way down and does much explaining.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 6.

“But intrinsic biological heterogeneity isn’t restricted to evolutionary biology. The geophysicist Walter Elsasser drew this out in his Atom and Organism with the contrast between physical and biological kinds….

“If Elsasser’s general contrast obtains, then we should expect to find manifestations of intrinsic heterogeneity throughout the biological sciences.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 6; reference: Elsasser, Walter. 1966. Atom and Organism: A New Approach to Theoretical Biology. Princeton UP.

“Our account of being an organism is called the Tripartite View of Organisms. At its core are the explicit claim [sic] that organisms are a type of living thing (or individual or agent), and the implicit claim that this kind is central to the biological sciences. Additionally, organisms are distinguished from other living agents by two properties: belonging to a certain sort of reproductive lineage, and having a certain type of autonomy. In summary, the Tripartite View holds that any organism is physically continuous and bounded and is:

“a. a living thing (individual, agent) during at least some of its existence
“b. that belongs to a reproductive lineage, some of whose members have the potential to possess an intergenerational life cycle, and
“c. which has minimal functional autonomy of the relevant kind.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). pp. 7-8.

“The fundamental, general feature of HPC [homeostatic property cluster] views of kinds concerns how an HPC kind term is defined by a cluster of properties rather than any one property….

“First, defining a kind term by a property cluster, rather than a single property, as HPC views do, acknowledges a complexity to the structure of entities that fall under the biological kind living thing…..

“Second, implying that no one of the properties in a given definitive cluster is strictly necessary for an individual to belong to the corresponding HPC kind recognizes the intrinsic heterogeneity of entities subsumed under living thing….

“Third, the HPC view doesn’t conceptualize a definitive cluster of properties as simply those properties that each kind member typically coinstantiates. Rather, coinstantiation of properties in the cluster is reliably underwritten by specific causal mechanisms and constraints. This gives definitive clusters their homeostatic character, and ensures the causal structure of the world plays a significant role in determining what is and what is not an HPC kind.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 8.

“So organisms are a kind of living thing. The next distinguishing feature of organisms according to the Tripartite View, something that helps separate organisms from other living things, is that they have life cycles that allow them to form reproductive lineages of a certain kind. Simply reproducing is not the distinctive feature here.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 9.

“On the Tripartite View, the third distinguishing feature of organisms is that they have a minimal level of functional autonomy of the relevant kind. This builds on the intuition that organisms are not simply living things or agents but have a life of their own: they are able to exercise some sort and degree of control over themselves and subsequently are relatively free with respect to relevant other things, including relevant other agents and environment.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 10.

“Thus, DST [developmental systems theory] involves broadening the conception of what the causal agents for organismic development are. But since there seems no barrier within DST to viewing developmental resources as forming part of an organism’s environment, it also returns us to a question about organisms that we raised earlier: where do individuals begin and end? Consider animal-built structures, such as nests and burrows. These often form a crucial part of the environment for the birth and development of offspring, and their particular properties often have a differential impact on the survival of those offspring. Such environmental resources seem no less (than genes) a crucial, causal part of what particular organisms need to develop, even if they are shared by multiple organisms.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 15.

“But how we should integrate sociality into our view of the evolution of biological individuals remains under-theorized. And however limited fossil evidence for individual structures and ecological niches may be, such evidence for the kinds and extent of sociality is significantly more sparse.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 17.

“Although the ‘evolution of sociality’ has been taken up by animal biologists and evolutionary anthropologists (where it is often viewed game-theoretically), this has served to reinforce a view of sociality that seems somewhat narrow, e.g., the view is not clearly applicable to structurally simpler organisms. Perhaps we need to take seriously the idea that sociality is not a relatively recent addition to multicellular life but a more sweeping feature of many if not all biological individuals.” Wilson, Robert A. & Matthew Barker. 2013. “The Biological Notion of Individual.” Revised edition. Stanford Encyclopedia of Philosophy. Zalta, Edward (ed). p. 17.

“But it is becoming clear that these accounts [of systems biology] need not resemble the kinds of explanation in physics and chemistry to which we are accustomed.

“Among the most obvious differences are: (1) the large number and dense interactivity of parts; (2) the hierarchical (and multi-scale) organization of biological systems; (3) the dependence of the identity of parts, and the interactions among them, on higher-order effects; and (4) the robustness and adaptability of biological structures.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 22.

“Indeed, both logically and historically, the notion of function with which I am concerned must precede the onset of natural selection, at least as that term is usually construed.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 23.

“In other words, reverting to another philosophical tradition, I use the term function in the sense of a simple feedback mechanism. Like a thermostat. As William Wimsatt puts it, ‘To say that an entity is functional is to say that its presence contributes to the self-regulation of some entity of which it is a part.’” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 24; reference: Wimsatt, William. 2002. “Functional organization, functional inference, and functional analogy.” In: R. Cummins, A. Ariew & M. Perlman (Eds). Functions: New Essays in the Philosophy of Psychology and Biology. pp. 174-221. Oxford UP.

“Indeed, if we think of reproduction as just one strategy for ensuring persistence … we can think of natural selection as a subset of this more general category of selection for persistence.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 24.

“An organism, in short, is ‘an organized natural product is one in which every part is reciprocally both end and means. In such a product nothing is in vain, without an end, or to be ascribed to a blind mechanism of nature.’” Kant, Immanuel. 1987. Critique of Judgment. Translated by: Pluhar, W. Indianapolis: Hackett Publishing. p. 558; subquote from Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 26.

“The chief difference between then and now, between Kant’s despair of ever being able to provide a mechanistic account of natural ends, and the optimism of our own time, came out of the development of mechanisms that promised a self-directed functioning, in the middle of the twentieth century…. not only a new machine, but also a new vision of a science of the inanimate: a science based on principles of feedback and circular causality, and aimed at the mechanical implementation of exactly the kind of purposive behavior that so worried Kant. I am referring to the birth of cybernetics, a science that would repudiate the very distinction between organism and machine on which Kant’s concept of self-organization was predicated.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. pp. 26-7.

“Turner is interested in ‘agents (or organs) of homeostasis’ and, referring to the famous physiologist most associated with homeostasis, Claude Bernard, he calls these agents Bernard machines. Bernard machines are devices for creating (and maintaining) a fixed milieu either inside the organism or immediately surrounding it; they are the mainstay of physiology, or, rather, they are embodiments of physiology.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 27; reference: Turner, S. 2007. The Tinkerer’s Accomplice: How Design Emerges from Life Itself. Harvard UP.

“In terms of my earlier discussion of function, a Bernard machine is exactly what is required to turn the rain-cloud-river cycle into a system with a function [by adding something like a thermostat to keep the rain matching the river flow or any other two steps in the cycle]; a Bernard machine is the mechanism that introduces function into such a system. Such devices are ubiquitous in biological systems, yet extremely complex from an evolutionary point of view.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 27.

“Turner answers the question as follows. The behavioral repertoire of the individual termite includes two actions: picking up grains of soil and gluing them down. Which action is performed depends on CO2 level, with a high probability of picking up the grain of soil when the level of CO2 is high concentration, and of gluing it down at low concentrations. In other words… each termite is equipped with a sensor that is coupled to its behavior…. The mound, one would have to say, has a function, namely, to maintain the atmosphere of the nest at comfortable levels…. Indeed, the net result is the construction and continual reconstruction of a mound that, at any given moment, operates as a well-designed wind tunnel adapted to the respiratory needs of the colony.” Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell. p. 29.

“But being a GAPDH [a protein, Glyceraldehyde-3-phosphate dehydrogenase], a molecule with that particular catalytic function, requires not merely a particular chemical structure, but an environment in which there is glyceraldehyde-3-phosphate to transform…. Chemistry, alone, cannot tell us that a particular protein is a GAPDH rather than one of the countless other functionally defined things it might have been. To be a GAPDH requires, in addition, an environment that includes the other elements that make the performance of its specific function possible.” Dupre, John. 2009. “It Is Not Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 32-47. Blackwell. p. 37.

“During its growth stage, a biofilm produces an extracellular polymeric substance (EPS) that performs a number of functions. A biofilm’s EPS provides a biofilm with structural integrity. It also traps nutrients from the environment and contains enzymes that break those nutrients down for digestion by a biofilm’s bacteria. EPSs even protect bacteria from threats, both predators and antibiotics, by providing a protective layer and by containing molecules that bind to antimicrobial agents that prevent them from attacking bacteria. Finally, EPSs serve as media for communication among bacteria through lateral gene transfer.” Ereshefsky, Marc & Makmiller Pedroso. 2015. “Rethinking evolutionary individuality.” PNAS. 112(33):10126-10132. p. 10126.

“Another indicator of evolutionary individuality is cooperation among the parts of an individual. Bacteria within biofilms frequently produce public goods. A public good is a cellular product that is costly to produce and enhances the fitness of other cells. Cheater bacteria within biofilms could receive the benefits of public goods without producing them. Cheating does frequently occur in biofilms; however, cheaters are often kept in check such that public good production is a common feature of biofilms….

“Sometimes cheaters do get an upper hand in a biofilm. Nevertheless, the production of public goods is a common feature of biofilms. Why might that be? Researchers cite a number of mechanisms within biofilms that reinforce cooperation. Some multispecies biofilms are spatially structured such that cooperative bacteria occur in dense clusters insulated from noncooperative mutants that arise from bacterial strains in other portions of a biofilm. Another mechanism that promotes cooperation in biofilms is the lateral gene transfer of mobile genetic elements that infect noncooperative bacteria and cause them to produce a public good. Some instances of quorum sensing and ecological disturbance are also thought to keep cheaters in check. Cooperation within biofilms–and the mechanisms that enforce it–occur over and over again. This is not to say that cheaters never win. Nor is it to say cooperation occurs in all biofilms or even all of the parts of a biofilm. Bacterial cooperation within a biofilm is often imperfect and patchy. Nevertheless, cooperation seems to be a reoccuring feature in some biofilms.” Ereshefsky, Marc & Makmiller Pedroso. 2015. “Rethinking evolutionary individuality.” PNAS. 112(33):10126-10132. p. 10127.

“Biofilms seem to achieve the outcomes of reproductive bottlenecks (genetic similarity and the transfer of novel mutations) by alternative means (ecological bottlenecks and lateral gene transfer).” Ereshefsky, Marc & Makmiller Pedroso. 2015. “Rethinking evolutionary individuality.” PNAS. 112(33):10126-10132. p. 10129.

“The existence of highly integrated multispecies biofilms and other consortia suggests that we need a more inclusive account of evolutionary individuality that allows individuals to have a variety of reproductive and trait transmission mechanisms. Furthermore, the existence of such multispecies consortia suggests that we need an account of individuality that is sufficiently open-ended to capture the contingent nature of individuality.” Ereshefsky, Marc & Makmiller Pedroso. 2015. “Rethinking evolutionary individuality.” PNAS. 112(33):10126-10132. p. 10130.

“During the second half of the twentieth century, two increasingly divergent approaches to ecological systems developed within ecology, which have gradually led to two distinct disciplines, community ecology and ecosystem ecology…. The focus in community ecology has traditionally been on species diversity: what exogenous and endogenous forces lead to more or less diverse communities? How do species interactions constrain the number of species that can coexist?… An ecosystem is the entire system of biotic and abiotic components that interact in some place. The ecosystem concept is broader than the community concept because it includes a wide range of biological, physical, and chemical processes that connect organisms and their environment….

“In a sense, community ecology provides a microscopic perspective on ecosystems because it analyses their parts, while ecosystem ecology provides a macroscopic perspective on the same systems because it studies them as a whole.” Loreau, Michel. 2010. “Linking biodiversity and ecosystems: towards a unifying ecological theory.” Philosophical Transactions of the Royal Society: B. 365:49-60. doi:10.1098/rstb.2009.0155. p. 49.

“Ecology has traditionally regarded, implicitly or explicitly, species diversity as an epiphenomenon driven by a combination of abiotic environmental factors (such as temperature, rainfall and soil fertility), ecosystem processes that are themselves determined by these abiotic factors (such as productivity, biomass and nutrient cycling) and biotic interactions within communities (such as competition and predation). This tenet is shared by community ecology and ecosystem ecology. Community ecology has been devoted historically to explaining patterns and processes of species coexistence and diversity. Ecosystem ecology has often ignored species diversity as some sort of ‘background noise’ irrelevant to ecosystem functioning…. But both have shared the basic assumption that species diversity is an epiphenomenon. The new biodiversity and ecosystem functioning research field has overthrown this central tenet by considering biodiversity–in particular species and genetic diversity–as a driver of ecosystem functioning.” Loreau, Michel. 2010. “Linking biodiversity and ecosystems: towards a unifying ecological theory.” Philosophical Transactions of the Royal Society: B. 365:49-60. doi:10.1098/rstb.2009.0155. p. 51.

“Two decisive features distinguish the new theoretical approaches to the diversity-stability relationship developed within the biodiversity and ecosystem functioning research agenda from earlier ones; first, these new approaches explicitly differentiate, and link, stability properties at the population level and at the aggregate community or ecosystem level, and second, they abandon the implicit assumptions that the environment is constant and that populations and ecosystems reach an equilibrium, to explicitly incorporate population dynamical responses to environmental fluctuations. They have led to two closely related hypotheses known as the ‘portfolio effect’ and the ‘insurance hypothesis,’ which predict a stabilizing effect of species diversity on aggregate ecosystem properties despite or, more exactly, through fluctuations of component species. The general mechanism that makes ecosystem properties less variable in more diverse communities is asynchrony of species’ responses to environmental fluctuations driven by niche differences between species. This asynchrony ensures that as one species decreases sharply in abundance, biomass or productivity, another species decreases less sharply, or even increases, thus compensating partly or wholly for the decrease of the first species. The more species there are and the more asynchronous their environmental responses, the larger the potential for stabilization of aggregate community or ecosystem properties. The realization of this potential, however, requires that population dynamics are not strongly destabilized by species interactions at high diversity….

“… the diversity-stability relationship is a complex, multifaceted one, which does not lend itself to sweeping statements.” Loreau, Michel. 2010. “Linking biodiversity and ecosystems: towards a unifying ecological theory.” Philosophical Transactions of the Royal Society: B. 365:49-60. doi:10.1098/rstb.2009.0155. pp. 53-4.

:The traditional slicing of ecology into autecology, population ecology, community ecology and ecosystem ecology has some value because different organizational levels obey partly different sets of constraints, and hence partly different laws. But it also has strong limitations because it tends to perpetuate arbitrary divisions and hamper the emergence of unifying perspectives.” Loreau, Michel. 2010. “Linking biodiversity and ecosystems: towards a unifying ecological theory.” Philosophical Transactions of the Royal Society: B. 365:49-60. doi:10.1098/rstb.2009.0155. p. 57.

“Although there has been some advance and evolution in the theoretical aspects of these principles, fewer empirical ecosystem studies have actually tested the MPP [maximum power principle] and, to a lesser extent, the MEPP [maximum entropy production principle].” Chapman, Eric, Daniel Childers & Joseph Vallino. 2016. “How the Second Law of Thermodynamics Has Informed Ecosystem Ecology through Its History.” Bioscience. 66(1):27-39. p. 28.

“During early succession and ecosystem development, when biomass is low, energy acquisition is used for net growth. During this period, the ecosystem operates under the MPP, because this objective function maximizes biomass accumulation rate; biomass increases exponentially (P:R>> 1 [P=production; R=respiration]). However, exponential growth cannot occur indefinitely, because either available energy or, more typically, elemental resources will eventually become limiting. As the ecosystem transitions into a mature, or climax, state (or pseudosteady state where P:R = 1), it follows the MEPP. Here, the ecosystem has organized either to consume all available energy (energy limited), or to consume as much energy as available resources allow (resource limited). In both cases, the energy consumed by the ecosystem is simply dissipated as heat by the actions of maintenance and predator-prey cycles…. Consequently, the MPP and MEPP may simply describe different phases in an ecosystems development.” Chapman, Eric, Daniel Childers & Joseph Vallino. 2016. “How the Second Law of Thermodynamics Has Informed Ecosystem Ecology through Its History.” Bioscience. 66(1):27-39. p. 35.

“Governing theories, such as the MEPP and MPP, are crucial for developing predictive models or theories, but they are not a panacea. Similarly, neither is the law of conservation of mass, but it is still a useful tool. Any proposed theory regarding ecosystem organization and function that contradicts mass conservation–or is at odds with the MEPP or MPP–is likelly to be wrong over sufficiently long time scales, but this simple litmus test is seldom applied.

“The second reason for the lack of acceptance of the MEPP or the MPP is the inherent propensity of ecosystem scientists–or all ecologists, for that matter–to focus on case studies. For instance, ecosystems, and associated specialists, are usually categorized by location–for example, tropical temperate, and polar–and are further subdivided into terrestrial or aquatic. But these ecosystems are all the same from the perspective of the MEPP and MPP, only the drivers and the temporary inhabitants differ.” Chapman, Eric, Daniel Childers & Joseph Vallino. 2016. “How the Second Law of Thermodynamics Has Informed Ecosystem Ecology through Its History.” Bioscience. 66(1):27-39. p. 37.

“Many prominent theories of macroevolution (evolution at or above the species level) share a focus on species interactions as a primary factor. The ecological theory of adaptive radiation describes how clades respond to ecological opportunity driven by a lack of competitive interactions with other species. The escape-and-radiate model, described in more detail below, supposes that diversification rates depend on trophic interactions. The Red Queen theory states that species constantly evolve in response to interacting species. Under theories of clade replacement, the extinction of one clade is coupled with the growth of another. In coevolutionary arms races, interacting species engage in constant adaptation to gain an advantage over one another. In the biotic interactions hypothesis, species interactions provide the impetus for novelty. Finally, the geographic mosaic theory postulates an ever-changing landscape of interactions that shape macroevolution.” Harmon, Luke J., Cecilia Andreazzi, Florence Debarre, Jonathan Drury, Emma Goldberg, Ayana Martins, Carlos Melian, Anita Narwani, Scott Nuismer, Matthew Pennell, Seth Rudman, Ole Seehausen, Daniele Silvestro, Marjorie Weber & Blake Matthews. 2019. “Detecting the macroevolutionary signal of species interactions.” Journal of Evolutionary Biology. 32:769-782. p. 770.

“Species interactions have long been thought to be critical in microevolution and macroevolution alike, but their actual impacts on evolution have remained unclear.” Harmon, Luke J. et al [see full list above]. 2019. “Detecting the macroevolutionary signal of species interactions.” Journal of Evolutionary Biology. 32:769-782. p. 777.

“Two appealing definitions of biological individuality have emerged in order to take into account ‘complex’ individuals: Wilson and Sober’s common fate definition, and Dupre and O’Malley’s homeostasis definition. Both focus in their own way on the functional integration of the parts into a whole.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. p. 384; references: Wilson, David S. & E. Sober 1989. “Reviving the superorganism.” J Theor Biol. 136:337-356; Dupre, John & M.A. O’Malley. 2009. “Varieties of living things: life at the intersection of lineage and metabolism.” Philosophy & Theory in Biology. doi: 10.3998/ptb.6959004.0001.003.

“In much of the symbiosis literature, symbiosis is defined as any association of individuals of different species that interact in a persistent fashion. This includes mutualism of course, but it also concerns sustained interactions even if one of the partners derives no apparent benefit from it (commensalism) or is demonstrably harmed by the interaction (parasitism). This understanding of symbiosis focuses on the persistence of the interaction, and is defined independently of the consequences of the interaction while it may be too inclusive, it remains empirically more useful, since most associations have shifting states of fitness costs of interaction.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. p. 385.

“One gets an additional interactor population (the fungus), an additional replicator population (fungus genes) [to help termites digest wood], but one can still track evolutionary changes. The real problem, however, is that it is not clear what would count as the replicator population for the community-level interactor. There is a community-level adaptation (digestion), but it is reducible neither to replicator A nor to replicator B populations alone. It exists only in the ecological interaction between termites and their fungus. To understand the digestive process present in this scenario, one must study the intricacies of fungus gardening within the mound on the part of the termites and how termites build wood combs and later consume the fungus-wood compost. Digestion is not solely fungus-based or termite-based. As such, to account for the adaptation that is digestion, the ecological and functional integration of two individuals is more telling than the coevolutionary history of symbiont partners.

“This is the general challenge of thinking about biological individuality and the evolution of communities. Community-level traits will have difficulty in general in matching any coherent replicator population because, while communities may have emergent adaptations (such as digestion), they do not have unified emergent genomes.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. pp. 386-7.

“The collections of symbionts that we may wish to treat as populations are actually meta-populations constituted of heterogeneous communities of vastly different types of individual organisms associated in complex and transient ways. Yet adaptations such as digestion emerge. For such systems, a functional or ecological approach is often more appropriate than a traditional population model.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. p. 388.

“Looking at ecosystems in an engineering way, by looking for functional subsystems and how they contribute to the overall persistence of the system, allows us to make sense of complex types of organization and their evolution.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. p. 388.

“If the efficacy of the functioning and the resulting capacity to persist is fine-tuned as a response to the resulting capacity to persist is fine-tuned as a response to pressures from the environment, as many ecologists have proposed occurs at the ecosystem level, then one seems to have adaptation by natural selection. This adaptation is in terms of increased persistence, not increased reproduction.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. p. 389.

“Many, if not most, definitions of biological individuality put a large burden on the idea of functional integration, implying that it is the systematic nature of these entities that is relevant. But criteria of shared fate or shared lineage history are less compelling in many cases of symbiosis where the symbionts are easily acquired, exchanged, and replaced.” Bouchard, Frederic. 2014. “Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction.” Biol Theory. 9:382-391. doi: 10.1007/s13752-014-0171-1. p. 389.

“An exciting recent development in systems biology of metabolism is the rise of methods to extend FBA [flux balance analysis] models from the genome scale to the ecosystem level. In addition to solving the resource allocation problem of metabolism for individual organisms in a given environment, these approaches take into account the fact that metabolites can be exchanged across species, giving rise to metabolically-driven ecological networks. These advances suggest that metabolism may be best understood as an ecosystem-level phenomenon…. The ecosystem-level nature of metabolism is another feature of present-day life whose roots likely date back to the early stages of life on our planet. For example, the chemical networks that gradually gave rise to reproducing protocells may have wandered for quite some time in a broader chemical space, effectively generating molecular ecosystems before the rise of spatially and chemically well-defined cellular structures.

“At an even larger scale, metabolism can be viewed as operating not just at the level of individual cells or ecosystems, but as a planetary phenomenon, in which cellular processes collectively affect (and are affected by) the flow of molecules at geological scales. The strong coupling between the metabolic processes of ecosystems and planetary-scale geochemistry suggest that biosphere-level metabolism should be viewed as one of the natural scales for the study of life’s history.” Goldford, Joshua & Daniel Segré. 2018. “Modern views of ancient metabolic networks.” Current Opinion in Systems Biology. 8:117-124. p. 118.

“Adding on to a large body of evidence on individual metabolic reactions being catalyzed by small molecules, recent experimental work has demonstrated that several key pathways found in modern day metabolic networks can be catalyzed non-enzymatically…. These experimental results support the hypothesis that the catalytic cores of some modern enzymes may represent evolved variants of simple geochemically available prebiotic catalysts like transition metals, iron-sulfur clusters or organic cofactors.” Goldford, Joshua & Daniel Segré. 2018. “Modern views of ancient metabolic networks.” Current Opinion in Systems Biology. 8:117-124. p. 119.

“As mentioned above, however, a major leap in the history of life must have involved the rise of a collectively autocatalytic chemical system. The feasibility of pre-enzymatic chemistry suggests a possible path for the rise of such collective autocatalysis: if the molecules produced by these reactions are themselves good catalysts, or if these reactions contribute to solubilize inorganic catalysts from rocks, there is a chance that a subset of reactions and molecules will effectively display a dynamic behavior that is equivalent to that of a single autocatalytic, exponentially growing entity.” Goldford, Joshua & Daniel Segré. 2018. “Modern views of ancient metabolic networks.” Current Opinion in Systems Biology. 8:117-124. p. 120.

“Experimentally, Whitesides and colleagues have constructed an autocatalytic chemical network based on simple, biologically relevant organic compounds. In particular, by using a continuous flow of nutrients into and out of their reaction vessel, they showed that simple mixtures of thiols and thioesters could display a wide range of dynamical properties, such as bistability, oscillations and autocatalysis. Notably, this work demonstrated that dynamical properties observed in biological networks can emerge from simple mixtures of prebiotically plausible chemicals held out of equilibrium.” Goldford, Joshua & Daniel Segré. 2018. “Modern views of ancient metabolic networks.” Current Opinion in Systems Biology. 8:117-124. p. 120; reference: Semenov, S.N., L.J. Kraft, A. Ainia, M. Zhao, M. Baghbanzadeh, V.E. Campbell, K. Kang, J.M. Fox & G.M Whitesides. 2016. “Autocatalytic bistable, oscillatory networks of biologically relevant organic reactions.” Nature. 537:656-660.

“However, autocatalytic networks have not been identified in non-enzymatic metabolic networks so far, and evidence for their existence during prebiotic evolution is lacking.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. p. 1.

“Of special interest for metabolic evolution are a class of mathematical objects called reflexively autocatalytic food-generated networks–RAFs–in which each reaction is catalysed by a molecule from within the network and all molecules can be produced from a set of food molecules by the network itself.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. p. 1.

“Modern cellular metabolism is enzyme-based but greater than 60% of enzyme mechanisms described to date involve one or more cofactors and 40% of all proteins crystallised have a bound metal relevant to their function.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. p. 2.

“The maxRAFs in the global prokaryotic O2-independent network were identified for different food sets,…. An inorganic food set containing H2O, H2, H+, CO2, CO, PO43-, SO42-, HCO3-, P2O74-, S, H2S, NH3, N2, all metals, FeS clusters and other metal clusters, a generalist acceptor, donor, and metal produced a minute maxRAF with eight reactions linking ammonia, carbon, and sulfide transformations. The addition of formate, methanol, acetate, and pyruvate, which are central metabolites with experimental evidence for synthesis from CO2 and metals, doubles the maxRAF size to 16 reactions. In principle, the addition of organic cofactors to the food set should generate larger maxRAFs. Sequential addition of the eight most frequent cofactors identified in the LUCA’s proteins to the metal-CO2 food set expanded the maxRAF from 16 to 914 reactions. The addition of all cofactors germane to the anaerobic network generates a maxRAF with 1335 reactions spanning 25% of the starting anaerobic network.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. pp. 2-3.

“Subsets of the global prokaryotic O2-independent network were obtained by parsing the genomes of the acetogen Moorella thermoacetica (Ace) and the methanogen Methanococcus maripaludis (Met). These were completed with reactions from corresponding manually curated genome-scale metabolic models, resulting in 1193 reactions for Ace and 920 for Met. Both the acetogen and the methanogen metabolic networks contain RAFs. When all organic cofactors are added to the food set, the maxRAFs contain 394 and 209 reactions for Ace and Met, respectively, spanning major KEGG [organic reaction database with ~11k known at time of publication] functional categories.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. pp. 3-4.

“The intersection of the Ace and Met maxRAFs should be more ancient than each of them individually. Three-quarters of the (smaller) Met maxRAF overlap with the (larger) Ace maxRAF in a connected network harbouring 172 reactions and 175 metabolites.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. p. 4.

“Crucial catalysts can be identified by removing them from the food set. NAD+ is strongly embedded in the RAF and its removal reduces the size of the maxRAF by approximately 50%.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. p. 5.

“Though Fe-S clusters are more ancient redox cofactors than NAD(P)H, they perform one-electron transfer reactions and have been replaced in evolution by NAD and other two-electron carriers. Fe-S clusters also heavily impact maxRAF sizes, together with pyridoxal-5-phosphate and divalent metals.

“Surprisingly, when we remove ATP from the food set of organic cofactors, this has no impact on the size of the maxRAF…. ATP is an essential intermediate in the maxRAF, but it is not required to kick-start it when other organics are present. This reflects the increasingly evident role of alternative energy currencies in primordial metabolism, such as acyl phosphates, thioesters, and reduced ferredoxin. Alternative energy currencies are particularly common in anaerobes.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. pp. 5, 6.

“Our analyses started with the enzymatic and spontaneous reactions charted in modern metabolism and used RAFs as a filter to uncover elements with self-organizational properties, to address the nature of processes in the earliest phases of evolution, before the origin of eukaryotes and before the appearance of oxygen. We found evidence for a role of autocatalytic networks at the onset of metabolism.” Xavier, Joana, Wim Hordijk, Stuart Kauffman, Mike Steel & William Martin. 2020. “Autocatalytic chemical networks at the origin of metabolism.” Proceedings of the Royal Society: B. 287:20192377. dx.doi.org/10.1098/rspb.2019.2377. p. 7.

“The ecological time frame might be defined as the time interval in which the extant species live under the same ecological conditions we know today. This has been called ecological time or real time, and has been defined as ranging from weeks to decades or, occasionally, centuries. It has been recognized that such time frame is often insufficient to fully resolve the ecological dynamics associated with succession, stability, biotic responses, biodiversity patterns, and so forth, underscoring the need for a historical or longer term view. Palaeoecology, defined as ‘the ecology of the past,’ is the discipline charged to provide this longer temporal scope.” Rull, Valenti. 2010. “Ecology and Palaeoecology: Two Approaches, One Objective.” The Open Ecology Journal. 3:1-5. p. 1.

“… while ecologists feel comfortable with the name of their discipline, a number of palaeoecologists do not. For this reason, some have coined the term neoecology, to refer to the ecological study of living ecosystems…. In this frame, ecology is implicitly considered a higher level discipline embracing both neoecology and palaeoecology.” Rull, Valenti. 2010. “Ecology and Palaeoecology: Two Approaches, One Objective.” The Open Ecology Journal. 3:1-5. p. 4.

“Homoeostatic Gaia [one version] implies resistance and resilience over long (Myr) time scales and at global spatial scales, compared with the much smaller spatiotemporal scaling of traditional ecology and evolution…. The issue of whether such an extrapolation of scale is justified is one of the most important and least resolved [sic: ‘issues’?] surrounding Gaia: although it seems that the diffuse nature of interactions between life and environment over large scales of space and time should make the global system less cohesive, the Earth system is more cohesive, in that it is essentially closed (unlike ecosystems) and subject to a single input flux (solar energy).” Free, Andrew & Nicholas Barton. 2007. “Do evolution and ecology need the Gaia hypothesis?” Trends in Ecology and Evolution. 22(11):611-19. p. 613.

“Lenton has separated life–environment feedback into two types: feedback on growth, in which traits selected for their individual fitness benefits have environmental side effects that affect the growth of those individuals and others; and feedback on selection, in which traits affect environmental variables which, in turn, directly affect the selective advantage of those traits. In both cases, the environmental effects are byproducts, not adaptations. We can add a third class, adaptive feedback, in which environmental feedback effects are selected for at the individual level (but might also control the environment at the system level).” Free, Andrew & Nicholas Barton. 2007. “Do evolution and ecology need the Gaia hypothesis?” Trends in Ecology and Evolution. 22(11):611-19. pp. 613-4; reference: Lenton, Tim. 1998. “Gaia and natural selection.” Nature. 394:439-447.

“If many issues raised by the Gaia hypothesis are also considered by conventional evolutionary and ecological science, do we need the hypothesis at all? Importantly, the hypothesis stimulates us to draw together these diverse lines of theory and experiment, appreciate their relatedness and ask whether they can be extended to the spatiotemporal scale of a closed system, the biosphere. Given current concerns about anthropogenic perturbation of the biosphere, all relevant scientific disciplines should contribute to predicting its response. These benefits would apply even if the Gaia hypothesis turns out to be unfalsifiable….” Free, Andrew & Nicholas Barton. 2007. “Do evolution and ecology need the Gaia hypothesis?” Trends in Ecology and Evolution. 22(11):611-19. p. 617.

“On Earth, tectonics and atmospheric photochemical processes continuously supply substrates and remove products, thereby creating geochemical cycles. These two geophysical processes allow elements and molecules to interact with each other and chemical bonds to form and break in a cyclical manner. Indeed, unless the creation of bonds forms a cycle, planetary chemistry ultimately will come to thermodynamic equilibrium….” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1034.

“Most of the H2 in Earth’s mantle escaped to space early in Earth’s history; consequently, the overwhelming majority of the abiotic geochemical reactions are based on acid/base chemistry, i.e., transfers of protons without electrons. The chemistry of life, however, is based on redox reactions, i.e., successive transfers of electrons and protons from a relatively limited set off chemical elements.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1034.

“On geological time scales, resupply of C, S, and P is dependent on tectonics, especially volcanism and rock weathering. Thus, biogeochemical cycles have evolved on a planetary scale to form a set of nested abiotically driven acid-base and biologically driven redox reactions that set lower limits on external energy required to sustain the cycles.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1034.

“Are the niches for all possible redox reactions occupied by microbial metabolism? Although some metabolic transformations, and the microbes that enable them, have been predicted to exist solely on the basis of thermodynamics, and only later were shown to actually occur, not all predicted pathways have been found.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1035.

“Due to physiological and biochemical convenience, elemental cycles generally have been studied in isolation; however, the cycles have coevolved and influence the outcomes of each other.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1035.

“The outcome of the coupled metabolic pathways is that on geological time scales, the biosphere can rapidly approach relatively self-sustaining element cycling on time scales of centuries to millennia. On longer time scales, perpetuation of life remains contingent on geological processes and the constant flux of solar energy.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1036.

“Oxygenic photosynthesis is the most complex energy transduction process in nature: More than 100 genes are involved in making several macromolecular complexes.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1036.

“The virtual explosion of genomic information has led to the hypothesis that there is limitless evolutionary diversity in nature. The vast majority of unexplored sequence space appears to encompass two categories of genes: a large and dynamic set of nonessential genes and pseudo-genes, under neutral or slightly negative selective pressure (which we call ‘carry-on genes’), and a set of positively selected environment-specific gene suites, tuned to very particular habitats and organisms (which we call ‘boutique genes’). In contrast, the evolution of most of the essential multimeric microbial machines (including the basic energy transduction processes, nitrogen metabolic processes, ribosomes, nucleic acid replication enzymes, and other multienzyme complexes) is highly constrained by intra- and internucleic acid, RNA-protein protein-protein, protein-lipid, and protein prosthetic group interactions, to the extent that even when the machines function sub-optimally, they are retained with very few changes.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1037.

“Dispersal of the core planetary gene set, whether by vertical or horizontal gene transfer, has allowed a wide variety of organisms to simultaneously, but temporarily, become guardians of metabolism. In that role, environmental selection on the microbial phenotype leads to evolution of the boutique genes that ultimately protect the metabolic pathway…. Hence, the same selective pressures enabling retention of fundamental redox processes have persisted throughout Earth’s history, sometimes globally, and at other times only in refugia, but able to emerge and exert ubiquitous selection pressure on ancillary genes. In essence, microbes can be viewed as vessels that ferry metabolic machines through strong environmental perturbations into vast stretches of relatively mundane geological landscapes. The individual taxonomic units evolve and go extinct, yet the core machines survive surprisingly unperturbed.” Falkowski, Paul G., Tom Fenchel & Edward F. Delong. 2008. “The Microbial Engines That Drive earth’s Biogeochemical Cycles.” Science. 23 May. 320:1034-38. p. 1038.

“Ecocentrism does indeed hold the Earth, including its ecosystems, places, processes, species, and individuals – including in turn, but far from only, humans – to be sacred, in effect, for the very good reason that the Earth gives rise to and sustains life.” Washington, Haydn. 2019. A Sense of Wonder Towards Nature: Healing the Planet through Belonging. Routledge. pp. xv-xvi; Foreword by Curry, Patrick.

“It is thus a positive development that the UN has now established a ‘Harmony with Nature’ programme (www.harmonywithnature.org) which states: The Harmony with Nature initiative speaks to the need to move away from a human-centered worldview – or ‘anthropocentrism’ – and establish a non-anthropocentric, or Earth-centered, relationship with the planet.’” Washington, Haydn. 2019. A Sense of Wonder Towards Nature: Healing the Planet through Belonging. Routledge. p. 83.

“For me it became clear in the 1950s that any approach to a philosophy of biology, essentially based on logic and mathematics rather than on the specifically unique concepts of biology, would be unsatisfactory.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 17.

“Biology could not be recognized as a science of the same rank as physics as long as most biologists accepted certain basic explanatory principles not supported by the laws of the physical sciences and eventually found to be invalid. The two major principles here involved are vitalism and a belief in cosmic teleology.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 22.

“… we find that biology actually consists of two rather different fields, mechanistic (functional) biology and historical biology. Functional biology deals with the physiology of all activities of living organisms…. These functional processes ultimately can be explained purely mechanistically by chemistry and physics….

“However, it [historical biology] is indispensable for the explanation of all aspects of the living world that involve the dimension of historical time – in other words, as we now know, all aspects dealing with evolution.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 24.

“I will now discuss four of these basic physicalist concepts for which it had to be demonstrated that they are not applicable to biology before it was realized how different biology is from the physical sciences.

“1. Essentialism (Typology)….

“2. Determinism ….

“3. Reductionism ….

“4. The absence of universal natural laws in biology….” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 26, 27, 28.

“Owing to the probabilistic nature of most generalizations in evolutionary biology, it is impossible to apply Popper’s method of falsification for theory testing because a particular case of a seeming refutation of a certain law may not be anything but an exception, as are common in biology.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 28.

“… biological systems are richly endowed with capacities such as reproduction, metabolism, replication, regulation, adaptedness, growth, and hierarchical organization. Nothing of the sort exists in the inanimate world.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 29.

“Evolutionary biology tries to find the answer to ‘why?’ questions. Experiments are usually inappropriate for obtaining answers to evolutionary questions. We cannot experiment about the extinction of the dinosaurs or the origin of mankind. With the experiment unavailable for research in historical biology, a remarkable new heuristic method has been introduced, that of historical narratives. Just as in much of theory formation, the scientist starts with a conjecture and thoroughly tests it for its validity, so in evolutionary biology the scientist constructs a historical narrative, which is then tested for its explanatory value.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 32.

“… questions that begin with ‘what?’ and ‘how?’ are sufficient for explanation in the physical sciences. However, since 1859 no explanation in the biological sciences has been complete until a third kind of question was asked and answered: ‘why?’” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 45.

“… function is sometimes used for physiological processes and sometimes for the biological role of a feature in the life cycle of the organism. ‘For example, the legs of a rabbit have the function of locomotion … but the biological role of this faculty may be to escape from a predator, to move toward a source of food, to move to a favorable habitat, [or] to move about in search of a mate.’… For this reason in my account I carefully avoid the word function when my concern is the biological role of a feature or process.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 48; subquote: Bock, W.J. & G. von Wahlert. 1969. “Adaptation and the form-function complex.” Evolution. 19:269-299.

“Accordingly, I distinguish five different processes or phenomena for which the word teleological has been used:

“(1) Teleomatic processes [automatic progression to end state as in the cooling of a heated piece of iron]
“(2) Teleonomic processes
“(3) Purposive behavior [as in animals such as jays who bury acorns and then return to get them]
“(4) Adapted features; and
“(5) Cosmic teleology.

“It is now realized that four of the five phenomena traditionally called teleological can be completely explained by science, while the fifth one, cosmic teleology, does not exist.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 49.

“… a teleonomic process or behavior is one that owes it goal-directedness to the influence of an evolved program. The term teleonomic thus implies goal direction of a process or activity. It deals strictly with ultimate causations….

“Truly teleonomic activities depend on the possession of a genetic program.

“All teleonomic behavior is characterized by two components. It is guided by ‘a program’ and it depends on the existence of some endpoint, goal, or terminus that is ‘foreseen’ in the program that regulates the behavior or process. This endpoint might be a structure (in development), a physiological function, the attainment of a geographic position (in migration), or a ‘consummatory act’ in behavior.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 51-2.

“However, after vitalism had become obsolete, a belief in strict reductionism was more and more confined to the physicalists, while most biologists adopted a holistic organicism. They accepted constructive analysis but rejected the more extreme forms of reductionism.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 69.

“‘What [reductionism] breeds is physics worship coupled with neglect of the ‘higher-level’ sciences.’” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 69; quoting Putnam, Hilary. 1973. “Reduction and the nature of psychology.” Cognition. 2:135.

“… the fundamental difference between analysis and reduction. Analysis is continued downward only as long as it yields useful new information and it does not claim that the ‘smallest parts’ give all the answers.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 70.

“As both Simpson and Lewontin have shown, the physicochemical approach is totally sterile in evolutionary biology. The historical aspects of biological organization are entirely out of reach of physicochemical reductionism.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 71; references: Simpson, G.G. 1974. “The concept of progress in organic evolution.” Social Research. pp. 28-51; Lewontin, R. 1969. “The bases of conflict in biological explanation.” J. Hist. Biol. 2:35-45.

“Analysis differs from reduction by not claiming that the components of a system, revealed by analysis, provide complete information on all the properties of a system, because analysis does not supply a full description of the interactions among the components of a system.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 71.

“The consistent failure of explanatory reductionism indicates that a different approach must be taken in biological analysis, based (A) on the insight that all biological systems are ordered systems, which owe much of their properties to this organization and not simply to the chemical-physical properties of the components; (B) on the insight that there is a system of levels of organization with the properties of the higher systems not necessarily reducible to (or explained by) those of the lower ones; (C) on the recognition that biological systems store historically acquired information, not accessible to a physicalist reductionist analysis; and (D) on the recognition of the frequency of the occurrence of emergence.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 73-4.

“One of the standard objections of the reductionists to emergentism is that nothing new is produced in a case of emergence. But this claim is only a half-truth. To be sure, no new substance is produced; a hammer consists of the same substance as its separated components, handle and head. But something new has nevertheless been produced, the interaction of handle and head. Neither its wooden handle by itself nor the hammer head can perform (with any efficiency) the functions of a hammer. When one puts the two together, the properties of a hammer ‘emerge.’ And this newly added interaction is the crucial property of every emerged system, from the molecular level up. Emergence originates through the new relations (interactions) of the previously unconnected components. Indeed, not to take the importance of such connections into consideration is one of the basic failures of reductionism.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 76.

“Even though living nature, from Buffon on, was increasingly important in the thinking of philosophers, it could not be properly organized until biology had become a recognized branch of science. And this happened not until the middle of the nineteenth century…. This revolution required more – and more drastic – modifications of the average person’s world view than had occurred in previous centuries. The reason why this is usually overlooked is that Darwin traditionally is considered simply an evolutionist. He was that undoubtedly; and it was clearly Darwin who established secular science….

“By replacing divine with secular science, Darwin profoundly revolutionized the thinking of the nineteenth century. But Darwin’s impact was not limited to evolution and the consequences of evolutionary thinking, including branching evolution (common descent) and humans’ position in the universe (descent from the primates); it also included a whole series of new ideologies. In part, they were refutations of time-honored concepts like teleology; in part they were the introduction of entirely new concepts, like biopopulation.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 84-5.

“The structural laws [i.e. physics] and the messages from the genetic program function simultaneously and in harmony, but genetic programs occur only in living organisms. They provide an absolute borderline between the inanimate and the living world.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 90.

“Let me now try to summarize Darwin’s contribution to the thinking of modern humans. He was responsible for the replacement of a world view based on Christian dogma by a strictly secular world view. Furthermore, his writings led to the rejection of several previously dominant world views such as essentialism, finalism, determinism, and the sufficiency of Newtonian laws for the explanation of evolution. He replaced these refuted concepts with a number of new ones of wide-reaching importance also outside of biology, such as biopopulation, natural selection, the importance of chance and contingency, and the explanatory importance of the time factor (historical narratives), and the importance of the social group for the origin of ethics.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 95.

“There is one particularly cogent reason why Darwinism cannot be a single homogeneous theory: Organic evolution consists of two essentially independent processes, transformation in time and diversification in (ecological and geographic) space.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 99.

“For Darwin himself these five theories [Mayr’s claim that Darwin consists in five separate theories] were evolution as such, common descent, gradualism, multiplication of species, and natural selection.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 99.

“None of Darwin’s theories was accepted as enthusiastically as common descent; it is probably correct to say that no other of Darwin’s theories had such enormous immediate explanatory powers. Everything that had seemed to be arbitrary or chaotic in natural history up to that point now began to make sense. The archetypes of Owen and of the comparative anatomists could now be explained as the heritage from a common ancestor. The entire Linnaean hierarchy suddenly became quite logical, because it was now apparent that each higher taxon consisted of the descendants of a still more remote ancestor.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 101.

“Darwin’s third theory was that evolutionary transformation always proceeds gradually and never in jumps.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 103.

“To find the solution to the problem of species diversification required an entirely new approach, and only the naturalists [those like Darwin who traveled the world to collect diverse but similar species] were in a position to find it… By adding the horizontal (geography) to the vertical dimension that had previously monopolized evolutionary thought, they all were able to discover geographically representative (allopatric) species or incipient species. But more than that, these naturalists found numerous allopatric populations that were in all conceivable intermediate stages of species formation.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 106.

“Darwin’s theory of natural selection was his most daring, and most novel, theory…. It replaced teleology in nature with an essentially mechanical explanation….

“Although I call the theory of natural selection Darwin’s fifth theory, it is actually, in turn, a small package of theories. This includes the theory of the perpetual existence of a reproductive surplus (superfecundity), the theory of the heritability of individual differences, the discreteness of the determinants of heredity, and several others.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 109.

“Neo-Darwinism is the designation for Weismann’s revised Darwinism (excluding any inheritance of acquired characters).” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 119.

“According to the more-or-less unified theory of Fisher and his colleagues, evolution was defined as a change in gene frequencies in populations, a change brought about through the gradual natural selection of small random mutations…. Unfortunately, this Fisherian synthesis of the late 1920s has been confused by many historians with a second synthesis involving biodiversity….

“Fisher, Wright, and Haldane were primarily interested in determining how a population evolves as the environment changes. This branch of evolutionary biology has been referred to as the study of anagenesis. The natuarlists, by contrast, were more interested in diversity and in determining how new species branch off from their parent species. This study of the origin of biodiversity is often referred to as cladogenesis. In other words, the mathematical population geneticists were concerned with the vertical or ‘time’ dimension of evolution (changes over time within a given population), whereas the naturalists were mostly concerned with the horizontal or geographic dimension of evolution (the production of new species at a given time)….

“Providing an explanation of how life proliferates into so many diverse forms at a given time – as opposed to just one form that continually changes over time – was the achievement of a second synthesis, initiated in 1937 by Dobzhansky’s work Genetics and the Origin of Species.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 121-2.

“Only one serious disagreement between the two camps [naturalists vs geneticists at time of synthesis] was left, relating to the object of selection. This, for the naturalists, as it had been for Darwin, was the individual, while for the geneticists it was the gene, in part for the sake of ease of computation.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 125.

“Actually, in spite of the synthesis, the definition of evolution (whether reductionist or holist) continued to be the major point of disagreement between the geneticists and the naturalists. For the naturalists, evolution is more than a change in gene frequencies; it is the acquisition and maintenance of a adaptedness and the origin of new biodiversity.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 125-6.

“According to one of these approaches [in how to understand ‘selection’ from agricultural breeders], those individuals are selected as breeding stock for the next generation that had special characteristics that represented the ideal of what the breeders aimed for in their selection. They would simply say that they would choose ‘the best individuals’ of their flocks as their breeding stock. It was this method that Darwin apparently had in mind when he used the word ‘select.’

“However, the breeders often used instead a different method to which they referred as ‘culling.’ In this method only the truly inferior individuals were eliminated and all the remaining individuals were used for breeding. This, of course, was not at all a ‘selection of the best.’ Nature uses the same two methods. In a harsh year as far as survival factors are concerned, only the best individuals survive, all others are eliminated. In a mild year only the worst are culled and most individuals survive.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 134-5.

“It has become clear since Darwin’s day that sexual selection is only one of a far wider realm of phenomena and that instead of sexual selection these activities are better referred to as ‘selection for reproductive success in direct competition with conspecifics.’ It includes also such phenomena as parent-offspring conflict, sibling rivalry, unequal parental investment, unequal rates of division in prokaryotes, and most of the phenomena studied by sociobiology.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 138-9.

“Evolution is not a change in gene frequencies, as is claimed so often, but a change of phenotypes, in particular the maintenance (or improvement) of adaptedness and the origin of diversity. Changes in gene frequency are a result of such evolution, not its cause. The claim of gene selection is a typical case of reduction beyond the level where analysis is useful.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 152.

“Is it [the problem of defining species] perhaps that different kinds of organisms actually do have different kinds of species? It turns out that this is definitely the case because what is designated as species in asexually reproducing organisms (agamospecies) is indeed something quite different from the species of sexually reproducing organisms.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 173.

“A species concept, as the word says, is the concept naturalists or systematists have of the role a species plays in nature. What kind of phenomenon do they have in mind, when use the word species?

“A species taxon is a population of organisms qualifying for recognition as a species taxon according to a particular species concept.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 174.

“… in many groups of animals and plants extremely similar and virtually indistinguishable cryptic species were discovered that, where coexisting in nature, did not interbreed with each other but maintained the integrity of their respective gene pools. Such cryptic or sibling species certainly invalidate a species concept based on degree of difference. They occur at lesser or greater frequency in almost all groups of organisms.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 176.

“Perhaps the greatest weakness of the typological species concept is that it fails to answer the Darwinian ‘why?’ question. It sheds no light on the reasons for the existence of discrete reproductively isolated species in nature. It tells us nothing about the biological significance of species.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 177.

“Members of different species, even when they coexist at the same locality, do not ordinarily interbreed with each other. They are separated by an invisible barrier into reproductive communities. Each reproductively isolated community is called a biological species. The concept that bases species recognition on reproduction is called the biological species concept (BSC).” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 177.

“An indiscriminate interbreeding of all individuals in nature would lead to an immediate breakdown of these harmonious genotypes. The study of hybrids, with their reduced viability and fertility, has demonstrated this abundantly. Consequently, there is a high selective premium on the acquisition of devices, now called isolating mechanisms, that would favor breeding with conspecific individuals and that would inhibit mating with nonconspecific individuals. This conclusion provides the true meaning of species. The species enables the protection of harmonious, well-integrated genotypes. It is this insight on which the BSC is based.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. pp. 178-9.

“Most of the criticisms of the BSC are directed against decisions made in applying the BSC in the delimitation of species taxa.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 182.

“To make the invalidity of the class nature of species more visible Ghiselin and Hull proposed considering species to be individuals. This called attention to some of the non-class properties of species such as their spatiotemporal localization, their boundedness, their internal cohesion, and their capacity for change (evolution).” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 187; references: Ghiselin, M.T. 1974. “A radical solution to the species problem.” Systematic Zoology. 23:536-544; Hull, D. 1976. “Are species really individuals?” Systematic Zoology. 25:174-191.

“Species in asexually (uniparentally) reproducing organisms are rather arbitrarily distinguished on the basis of phenotypic characters. Lateral gene transfer makes the delimitation of many bacterial agamospecies against each other a rather arbitrary matter. These agamospecies have little in common with the traditional species of the eukaryotes.” Mayr, Ernst. 2004. What Makes Biology Unique. Cambridge UP. p. 190.

“Tectonic processes can therefore exert a significant control on Earth surface redox and climate through their involvement in global nutrient cycling and primary productivity. These ‘biogeodynamic’ controls fall under two categories: (1) a direct control via subduction and volcanism (e.g. for CO2 and N2); or (2) an indirect control via burial, uplift and erosion (e.g. for phosphorus and some bioactive trace elements).” Zerkle, Aubrey. 2018. “Biogeodynamics: bridging the gap between surface and deep Earth processes.” Philosophical Transactions of the Royal Society: A. 376: 20170401. dx.doi.org/10.1098/rsta.2017.0401. p. 2.

“Sediments subducted into the mantle are highly influenced by biological activity, and their composition and abundance will vary following the evolution of life and biogeochemical cycles over Earth history. Similarly, the local environment of the mantle wedge can directly control the speciation and volatility of elements that are subducted within these sediments, with critical consequences for their storage or release from the mantle into the atmosphere.” Zerkle, Aubrey. 2018. “Biogeodynamics: bridging the gap between surface and deep Earth processes.” Philosophical Transactions of the Royal Society: A. 376: 20170401. dx.doi.org/10.1098/rsta.2017.0401. p. 7.

“The interest of the concept of self-maintenance is that it relates function to the self-maintaining system by interpreting it as a specific causal effect of a component or trait which contributes to the maintenance of the system and, consequently, of the component itself in an organizationally closed way. Then, in this context appears a basic idea of functionality understood as the contribution of a component of the self-maintenance of the system.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. p. 3.

“Specifically, the flame makes a crucial contribution to maintaining the microscopic chemical reactions by keeping the temperature above the combustion threshold, vaporizing wax, and inducing convection (which pulls in oxygen and removes combustion products)…. In particular, the emerging configuration (i.e., the flame) constrains the surroundings (temperature, wax, oxygen), by turning them into appropriate boundary conditions required for its own maintenance. … the candle flame is a simple SM [self-maintaining] system, whose maintenance depends on the work of a single constraint acting on its own boundary conditions.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. p. 4.

“[According to Fox Keller] … for a concept of function that preceded natural selection, what is needed is … the existence of a property that contributes to the persistence of the system to which that property belongs, which will be enough to trigger a different (simpler) selection process for stability and persistence. In other words, the application of feedback mechanisms, which result in the generation of stabilities in a system, is enough for the operation of simpler evolutionary competitive dynamics that will result in different degrees of maintenance to those stabilities.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. p. 5; reference: Keller, Evelyn Fox. 2009. “It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics.” Contemporary Debates in Philosophy of Biology. Ayala, Francisco & Robert Arp (eds). pp. 19-31. Blackwell.

“Considering the low levels of membrane phospholipids in the early stages of prebiotic evolution, they [Budin & Szostak] inquire on the selective advantage that could have driven the evolution from self-assembled simple single-chain lipids membranes to phospholipid membranes….

“What is important concerning the quest for minimal FD [functional differentiation], is that they suggest that the resulting decrease of membrane permeability–due to the increase in membrane phospholipid content during the passage from self-assembling to self-produced membranes–would impose the cascading of new selective pressures on early protocells, allowing the internal evolution of a metabolic and transport machinery that would overcome the reduced permeability, protocells could have started to evolve membrane transporters along with proto-metabolic networks for synthesizing their own building blocks, as well as exploring new environmental niches compatible with compounds that were otherwise rapidly decaying in fatty acid membranes. They concluded that at this point of transition, from highly permeable vesicles to less permeable and more stable protocells, a primitive type of selection begins to operate accompanied by a parallel evolution of the functional domain of the protocells.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. p. 7; reference: Budin, L. & J.W. Szostak. 2011. “Physical effects underlying the transition from primitive to modern cell membranes.” PNAS. 108(13):5249-5254.

“Considering the gradual alteration in the degree of the membrane’s permeability, and that the respective competitive-evolutionary selective dynamics mirror the emergence of internal metabolic and transport machinery, there should had [sic] been a point where the underlying proto-cellular organization would had [sic] started to produce the main phospholipid components of its membrane. What should be noted now is that since the transition was gradual, the primitive operation of the competitive-evolutionary selective dynamics would had corresponded to small differences in phospholipid content. Accordingly, the beginning of the internal production of the phospholipid parts of the boundary in protocells is a case where internally generated structural complexity begins to get related to the dynamics of its production. This point is reached in a developing protocell only when its membrane permeability starts to decrease and a proto-metabolic SM [self-maintaining] network begins to be internally formed and sets about to operate, thus producing the main phospholipid components of the membrane. In the evolutionary transition from a self-assembled vesicle to a self-maintaining protocell, certain structural components and related processes (the membrane and the self-maintaining chemical proto-metabolic network) begin to play the role of parts in a whole (the self-maintaining organization of the protocell)….

“Accordingly, the resulting increase in membrane phospholipid content is a kind of ‘control’ of the boundary conditions, which in turn increases the internal synthesis of phospholipids residing in the membrane.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. pp. 7-8.

“In a more formal description, we consider a SM organization as constituted by a set of structures (C1, …, Cn) operating as constraints. Since in this context each constraint is not able to achieve self-maintenance on its own, the persistence of a constraint depends on the process it harnesses, and hence, there should be a form of mutual dependence between the set of constraints operating in the organization…. As such, each Ci (as well as any group of constraints) contributes to the maintenance of the web of the rest of the constraints which, in turn, maintains in a recursive way (at least some of) the boundary conditions necessary for the re-appearance and/or maintenance of Ci. We will call this form of SM organization a closure of constraints because it is maintained due to the action of these constraints and, in turn, these very constraints are recursively re-produced and/or maintained by the system. Since the constrained processes generated and maintained in the system make a distinguishable contribution to its maintenance, they become candidates for differentiated functional ascriptions.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. p. 10.

“Macromolecular structures tend to be highly vulnerable to disruption by impinging signals and are constantly in need to replenishing their dissipating energy and order as their structural bonds have energies measured in electron volts, even fractions. Although some relatively complex structures could be maintained due to spontaneous processes of self-assembly compensating their decay, most of them (as we see in present day cells) can only be maintained through operations of repair and reproduction. Hence, though initially relatively complex structures could be formed in different environments, driven by geological or other types of abiotic processes, an accumulative production of complex structures leading to the appearance of interesting macromolecular structures is not likely to occur outside the frame of SM systems. The reason is that within SM systems these increasingly complex structures could be recruited to perform functional activities and, therefore, by entering in a SM organization of mutually dependent constraints, they ensure their maintenance. In other words, the formation of new and more complex structures can be ensured if they become functional parts within SM organizations. Thus, although a large part of biological organization depends on complex structures formed by self-assembly processes that do not involve energy dissipation (thermodynamic equilibrium), the variety of functional processes of the cell results from a combination of complex self-assembly and self-organizing processes.” Arnellos, Argyris & Alvaro Moreno. 2012. “How functional differentiation originated in prebiotic evolution.” Ludus Vitalis. XX(37):1-23. p. 16.

“To address this need [access to best estimates of key biological values], BioNumbers, the database of key numbers in molecular and cell biology, was constructed as a Wikipedia-like community effort (www.BioNumbers.org).” Phillips, Rob & Ron Milo. 2009. “A feeling for the numbers in biology.” PNAS. 106(51):21465-21471. p. 21466.

“The idea of medium number and failed prediction was developed by Gerald Weinberg, originally in 1975. The notion cleaves systems into three categories. Two are predictable, and occur in the more successful disciplines. The third is medium number system and they are intrinsically not predictable. Medium number system specifications do not yield even to experimentation, because the results are different every time.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 3-4; reference: Weinberg, Gerald. 1975. A Introduction to General Systems Thinking. NY: Wiley.

“Large and small number systems are predictable, medium number systems are not. Low randomness means good behavior, like planets. High randomness gives reliable statistical values. Medium number systems are statistically unreliable.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 4.

“To understand the nature of prediction it is useful to follow Ken Boulding, who said all predictions are that nothing happens. What did not happen in the past will generally continue not to happen in the future.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 9.

“‘Essentially, all models are wrong, but some are useful.’ If the things that are posited in a question are unstable over the time span implied by the question, then the question invokes a medium number system.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 13; subquote: Box, George & N.R. Draper. 1987. Empirical Model Building and Response Surfaces. NY: John Wiley & Sons. p. 424.

“Engineers try to create something open in a closed system. Meanwhile scientists try to create something closed in an open system. The ‘open’ that is sought by engineers is a process that captures creative and elegant solutions in reaching the prescribed goal. The ‘closed’ that is sought by scientist is the internally consistent model, which is more closed because distracting alternatives are pruned away, leaving only the closed intellectual structure in an unambiguous model that leaves few alternatives.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 18.

“Unable to machine parts with sufficient precision, workers made each part for each gun and then adjusted relative to the other parts on that particular weapon; a blow with a hammer here, a bit of filing there…. Before the industrial age, making guns was a medium number problem that was solved by something like calibration. So how did they manage to generalize in what was a medium number world of gunsmithing? Medium number failure comes from parts (particles) being so individual that the particularity of some part reliably causes failure. The economies of scale of industrial production were not possible until there was machine tooling to a thousandth of an inch…. Once you could say ‘when you have seen one Smith and Wesson barrel you have seen them all,’ an individual barrel would not create failure in a medium number emergence. In this way medium number gunsmithing was translated into a large number process…. So there are various ways to escape the failure of medium number to predict. One is to change the question. Another is to calibrate. Yet again one could impose tight constraints, as in the barrels of Smith and Wesson all machined to be functionally identical.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 25.

“In a sense post-normality [or post-normal science] is the context for using hierarchy theory. In their terms, difficulties cited above [socio-ecological problems] arise ever more often, particularly when science attempts to solve practical problems. Not all applied science is medium number, but applied science is often the place where medium number comes into play. In those practical situations the stakes are high, time is short, values are in conflict, and variability is large and intrinsic….

“Ravetz accepts that science as an institution in the service of society has great potential to be corrupt, taking more money to do more of the same research. He says the system is simply broken. What to do? After procrastination has run its course, in the end pressing resource issues will become so urgent that remedial action will be taken…. Ravetz suggests that the only thing to be done [as post-normal science] ahead of an actual good faith effort at remedy is to clear the decks ready for the crisis…. With Ravetz’s protocol, when political players are forced to enact a remedy because of scarcity, the path of the overdue correction is at least cleared of debris. Then there is a shot at not going over the cliff.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 26-7; reference: Ravetz, J. 2007. “When communication fails.” In: Interfaces between Science and Society. Pereira, A.G., S. Guedes Vaz & S. Tognetti (eds). pp. 16-34. Sheffield, UK: Greenleaf.

“The deterministic approaches use exact results of running simulations of some sort. They are hampered by their strong simplifying assumptions, which keep the meaning local or time specific. Meanwhile the stochastic, statistical approaches are less and less justified in their use of averages.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 27.

“Relational biology stands against reductionism in that it addresses what is lost when biological systems are taken apart. Louie starts his book defining relational biology as that which is left in biology after all the materiality of life has been removed. Hierarchy theory addresses organization. In this book we do consider material organisms and the like, but in the end the nub of it is organization, which is not in itself material.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 30; reference: Louie, A.H. 2009. More than Life Itself: A Synthetic Continuation in Relational Biology (Categories). Heusenstamm, Germany: Ontos Verlag.

“The error in assuming increased size increases complexity is to imagine that complexity is a material issue as opposed to a matter of how the system is observed.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 36.

“The conduct of normal science includes a narrowing of discourse, so the universe is highly contrived. In a narrow discourse we can be more confident about the reliability of what emerges with that exact protocol but will be less confident as to general application.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 37.

“In this epistemological discussion we wish to deepen the definition of holon so as to emphasize that it is not the parts themselves that become blended, but it is rather information from the parts that is integrated. If a holon is defined only as an integration of information from the parts, then clearly what is included and excluded may be freely chosen by the observer. We suspect that, in part, it is Koestler’s failure to exclude explicitly ontological reality from his definitions of holons that has slowed the acceptance of his hierarchical approach. We feel he is mistaken to allow ontological inferences to arise.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 45; reference: Koestler, Arthur. 1967. The Ghost in the Machine. NY: Macmillan.

“… we can quote Levins and Lewontin in their writing proposing dialectical materialism as a philosophy for biology. In a negation of alternative views they say

“‘Idealism and reductionism in ecology share a common fault: they see ‘true causes’ as arising at one level only with other levels having only epistemological but not ontological validity.’

“We share their view that reification of just one level alone is misguided. In fact we generally mistrust reification altogether. A difference between their approach and ours is that they seem prepared to give ontological validity to multiple levels while we avoid this issue.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 45-6; subquote: Levins, R. & R. Lewontin. 1980. “Dialectics and reductionism in ecology.” Synthese. 43:47-78.

“Emergence is not simply an explosion driven by a steep gradient that drives positive feedbacks. It arises when those positive feedbacks encounter some limit, perhaps in the form recognizable as a negative feedback.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 48.

“Inertial memory keeps a whirlpool turning in the same direction….

“Einstein viewed it as most remarkable that mass in gravity is the same as mass in acceleration. The one is an expression of rate, and so is rate-dependent. The other is static, and so is rate independent. Thermodynamics is rate-dependent. Efficiency is a matter of some preferred state. Preferences and states are rate-independent. Physical systems work without preferences but do have rate-dependent explanations as in the memory of the whirlpool with regard to direction.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 53.

“True, it takes thermodynamics to make and read DNA, but the coding itself is not thermodynamic. Codes are rate-independent. So the coding is inside the organism or whatever is the holon, but the coding is separate from the thermodynamics. Codes invoke plans. Plans constrain the thermodynamics by imposing constraints. Plans change as the holon becomes something else, such as an adult derived from a child.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 54.

“Becoming is driven by the story told by the holon. Note that a role comes from the outside. The US president has a role to play, imposed by the US presidency.

“If the holon is political and social, the US presidency has a history, which is updated by public reaction to the action of the most recent incumbent. So the dual nature of the holon is at the core of its functioning. It communicates to its world. That changes the holon’s context, which then steers the way that the role of the holon is played out.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 54-5.

“Changes in the scale of thermodynamics force changes in scaling effects because the larger spaces influence flux. While information can change with the application of a filter, change in information is not forced by shifts in scale as it is in thermodynamics.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 55.

“After Noble’s recent work the central dogma and neo-Darwinism are now in tatters, but as a paradigm change the Darwin Police will not notice the problem. The old guard in a paradigm change will only complain that the old important questions are not being asked. The old important questions do not matter anymore.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 56; reference: Noble, D. 2013. “Physiology is rocking the foundations of evolutionary biology.” Exp Physiol. 98:1235-43.

“A nerve fiber fires through disorder not ordering. The constraints on the potassium and sodium are relaxed as membranes become permeable, and the ions simply move to a more likely position….

“Hierarchies can be profitably viewed as systems of constraint. Any holon higher in the hierarchy exerts some constraint on all lower holons with which it communicates.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 60.

“A holon’s environment can be defined as being made up of all things with slower behavior with which it interacts. The holon itself can be seen as part of the environment of all faster behaving holons with which it interacts.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 61.

“We define sister holons as having no asymmetric effect on each other. Holons may be sisters in one discourse while failing to meet the criteria for sorority in another discourse. Therefore constraint is seen as relative to defined information exchanges between holons. There is no direct constraint between sister holons at the same level in the hierarchy because there is no asymmetry in the exchange.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 61.

“In summary, entities (holons) in a hierarchy may be viewed as the interface between the parts and the rest of the universe. On its journey to the outside, signal from the parts is integrated through the whole (holon). The same applies to signals reaching the parts from the rest of the universe. The holon itself is the surface between the parts and the whole. Stan Salthe refers to the triadic aspects of holons: the level of the holon itself; the level of the parts; and the level of the holon seen from the environment….

“The holon itself is simply the surface around its parts.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 64; reference: Salthe, Stan. 1985. Evolving Hierarchical Systems: Their Structure and Representation. Columbia UP.

“The order in hierarchy is often fully apparent, but unlike more restrictive ordering systems, such as seriality, hierarchical order is more emergent and less imposed.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 65.

“A scale is the period of time or space over which signals are integrated or smoothed to give message.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 73.

“Patten and Auble also split up the enviornment as that which transmits inputs to the holon as opposed to that which receives the signal from the holon…. Patten and Auble show how network theory carefully steps upscale, while hierarchy theory reaches farther over greater differences in scale and type. Network and hierarchy theory are twins.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 73; reference: Patten, B.C. & G.T. Auble. 1980. “Systems approach to the concept of niche.” Synthese. 43:155-181.

“As the soldier makes his report to his platoon leader, information begins its return passage up the hierarchy. This time, instead of a chain of trigger reactions to ‘do this,’ the information passes up through a series of successively coarser filters, becoming a broader account of the enemy position until the general receives the intelligence that he requested. While the trigger-filter duality is a helpful way to emphasize the asymmetry in hierarchical control, it also has the unfortunate property of masking the essential similarity of filter and trigger.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 79.

“He [William Wimsatt] notes that a checkerboard of environmental patches of ten meters on a side, varying between patches discretely from 0̊C to 40̊C, would kill a Drosophila by either freezing or overheating but would not even activate thermoregulatory systems in a cow or human walking through such an environment.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 82; reference: Wimsatt, William. 1980. “Randomness and perceived randomness in evolutionary biology.” Synthese. 43:287-329.

“Information may pass between two holons without alteration only if they both use the same filters–that is, only if they work at the same scale (like movie camera and projector).” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 83.

“Usually there are three scales in any observation: the scale of the transmitting holon, the scale of the receiving holon, and the scale assumed by the observing scientist. The first two scales determine the structure of the models. The third (human) scale will be different from the scale of either of the observed holons.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 84.

“Both scientist and artist are conscious of the human scale, but the artist celebrates it while the scientist tries to eliminate its effect. Scientists make every effort to measure the holon interaction at the scales of the holons themselves as directly as possible. They try to avoid distortions of human perception; the scientist tries to look at what is modeled the way it looks at itself and exists in itself.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 85.

“If scientists are to observe their subjects completely and accurately, they must observe at close proximity with the same scale as the observed holon. The problem then becomes one of intrusion. Since the identity of a holon is determined by its scale, when they apply an identical scale at close quarters, the scientists become part of the phenomenon. R.D. Laing in Politics of Experience, an early postmodern work in psychiatry, notes that psychiatrists cannot observe the patient; they can only observe the patient being observed by the doctor, and that is different.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 87.

“In an ecosystem view, animals simply melt into pathways.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 102.

“Evolution does not apply to organisms seen in an ecosystem, because the organizing principle in ecosystems is mass balance and the first law of thermodynamics. As a rule some other species can often be substituted without affecting ecosystem function.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 102.

“The bookkeeping in evolution is of animals largely as individual units that are vessels for genetic material. The bookkeeping in ecosystems is not of animals as units, but as crosswalks through which matter and energy flow. Communities are held together by processes that surround evolution. Community and ecosystem are types of biological entity, not entities that are distinguished on scale.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 102.

“An example of a non-nested hierarchy might be a food chain or a pecking order.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 105.

“The nested hierarchical model is the one which generally facilitates a reductionist model. Holistic science, on the other hand, can always operate perfectly well with the non-nested condition.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 107.

“‘The basic distinction between laws and rules can be made by these criteria: laws are a) inexorable, b) incorporeal, and c) universal; rules are a) arbitrary, b) structure-dependent, c) local. In other words, we can never alter or evade laws of nature; we can always evade and change rules. Laws of nature do not need embodiments of structures to execute them; rules must have a real physical structure or constraint if they are to be executed.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 109; quotation of: Pattee, H.H. 1978. “The complementarity principle in biological and social structures.” J. Soc. Biol. Structures. 1:191-200.

“In a similar use of dual modes of description, Southwood factors pattern from process. ‘Thus the whole concept of evolution may be seen to have two components: the patterns (of taxonomy, classification and variation, and of biogeography) and the mechanism. Darwin’s theory.’ Southwood’s taxonomic patterns are rate-independent and linguistic. His mechanism, Darwin’s theory, is rate-dependent.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 111; reference/subquote: Southwood, T.R.E. 1980. “Ecology–A mixture of pattern and probabilism.” Synthese. 43:111-22.

“Any nonlinear system can be linearized by narrowing the discourse. Curved lines on graphs can be made straight by only looking at a short enough segment. The close-to-serial patterns in mechanisms come from narrowing the scope to get rid of nonlinearity. Removing the shoulder allows the effects of the bicep on the arm to appear as a linear structure, a lever…. That means that mechanism is a linear approximation.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 115-6.

“As a moving fluid encounters an obstruction it must take a track that bends around the obstacle. The bent track must therefore go further than that part of the fluid that passes straight and unimpeded to either side of the obstruction. Since all tracks meet on the far side of the obstruction, the longer track must go faster to catch up, and so bending translates as moving faster. There is therefore sheering stress in the fluid as that part going the long way round cannot quite keep up with the linear flow of adjacent fluid. That sheering stress causes wrinkles in the fluid. Increase the speed of the flow and the wrinkles become circulating gyres characteristic of turbulent systems. The turbulent gyres dissipate the stress, passing it down to smaller gyres that hang off the big ones…. If turbulence is started a second time under what are apparently identical conditions, the pattern of turbulence will turn out differently….

“Even so there are regularities in the gyres. They are always evenly spaced and counter rotational to their nearest neighbor. To explain this regular and predictable pattern we need a different device that cascades upscale not down. As the turbulence starts with many wrinkles in the fluid, those that are close together will share the shearing stress in the vicinity. With sharing of resource the wrinkles get smaller not bigger and eventually disappear. That shared stress then becomes available to more distant but still adjacent wrinkles. With that extra stress, those wrinkles get bigger and start to form gyres. The regularity of the gyres is a pattern formed by competition for sheering stress. Competition usually leads to even separation in space as closer structures are removed. Gyres that are con-rotational rub each other up the wrong way. That friction causes the gyres to slow and disappear. By contrast counter rotational gyres merely kiss each other, and can persist next to their neighbor….

“While removal of stress goes downscale, the emergence of larger gyres expresses a relationship that moves upscale.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 122-3.

“At a level of organization higher than the individual instructions are governors that regulate the rate of the development rather than the course of development…. For the development of the hierarchy that is an organism, the governors are often manifested as growth hormones. A changed instruction from a governor is likely to produce dramatic departures in form but without intrusion into the orderly process of local step–by-step development. Thus change in a large number of characters is achieved without the disorder produced by a change within the developmental chain.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 133.

“Pattee argues a similar case, but more generally, he points out that evolution is likely to produce increasing elaboration in developmental instructions, but that organized modification, which is on balance beneficial, becomes more difficult as its complications accumulate. He uses the compelling image of a computer programmer modifying code in a long algorithm. At first, modifications are simply made and their utility is clear. There is a natural selection of lines of code. But soon, problems begin to arise through secondary effects of the modifications, and improvement is made at a price…. The same argument is made by Tainter where he identifies diminishing returns on problem solving in societies. An example is the greater cost of higher levels of education over primary and elementary school. Tainter’s worrying message is that the later stages of societal change lead inexorably to collapse.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 134; references: Pattee, H.H. 1972. “The evolution of self-simplifying systems.” In: The Relevance of General Systems Theory. Lazlo, E. (ed.) pp. 31-42. NY: Braziller; Tainter, J.A. 1988. The Collapse of Complex Societies. Cambridge UP.

“Essences [core identity of biological category that is assumed to be independent of observer] are like roles, they are the bounded infinities like we find in chaos theory. Roles limit what applies, but there is an infinite number of ways to fulfill a role. Many categories in biology can be seen as being bounded infinities. Consider for instance elm trees. No two elm trees have ever been exactly the same, so there is an infinity of elms past, present, and future.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 147.

“The rate independence of coded information allows evolution to work with a ratchet. It encodes history, giving it a larger influence in a longer future.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 149.

“Evolution is tricky in that denies biology a time zero [the usual assumption in physics].” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 153.

“Prudent exploitation of an abundant resource will always lose in competition. If the resource is high quality than profligate exploitation of high quality is the best plan. But the quality of the resource declines over time. There are high gain termites that live in high quality wood and eat it. They literally eat themselves out of house and home. At that point high gain termites have to move to a new chunk of good wood. In contrast to eating the good wood in which they live there is an alternative: increasing efficiency of processing allows for a move to low quality wood resources. This move leads to selective advantage in gathering dead wood fragments and bringing them to the termite nest. These are classic low gainers; the twigs and fragments are only 40% as good as a chunk of good wood in which the high gain termites live. But critically there is so much more total resource in dead twigs and fragments of wood.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 159-160.

“However, for some questions, it is of less general utility than the following stronger statement. Those individuals whose form and function best anticipate the new environment are those who are stable enough to pre-empt the material otherwise to be used for construction of alternative forms; in reproductive forms in biology, it is those who reach a breeding state…. This depends on the critical difference between thermodynamic flux and coded particularity. The kicker is that only coded information can pass unchanged between levels….

“To the extent it is valid, chance focuses on the dynamics of the evolutionary process; our anticipation-oriented view draws attention to the rate-independent significance of the evolutionary end product. A limitation of the perspective that emphasizes chance rather than anticipation is that it does not take the end products of the evolutionary intensification at face value.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 162-3.

“With very short time constants the holon comes to live functionally in such a local time/space that the constraints of the larger environment are never encountered. A holon scaled very locally reaches such a small scale that the constraining environment passes very little information of any sort, constraining or otherwise. It seems to be this second strategy that allowed incipient life to evolve the distinctive characters that distinguish the contemporary biosphere from its physical environment. By developing biochemistry, life started to move so fast that the organic chemistry environment is outmaneuvered and falls away as only a part of the environment.

“The particular characters that allowed this change in scale were enzymes. Enzymes do not change the chemical reaction they address; they merely increase the reaction rate….. The emergent properties of life come not from new organic reactions but rather from the consequences of new rates for chemical reactions. Thus the qualitative differences in the chemistry of life are attributable not to new reactions per se but to a new scale for these reactions….

“By increasing the reactivity of living systems, enzymes functionally isolate the system from its environment.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 165-6.

“In a sense it [a membrane] is the inverse of an enzyme, for enzymes isolate reactions by increasing their rates while cell membranes isolate by slowing down intrusion.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 168.

“The identification of holon surfaces by decomposition is important if the world is to be manageable.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 177.

“At right angles to surfaces, the ratio between changes in rate constants and changes in spatial position is very large. At surfaces a narrow part of space manifests big changes in time constants. The character of most other places in space–that is, places between boundaries, gives a medium-range ratio where size and behavior rates increase gradually together.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 181.

“Blum suggests an alternative geometry where the primitives are the point and the disc. A disc is the consequence of growth about the point. A line is not a primitive and must be derived by growth about two points. As the discs touch, they form the midpoint of the line; as the discs overlap, the two points of intersection move away from the midpoint to trace out the growing line.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 183; reference: Blum, H. 1973. “Biological shape and visual science. Part I.” J. Theoret. Biol. 38:205-87.

“Reduction of dimensionality is one of the strategems of living systems. An example would be male moths whose problem is detecting pheromones from females in a massive 3D space. Antennae shaped as combs sweep the signal onto the plane of the antenna. Pheromones pass down to the stem of the comb and so become ordered in one dimension. The molecules pass to the base of the stem and are counted as zero-dimensional points ticked off as they pass. Male moths solve their problems by changing dimensionality.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 185-6.

“Enzymes are a transition point between two fundamentally different systems or universes. There is chemistry, which is largely a matter of electrical charges, and there is shape where surface and volume are connected by surfaces.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 186.

“With the advent of sexual reproduction, further highly integrated holons with their particular characteristics may be seen as part of phenotypic hierarchy. These holons are the reproductive pair, the recombinant individual, and the breeding population. They are part of the reason for the fast pace and great creations of biological evolution.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 188.

“Parallel to the phenotypic hierarchy, and interacting with it, is a genotypic hierarchy. Here we find messengers and masters in protein synthesis, the Mendelian genes and polygenes, gene complexes, duplicated segments, and crossover segments. The hierarchy of genetic components has level structure that is well considered as temporal…. Each of the levels in the genotypic hierarchy holds genetic signal constant for certain periods of time, and is associated with certain rates of genetic change.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 189.

“It should be clear from the above discussion that a regular perturbation is a contradiction in terms [since biological phenomena such as fire-adapted plants allow for it as different time-scaled regularities].” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 201.

“The fate of a litter of baby hamsters depends on the food supply to the parent at the time the litter is born. If food is abundant, then the young are reared in a normal fashion, as a contribution to the population holon. If, however, food is in short supply, the parent kills and eats the young. Lotka suggested that birth does not contribute to population growth directly, it only provides vessels. If there is food to fill those vessels than a new individual survives. Sometimes birth only generates a food resource for adults….

“For hamsters, food is a constraining holon at a physiological level of organization. This would be well and good, but if the food supply behaves at a higher frequency than the individual life span, then the hamster depends upon a highly variable compartment, the behavior of which is likely to be fatal. Somehow the hamster must alter its relationship to the food compartment either by changing its own relaxation time or by stabilizing the food supply. As is characteristic of selected holons in such circumstances, the hamster runs the food through a buffer compartment, its offspring. Signals from the food supply are integrated over a long enough period so that the adult hamster reads food messages that are essentially constant. Thus the food holon is seen by the hamster to behave in such a way that it protects the organismal holon; environments (food here) must behave more slowly than that for which they are the environment in a stable hierarchy. eating babies stabilizes the food supply.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 205, 206; reference: Lotka, A.J. 1956. Elements of Mathematical Biology. NY: Dover.

“Because it was so abundant, the loss of the passenger pigeon will have increased diversity of birds in North America. The explanation is that some measures of diversity very reasonably do more than simply count species, they give account to evenness of numbers of individuals in species. High evenness refers to diversity in the experience of the average individual. In the most even situation the chances are greatest that an individual will be next to another individual of a different species. For instance, if there are one hundred total individuals split into five species, diversity is highest if all species contain the same number of individuals, twenty.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 270.

“The same term [stability or diversity] can have opposite meanings for different authors. Stability is set in the context of disturbance. First there is the notion of resistance, the capacity of the system to resist being displaced by a given size of perturbation. Then there are various notions of resilience. Resilience can refer to the capacity of the system to return after perturbation from a given displacement. Resistance will of course minimize the displacement, but resilience indicates a certain response to the displacement. So there is recovery associated with the degree of displacement, but even that can be addressed in two ways. First is the degree of displacement from which there is still recovery, and second is the speed of recovery if there is a recovery. Then there is the added dimension of what qualifies as recovery. If there is a singular pattern before the disturbance, how much of that pattern must be reestablished for recovery to be recognized? It might be recovery to an equilibrium point or a stable limit oscillation. But if the system at rest is chaotic, it is only possible to recover to the track of the strange attractor, which will of course never return to any particular value or set of values. There recovery will be recognized not by what happens, but by what never happens.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 274-5.

“Diversity by itself has little to say about stability precisely because it does not consider connectedness.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 277.

“Paradigms are narratives about what is interesting. One takes it on its face that what an accepted paradigm says is interesting. A narrative is not a truth but is rather an announcement of a point of view. The paradigm says what is studied in the prescribed way is self-evidently worthwhile.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 284.

“Hierarchy theory articulates a narrative for undefined situations, which in science amounts to a paradigmatic statement not a hypothesis.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 284.

“The junction point in the hierarchy is a holon in its own right. Two people talking in a room saturate the room so that the respective other person can hear the communication. The room is the junction compartment and is a holon. The signal must not so much pass between the lower-level communicating holons as it must saturate the junction holon that contains or is the context of the lower-level pair.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. pp. 284-5.

“A standard nonhierarchical model couples the holons by a direct communication channel that makes the holons simultaneous functions of each other. The hierarchical alternative has certain attractive features. It alerts us where to expect new pertinent filters. For instance, information theoretic discussions of groups of people predict that up to six members in a group do not apparently organize. But at seven members it is more economical in terms of monitoring channels to have a leader. It takes two communications between members via the leader, but it is more reliable than direct connection to the tangle. That is why sports teams get a captain once more than seven are involved.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 285.

“Formal models are scale-relative statements, and are therefore in themselves scale-independent.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 301.

“Engineers are particularly attentive to scaling issues because relationships change in what they construct across scales. They are cautious in scaling, always trying to avoid emergent properties.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 302.

“When we consider scaling in our work, we are actually interested in sudden change–that is, in emergent properties, the very thing engineers eschew. Hierarchy theory addresses rescaling where qualitative differences appear. Hierarchy theory looks for emergence and tries to deal with it, not stop it.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 303.

“The mathematics of collapse and emergence is positive feedback.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 304.

“The one thing that does map onto exponential economic growth is energy, so there is no weaseling out there. Murphy shows, with elementary graphing, that at 3% growth, in 300 years all sunlight hitting the Earth would need to be captured with 100% efficiency. At 400 years waste energy would boil the oceans.” Allen, T.F.H. & Thomas Starr. 2017. Hierarchy: Perspectives for Ecological Complexity, Second Edition. U of Chicago Press. p. 341; reference: Murphy, Thomas. Has 1988 book and blog – “Do the Math: Using Physics and Estimation to Assess Energy, Growth, Options.”

“Despite intense debate on the matter, there have been numerous attempts to delineate a universal definition for life…. Among the properties of life most amenable to this approach is autonomy. Roughly speaking, autonomous systems can be characterized as forming a unitary ‘whole’ from their own intrinsic perspective, and being able to maintain themselves in the face of changing internal and external states. That is, autonomous systems are integrated wholes with self-defined and self-maintained borders….

“Moreover, autonomy requires a system to construct its own ‘umwelt’, causally separating itself from its environment. Nevertheless, living systems are open systems that dynamically and materially interact with their environment. For this reason, a purely dynamical approach cannot distinguish between a living entity and its environment.” Marshall, William, Hyunju Kim, Sara Walker, Giulio Tononi & Larissa Albantakis.” 2017. “How causal analysis can reveal autonomy in models of biological systems.” Philosophical Transactions of the Royal Society: A. 375:20160358. dx.doi.org/10.1098/rsta.2016.0358. p. 2.

“To fully characterize the causal mechanisms involved in the fission yeast cell-cycle model we employ the formalism of integrated information theory (IIT)…. By IIT’s composition principle, any subset of elements within the system can be a mechanism of the system if its intrinsic cause-effect power is irreducible. Emergent mechanisms composed of more than one element are termed ‘high-order mechanisms’.” Marshall, William, Hyunju Kim, Sara Walker, Giulio Tononi & Larissa Albantakis.” 2017. “How causal analysis can reveal autonomy in models of biological systems.” Philosophical Transactions of the Royal Society: A. 375:20160358. dx.doi.org/10.1098/rsta.2016.0358. p. 3.

“The results of the causal analysis reveal several properties of the cell-cycle network that cannot be uncovered by a purely dynamical approach, namely that the Boolean network mode of the fission yeast cell cycle is a robustly integrated whole and is self-regulating. In summary, we have demonstrated how IIT’s causal analysis can be applied to reveal defining features of biological autonomy–the ability of a physical system to self-define, and self-maintain its borders.

“Previous analysis of the cell-cycle network identified a control kernel that, when externally intervened upon, dictates the dynamics of the network. However, studying the high-order mechanisms within the system reveals an intrinsic, causal mechanism which self-regulates not only the network’s function, but also its causal borders, without the need for external manipulation.” Marshall, William, Hyunju Kim, Sara Walker, Giulio Tononi & Larissa Albantakis.” 2017. “How causal analysis can reveal autonomy in models of biological systems.” Philosophical Transactions of the Royal Society: A. 375:20160358. dx.doi.org/10.1098/rsta.2016.0358. p. 9.

“Implicit in this analysis [previous paragraph above] is a rejection of the reductionist assumption according to which only individual micro elements have true cause-effect power. Reductionist approaches, as well as holist approaches that lack composition cannot account for how subsets of elements work together, constraining the system jointly and irreducibly to achieve a specific state transition.” Marshall, William, Hyunju Kim, Sara Walker, Giulio Tononi & Larissa Albantakis.” 2017. “How causal analysis can reveal autonomy in models of biological systems.” Philosophical Transactions of the Royal Society: A. 375:20160358. dx.doi.org/10.1098/rsta.2016.0358. p. 9.

“Furthermore, a causal approach allows us to disentangle the intrinsic mechanisms within a system from the contributions of its external environment and thus establish self-defined borders necessary for autonomy. A functionalist approach, which only cares about what happens and not why it happens, has no way to distinguish the two contributions, and thus cannot firmly identify the borders between an entity and its environment…. This establishes a distinction between function and integration, which may be important to the origins of life. A prebiotic system, such as an autocatalytic network or a protocell, even if functional, may not be integrated and thus would not be an autonomous system.” Marshall, William, Hyunju Kim, Sara Walker, Giulio Tononi & Larissa Albantakis.” 2017. “How causal analysis can reveal autonomy in models of biological systems.” Philosophical Transactions of the Royal Society: A. 375:20160358. dx.doi.org/10.1098/rsta.2016.0358. p. 10.

“The great systems scientist Weaver once classified systems into three categories: (1) organized simplicity, (2) disorganized complexity, and (3) organized complexity.” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. p. 1; reference: Weaver, W.A. 1958. Quarter Century in the Natural Sciences. NY: The Rockefeller Foundation Annual Report.

“Successful measures of ecological complexity include structural AND functional aspects, or function embedded in (network) structure. An unwritten consensus was reached, borrowing from physics, that a good measure of complexity should have both an extensive and an intensive aspect to it. Just as we measure energy as volume (extensive) times pressure (intensive) or entropy (extensive) times temperature (intensive), our measure of ecological complexity should include the amount or quantity and characteristic or quality of the thing being measured. Three different approaches, in particular, are worth noting here.

“The first metric … is termed eco-exergy and is based on the concentration of biomass of a species (extensive) weighted by the informational complexity of the species (intensive). Specifically, the information in this approach is measured as genetic complexity such that there is information in the order of nucleotides within the DNA. Species with a longer alignment of nucleotides in its genome are given a correspondingly larger weighting factor. A second method, developed by Odum uses the species biomass as the extensive variable and weights it by a species-specific transformity, which is a measure of how much solar energy is needed to generate biomass of that species. For example, since it is impossible to have a lion without prey and the prey without forage, the lion indirectly consumes an amount of forage, which in turn had captured solar radiation. This gives a path dependent metric in terms of the total solar energy embedded in the ecosystem, and has been called emergy (for embodied energy). A third approach developed by Ulanowicz uses the network as the scale of study rather than the species. In this case, the network is comprised of energy flows within entire food webs. The extensive variable is the total energy flow through the entire network and the intensive variable is the information within the network flow structure. In other words, information is gained when there is a reduction of uncertainty such that the network constrains or articulates flow. The lower the redundancy, the greater information there is about the system.” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. pp. 4-5; references: Odum, H.T. 1988. “Self-organization, transformity, and information.” Science. 242:1132-1139; Ulanowicz, R.E. 1986. Growth and Development: Ecosystem Phenomenology. NY: Springer.

“A number of ecological goal functions, including the ones above, such as increasing the energy cycling, storage, dissipation, residence time, degree of mutualistic relations, and minimizing specific dissipation (dissipation per unit of biomass) have been proposed.” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. p. 5.

“Some scholars have promoted the idea that degrading the energy gradient IS the purpose for the structure and therefore the evolution toward more complex structures is actually a trend toward greater dissipative ability. Others have focused on the organization of the structure and its increased complexification as the primary motive trend. The critical duality is that of aggradation and degradation, construction and dissipation. The insight that far from equilibrium physics brings us is that we are working with systems that are obligate open, linked to a continued and sustained flow of energy: these systems reside in an energy gradient.” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. p. 5.

“‘In the forest, energy flow is anything but swift and simple, because the diverse and roundabout ways that the system’s web of teeming, interdependent organisms uses energy. Once sunlight is captured in the conduit, it’s not only converted but repeatedly reconverted, combined and recombined, cycled and recycled as energy/matter is passed around from organism to organism. Energy flow through an intricate conduit of this kind is dilatory and digressive. It leaves behind, in complex webs of life, ample evidence of its passage.’” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. p. 7; quotation from: Jacobs, Jane. 2000. The Nature of Economies. NY: Vintage. p. 46.

“In the end, we showed the complementarity of all goal functions considered, and identified three as summative: (1) increasing energy acquisition, (2) increasing retention time (i.e. biomass), and (3) increasing cycling. These results engendered the quip: Ecosystems get as much as they can, hold on to it for as long as they can, and if they must let if go, then try to get it back.” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. p. 7; referring to a study done in the paper – Fath, B.D., B.C. Patten & J.S. Choi. 2001. “Complementarity of ecological goal functions.” Journal of Theoretical Biology. 208:493-506.

“We distinguish four stages of EGD [ecosystem growth and development]. The first EGD stage is boundary growth, which simply means how much energy the system is able to capture across its boundary. Obviously, an increase in input can result in an increase of both throughflow and storage. The second EGD stage, also growth dominated, is biomass growth. This is the stage in which the energy flow is converted to additional biomass storage, greater plant and animal material, and represents a true measurably quantitative increase. As the ecosystem fills with biomass, the next stage represents the network development, an increase in the diversity (differentiation of nodes) and connectivitiy. A richly connected system is able to retain and utilize the energy inflow more effectively and extract our more structure and organization for the same amount of energy flow…. The fourth EGD stage captures information development. This represents the changes that take place within the storage compartments to increase efficiencies and processes through biochemical or even genetic evolution.” Fath, Brian. 2017. “Systems ecology, energy networks, and a path to sustainability.” Int. J. of Design & Nature and Ecodynamics. 12(1):1-15. pp. 8-9.

“… Julian Adams and co-workers initiated long-term chemostat cultures of Escherichia coli in glucose-limited conditions. An intriguing observation from their continuous cultivation experiments was that bacterial strains repeatedly evolved mutations in the acetyl CoA synthetase enzyme. This mutation allowed the uptake of exogenous acetate, resulting in a stable coexistence of these mutants with wild type strains that secreted acetate as a by-product of glucose metabolism. Several subsequent studies analysed similar cases of diversifying selection in initially clonal populations that resulted from the evolution of metabolic cross-feeding interactions.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 458; reference: Treves, D.S., S. Manning & Julian Adams. 1998. Mol. Biol. Evol. 15:789-797.

“Our classification framework categorizes metabolic interactions along two main axes: (i) the degree of reciprocity (i.e. unidirectional versus bidirectional metabolite flow), and (ii) the investment by the involved partners (i.e. the cost to produce the exchange metabolite). The first parameter, degree of reciprocity, categorizes cross-feeding interactions based on whether the metabolite exchange is unidirectional (one-way) or bidirectional (reciprocal). The second parameter, investment, divides cross-feeding interactions according to the cost of biosynthesis that the interacting partners bear during the interaction, resulting into two sub-categories (i) by-product cross-feeding and (ii) cooperative cross-feeding. By-product cross-feeding is the exchange of metabolites that results from a selfish act of the producer. For example, by-products can be secreted due to the degradation of complex hydrocarbons, the accidental leakage of metabolites through the bacterial membrane, or overflow metabolism. In general, the production of metabolic by-products is independent of the presence of an interaction partner and positively correlated with producer’s growth.

“In contrast, cooperative cross-feeding occurs if one partner actively invests resources to produce metabolites that benefit an interaction partner.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 458.

“Cross-feeding interactions can be classified based on the degree of reciprocity and the investment of the interacting partners. (A) Unidirectional by-product cross-feeding: one partner produces a metabolic by-product that benefits the respective other. (B) Bidirectional by-product cross-feeding: reciprocal exchange of metabolic by-products between two partners. (C) By-product reciprocity: one partner produces a costly metabolite to benefit another cell, which in turn supplies the producer with increased amounts of a metabolic by-product. (D) Unidrectional cooperative cross-feeding: one partner bears a cost for producing a metabolite that benefits the respective other one. …this case is hypothetical and expected to be strongly disfavoured by natural selection. (E) Bidirectional cooperative cross-feeding: reciprocal exchange of a costly metabolite that benefits both partners.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 459.

“The results of this meta-analysis indicated that metabolite cross-feeding is indeed very common both among different bacterial species and between bacteria and members of other kingdoms including archaea, fungi, animals, protists, and plants.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 461.

“Interestingly, even seemingly identical members of the same bacterial species can differ greatly in their gene repertoire. Observation of this recurring pattern in several bacterial taxa like Salmonella, Escherichia, and Prochlorococcus has led to the development of a concept called the pan-genome. In this framework, all genes that are found in all isolates/genotypes of a given species are called the core genome, while genes that are only present in some genomes are referred to as the pan- or auxiliary genome. Systematic analyses, in which the ability of known bacterial genomes to produce all primary metabolites a bacterium requires for growth was scrutinized, revealed that in fact 76% of all 949 eubacterial genomes analysed were unable to produce at least one of 25 different metabolites.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 468; study referenced in last sentence: D’Souza, G., S. Waschina, S. Pande, K. Bohl, C. Kaleta & C. Kost. 2014. Evolution. 68:2559-2570.

“… obligate cooperative cross-feeding interactions are commonly stabilized by negative frequency-dependent selection. Frequency dependence describes an evolutionary process, in which the fitness of a given genotype depends on the relative frequency of other genotypes in the total population. In the case of negative frequency-dependent selection, the fitness of a certain genotype decreases as it becomes more common in a given population. From this, results a stabilizing force that maintains interacting genotypes in the long-run.

“Negative frequency-dependence has been shown to operate in both one-way by-product and two-way cooperative cross-feeding interactions. In both cases, frequencies of the two interacting cell types oscillated around a stable equilibrium point that most likely was determined by rates of metabolite production and consumption. Interestingly, the same pattern prevails when non-cooperators are included…. Observing negative frequency-dependent selection for different types of metabolic interactions in both spatially structured and unstructured environments suggests this pattern is a common principle emerging in synergistic microbial communities.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 476.

“However, cooperators and non-cooperating individuals of the abovementioned examples are unlikely to have equal access to the cooperatively produced metabolite. Instead, mechanisms of positive assortment, which have either evolved or result as a by-product from other features of the interaction, ensure the cooperatively produced metabolite is predominantly benefitting other producing genotypes. Examples of such mechanisms include a privatization of metabolites or biosynthetic functions due to contact-dependent exchange mechanisms or the localization of public goods in spatially structured environments.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 476.

“Coevolution experiments with syntrophic consortia consisting of a sulfate reducer (Desulfovibrio vulgaris) and a hydrogenotrophic methanogen (Methanococcus maripaludis) for 1000 generations documented an extremely rapid loss of functional independence of Desulfovibrio vulgaris, which was driven by a mutational inactivation of genes involved in sulfate respiration. Also pairs of lactic acid bacteria that have been serially propagated in coculture to ferment yoghurt reciprocally exchange a larger number of metabolites in a mutualistic manner. This striking metabolic complementarity, which likely evolved in response to the ecological interaction between both species, is largely due to gene loss. Given that consortia of co-occurring bacterial endosymbionts display a similar pattern on a genomic level, it is tempting to speculate that metabolic complementarity is a common outcome of a synergistic metabolic coevolution.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 476.

“The frequent loss of metabolic genes from microbial genomes along with intricate patterns of cross-feeding, where other coexisting genotypes compensate the functional deficiency, suggests that within bacterial consortia, metabolism is often a community-level property and not a feature of an individual cell any more. If true, this implies that a bacterial communities’ metabolism is in essence a super-metabolic network, where many of its constituents perform specialized biosynthetic or catabolic tasks that also benefit other members of the community.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. pp. 476-7.

“Moreover, coevolved symbiotic interactions between bacteria and higher organisms often show signatures of a functional fusion, in which interacting parties operate as one integrated metabolic unit.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 477.

“… microbiologists have repeatedly corroborated that less than 1% of all archaea and bacteria can be grown in vitro – a problem that has been popularized as the great plate count anomaly….

“Many potential explanations have been proposed to account for the unculturability of most bacterial species. These can be grouped into four main categories:

“(1) Niche mismatch: Mismatch between the physiological and nutritional requirements of a bacterial strain and the conditions provided (e.g. pH, temperature, salts, minerals, and nutrient levels).

“(2) Dormancy: Bacterial cells might be viable, but unculturable.

“(3) Antagonistic effects: Competitively superior strains outcompete others and/or produce toxic compounds to kill or inhibit other strains.

“(4) Obligate metabolic interactions: Bacterial strains have evolved obligate metabolic relationships with other neighbours in their environment. Thus, attempts to isolate a single species must fail, because of the lacking nutrients or biochemical functions….

“… accumulating experimental evidence suggests that an obligate exchange of metabolites or biochemical functions among bacterial strains is particularly important in this context…. Taken together, the available evidence suggests that metabolic interdependencies within natural microbial communities are an important determinant of the commonly observed unculturability of natural bacterial isolates.” D’Souza, Glen, Shraddha Shitut, Daniel Preussger, Ghada Yousif, Silvio Waschina & Christian Kost. 2018. “Ecology and evolution of metabolic cross-feeding interactions in bacteria.” Natural Products Reports. 35:455-488. p. 477.

“In an 1898 essay, Thorstein Veblen asked: ‘Why is Economics not an evolutionary science?’ This question remains surprisingly relevant today. Veblen distinguished between teleological and evolutionary modes of scientific thought, arguing that the economics of his day was built on the former approach because of a presumption that the economy is propelled toward a state of normalcy or equilibrium. Veblen was not alone: a number of leading economists, such as Marshall and Schumpeter, argued that economics has more to learn from biology than from the physics on which its formal structure is based.” Axtell, Robert, Alan Kirman, Iain Couzin, Daniel Fricke, Thorsten Hens, Michael Hochberg, John Mayfield, Peter Schuster & Rajiv Sethi. 2016. “Challenges of Integrating Complexity and Evolution into Economics.” In: Complexity and Evolution: Toward a New Synthesis for Economics. Wilson, David S. & Alan Kirman (eds). MIT Press. pp. 65-81. p. 81; reference: Veblen, Thorstein. 1898/1998. “Why is economics Not an Evolutionary Science?” E:CO 12:41-69.

“… the aggregate outcomes in a market or an economy could be equally well attributed to the structure of the system or to the behavior of the individuals within it. The former view attributes much less knowledge and reasoning capacity to the participants and allows one to model agents as using simple rules and adapting to their environment rather than as the omniscient individuals common to economic and particularly macroeconomic models.” Axtell, Robert, Alan Kirman, Iain Couzin, Daniel Fricke, Thorsten Hens, Michael Hochberg, John Mayfield, Peter Schuster & Rajiv Sethi. 2016. “Challenges of Integrating Complexity and Evolution into Economics.” In: Complexity and Evolution: Toward a New Synthesis for Economics. Wilson, David S. & Alan Kirman (eds). MIT Press. pp. 65-81. p. 81.

“From classical thermodynamics two principles are firmly established for systems near equilibrium. The first is the second law which applies to isolated systems: entropy always increases with time and approaches a maximum at equilibrium. The second is for open systems: entropy production always decreases with time and approaches a minimum at steady state. Far from equilibrium, which is where many physical systems and all living systems operate, these principles do not apply.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 493.

“More recently, Schneider & Kay, who take a thermodynamic approach, proposed seven ecosystem properties as basic orientors: exergy capture, energy flow, cycling of energy and materials, respiration and transpiration, biomass, average trophic structure, and types of organisms.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 494; reference: Schneider, E.D. & J.J. Kay. 1994. “Life as a manifestation of the second law of thermodynamics.” Math. Comput. Modeling. 19:25-48.

“Here, we take this a step further by demonstrating consistency of ten goal functions….

“1. Maximize power. Lotka’s maximum power principle states that systems become organized to maximize their energy throughput…. In networks, power is reflected in energy throughput or total system throughflow (TST), the sum of flows into, or alternatively out of, all compartments. Thus, in the network context, maximizing power is equivalent to maximizing total system throughflow….

“2. Maximize storage. Jorgensen & Mejer proposed a maximum storage principle in which energy systems maximize their distance from a thermodynamic reference point by storing usable energy (exergy)…. For entire systems, this principle asserts that total system storage (TSS) is maximized. For biotic systems this means maximizing biomass….

“3, 4. Maximize empower and emergy. Odum developed the concept of emergy (embodied energy) to describe energy quality as referenced to solar radiation. As solar energy passes through a series of energy transformations, its quality increases in proportion to the amounts of original solar energy required at each step. Emergy measures this stored energy quality, and empower the associated energy flow…. Maximizing empower (EMP) is consistent with reference condition 1 and…maximizing emergy (EMG) is consistent with reference condition 2.

“5. Maximize ascendency. Ulanowicz… where ascendency quantifies network organization as the product of the total system throughflow (TST) and average mutual information (AMI)…. As a result, throughflow dominates the ascendency measure such that power and ascendency give strongly correlated results….

“6. Maximize dissipation…. Schneider & Kay elaborated this in exergy terms, stating that systems supplied with an external exergy source will respond by all means available to degrade the received exergy…. Maximizing total system export (TSE) is the sum of dissipative processes over all components. Maximizing total system export (TSE) seems counter to the maximize storage principle above. This incongruence has produced a divergence in contemporary discussion between proponents of maximizing storage and maximizing dissipation….

“7. Maximize cycling. Morowitz considered that energy flow caused cycling and this produced organization:…

“The flow of energy causes cyclic flow of matter. The cyclic flow is part of the organized behavior of the system undergoing energy flux. The converse is also true; the cyclic flow of matter such as is encountered in biology requires an energy flow in order to take place. The existence of cycles implies that feedback must be operative in the system…. [Morowitz, Harold. 1968. Energy Flow in Biology; Biological Organization as a Problem in Thermal Physics. NY: Academic Press. p. 120]

“Glansdorff & Prigogine and Nicolis & Prigogine hypothesized an order-through-fluctuation principle. These authors noted that small deviations in energy flow exist statistically in any thermodynamic systems. These are generally damped out by dissipative processes, but as energy gradients (including those reflected in storage) increase, deviation amplification becomes more and more probable…. In far-from-equilibrium thermodynamics pulsing organizations have been referred to as ‘dissipative structures’, and the significance of their oscillations is the acceleration of energy flux toward the realization of maximizing power. Maximizing cycling contributes to both reference conditions 1 and 2, and hence is consistent with all of the foregoing principles.

“8. Maximize residence time. Cheslak & Lamarra proposed that ecological systems organize to maximize the residence time of energy….

“9. Minimize specific dissipation. Internal constraints, such as caused in living systems by inefficient energy transfer or limited availability of metabolites, modulate throughflow maximization and divert free energy (exergy) to storage as chemical potential. This tends to minimize dissipation per unit mass or volume, which expresses the least specific dissipation principle. Although this least-specific dissipation principle was developed for systems near thermodynamic equilibria, we contend that even if the global system is ‘far from equilibrium’, sub-systems at finer spatio-temporal-organizational scales may be considered to be in some proximity to a quasi-local steady state–close enough at least for the principle to provide an understanding of ‘how a system should change.’ A question for future research is to determine whether a system is too far or near enough for this to be valid. Choi et al used the respiration biomass ration (TSE/TSS in our notation) of lacustrine communities as an empirical measure of least-specific dissipation at the ecosystem level. With the dimensions of reciprocal time, TSE/TSS (to be minized) approximates how efficiently structure (TSS) can be created for a given amount of work performed (reflected in the unusable released heat portion of TSE)….

“10. Minimize empower to exergy ratio. Bastianoni & Marchettini proposed that system organization can be measured by a ratio of empower to exergy (in their paper they inadvertently label empower, a throughflow metric, as emergy, a storage metric). The empower to exergy ratio measures the total environmental cost (throughflow) required to produce a unit of organization (structure).” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. pp. 494-6.

“The two principles that seem most contradictory are maximize dissipation and minimize specific dissipation. However, both can co-occur if total system storage increases faster than total system export.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 503.

“The consistency of the goal functions investigated here by network methods is more than just the sharing of several notated variables…. Only those pertaining to empower, emergy, and ascendency were originally conceived in an explicit network context, yet it is global systemic organization that is behind the similarities inherent in all the studied goal functions. The implication is that the network perspective is fundamental, and somehow the originators of different orientors managed to capture this intuitively in their concepts.

“At steady state all ten energy organizing principles are founded on increasing boundary flow, and three primary internal properties: first-passage flow, cycling, and residence time.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 504.

“In addition to the inputs and transfer efficiencies, cycling is also a function of system connectivity and organization. Retention time depends on cycling and system structure because cycling retains and stores flow, thus increasing the turnover time. Cycling at one scale is structural storage at another.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 504.

“The primary boundary and internal properties that are common to these organizing principles can be summed up in the following maxim: Get as much as you can (maximize input and first-passage flow), hold on to it for as long as you can (maximize retention time), and if you must let it go, then try to get it back (maximize cycling).” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 504.

“… we find that specific dissipation rather than storage per se is the primary goal function. Minimizing specific dissipation is most encompassing because it captures all three properties above and is dependent on maximizing storage faster than maximizing dissipation, which is empirically observed.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 504.

“In conclusion, we support the use of a plurality of goal functions because each organizing principle reflects a slightly different aspect of overall system function. In fact, it is probably their complementarity and interdependency that has made the identification of a single universal extremal principle difficult.” Fath, Brian D., Bernard Patten & Jae Choi. 2001. “Complementarity of Ecological Goal Functions.” J. theor. Biol. 208:493-506. p. 504.

“Based on the universality of the genetic code, amino acid chirality, and universal metabolic currencies, there is an agreement that a last universal common ancestor (LUCA) predated the divergence of bacteria and archaea. Because the bacterial and archaeal domains are monophyletic, there is evidence for one clear ancestor for each domain–the last bacterial common ancestor (LBCA) and the last archaeal common ancestor (LACA).” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metabolic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 2.

“The most important difference between anaerobes and aerobes is related to energy; acetogenesis, and methanogenesis yield only a fraction of the energy when compared to aerobic pathways, but this is compensated by the circumstance that the synthesis of biomass costs 13 times more energy per cell in the presence of O2 than under anoxic conditions. This is because, in the reaction of cellular biomass with O2, the thermodynamic equilibrium lies very far on the side of CO2. That is, the absence of O2 offers energetic benefits of the same magnitude as the presence of oxygen does.” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metabolic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 2.

“Metabolic networks include multiple redundant paths, and in different species, different routes can lead to the same functional outcome.” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metaboic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 2.

“Here we take a simple but effective approach at inferring the metabolism of LBCA, by focusing on anaerobic genomes and genes that are widely distributed among them. We reconstruct the core metabolic network of LBCA independent of any single backbone phylogenetic tree for the lineages in question.” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metaboic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 2.

“Only nine compounds were required to complete intermediary metabolism in LBCA. The list of LBCA genes is conservative because our criteria, although not imposing bacterial universality, do require the presence in 25 higher taxonomic groups. However, even though the list is short, the 146 protein families of LBCA generate a tightly connected metabolic network of 243 compounds with only one reaction out of 130 disconnected from the rest. The network is close to complete in that it generates 48 of the 57 universally essential prokaryotic metabolites: the 20 amino acids, four DNA bases, four RNA bases, eight universal cofactors, glycerol 3-phosphate as a lipid precursor, and 20 charged tRNAs. The compounds missing are the charged tRNAs for Lys, Met, Ile, Pro, Asn, Gly, and Gln and two cofactors. Using a network expansion algorithm, adding all reactions encoded by non-LBCA genes to the network, and then sequentially and gradually removing them until the production of all universal metabolites was possible with the minimal set of reactions, we found that the addition of only nine genes… completes the network to generate all 57 universal compounds.” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metabolic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 3.

“LBCA’s network is highly structured around three major metabolic hubs: (i) ATP/diphosphate, (ii) NADP(H)/H+, and (iii) CO2/ACP/malonyl-ACP. These represent the cores of (iii) energy, (ii) hydride transfer, and (iii) carbon metabolism of LBCA.” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metaboic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 3.

“The analyses so far suggest that the 146 protein families conserved in all groups of anaerobic bacteria were present in LBCA, not only due to their ubiquitous and nearly universal nature but also because they form a functional unit: a highly connected, nearly complete core metabolic network.” Xavier, Joana, Rebecca Gerhards, Jessica Wimmer, Julia Brueckner, Fernando Tria & William Martin. 2021. “The metaboic network of the last bacterial common ancestor.” Communications Biology. doi.org/10.1038/s42003-021-01918-4. p. 5.

“… Isaac Newton never presented his second law in its familiar form: force equals mass times acceleration (F = ma). That formulation belongs to Leonhard Euler, who saw the world as a continuum. Newton’s statement, by comparison, was discrete and irreversible, and he argued strenuously against the continuum assumption, because it equates cause with effect. The ensuing mathematics of Leibniz and Euler gave rise to a physics of ‘objects moving according to universal laws’. Ecology, however, is intended to focus, not upon objects, but on relationships, most of which appear as irreversible processes. Processes explicitly involve time and thus cannot be fully characterized by the time-reversible force laws of physics.” Ulanowicz, Robert E. 2018. “Dimensions Missing from Ecology.” Philosophies. 3(24). doi:10.3390/philosophies3030024. p. 2.

“Biology, by contrast [to the continuum of physics], involves heterogeneity–in fact massive heterogeneity. The problem posed by heterogeneity is that the combinations and possibilities among differing types quickly become hyper-astronomical….

“This enormity of possible combinations hampers efforts to represent heterogeneous systems in terms of homogeneous laws.” Ulanowicz, Robert E. 2018. “Dimensions Missing from Ecology.” Philosophies. 3(24). doi:10.3390/philosophies3030024. p. 2.

“Conditional probabilities, for example, refer to events that exhibit some degree of bias in directions that are influenced by surrounding events. Such bias can grow quite dominant, resulting in almost law-like propensities that yield the same outcome in a large preponderance of instances. Hence, we see that there exists an entire spectrum of contingencies, ranging from radical unique happenings through blind chance to conditioned outcomes to propensities that border on determinism.” Ulanowicz, Robert E. 2018. “Dimensions Missing from Ecology.” Philosophies. 3(24). doi:10.3390/philosophies3030024. p. 3.

“An autocatalytic cycle is one wherein every constituent process benefits its succeeding one. Such serial mutual beneficence grows whenever any component process becomes more beneficial to its successor and it declines whenever any benefit diminishes. The result is a ratcheting dynamic that will promote those changes that benefit the ensemble–a form of endogenous group selection. Furthermore, because living entities always require energy and materials to survive, such selection will favor any change that augments the acquisition of resources. Such a contribution can be made by any member of the cycle, cumulatively resulting in ever greater flows of resources into the loop, or what might be called ‘centripetality’. None other than Bertrand Russell identified this dynamic as ‘the drive behind all evolution’. Centripetality, after all is what induces competition. If two independent autocatalytic configurations exist within a field of resources, their respective centripetalities will grow eventually to intersect one another, the group that builds faster under prevailing contingencies will come to dominate or extirpate the other in a form of group selection.” Ulanowicz, Robert E. 2018. “Dimensions Missing from Ecology.” Philosophies. 3(24). doi:10.3390/philosophies3030024. p. 3; reference: Russell, Bertrand. 1960. An Outline of Philosophy. Cleveland, UK: Meridian Books.

“In any event, the time is ripe for ecology to advance to center-stage and become the ‘new integrative discipline’ for the science of life.” Ulanowicz, Robert E. 2018. “Dimensions Missing from Ecology.” Philosophies. 3(24). doi:10.3390/philosophies3030024. p. 5.

“What is an organism”… The first type of answer endorses a broadly mechanistic ontology wherein organisms are conceptualised as the mereological sums of organised collections of entitites bearing certain spatial and causal relations to one another – they are in other words, specialised sorts of machines…. The second type of answer to the organism question endorses a processual ontology wherein organisms are conceptualised as spatio-temporally extended, causally continuous patterns of activity – they are, in other words, dynamically stabilised processes.” Austin, Christopher J. 2020. “Organisms, activity, and being: on the substance of process ontology.” European Journal for Philosophy of Science. 10: 13. doi.org/10.1007/s13194-020-0278-0. pp. 1-2.

“In other words, in line with its rejection of the metaphysical stasis inherent in SO [substance ontology], PO [process ontology] is a system in which identity is determined by activity – it is a specialised sort of autopoietic activity which functions as the connective ‘glue’ among temporal slices which connects those slices into properly unified, singular series – i.e. particular organisms.” Austin, Christopher J. 2020. “Organisms, activity, and being: on the substance of process ontology.” European Journal for Philosophy of Science. 10: 13. doi.org/10.1007/s13194-020-0278-0. p. 9.

“The starfish and the crinoid [floating, flowery heterotroph] are distinct sorts of organisms not (or, at least, not principally) because the segments of their four-dimensional ‘worms’ [series of time slices to make the organism-as-process] are fastened together in different fashions, but because the respective segments of which they are composed are of a different sort: ‘what it is to be’ either one of them is, to be these sorts of slices in this sort of arrangement. We might say then that the identity of an organism is better conceptualised as being constituted by the patterned progression of its slice-series – its unique life-cycle….

“With the incorporation of the life-cycle concept, I think it’s clear that the first question posed at the beginning of this section – whether the metaphysical framework of PO can answer the organism question in a way that is capable of delivering a sufficiently adequate ontological inventory of the living world – should be answered in the affirmative.” Austin, Christopher J. 2020. “Organisms, activity, and being: on the substance of process ontology.” European Journal for Philosophy of Science. 10: 13. doi.org/10.1007/s13194-020-0278-0. p. 11.

“To put the point more simply: while PO’s answer to the organism question is capable of saving the phenomena – of sufficiently cataloguing the natural world by sufficiently distinguishing this organism from that one – it is incapable of explaining the phenomena – of producing that catalogue by its own means. As I illustrate in what follows, PO can only successfully perform that important latter task by appealing to the central principles of SO.” Austin, Christopher J. 2020. “Organisms, activity, and being: on the substance of process ontology.” European Journal for Philosophy of Science. 10: 13. doi.org/10.1007/s13194-020-0278-0. p. 11.

“According to SO, ‘what it is to be’ an organism is grounded in a privileged collection of unchangingly stable and modally rich properties the organism in question possesses. In other words, the identity of an organism is determined by (I) a set of properties it could not fail to possess as long as it exists which (II) define and delimit its range of possible developmental trajectories and determine its characteristic mereological-cum-morpholgical featues. As we have seen, PO challenges (I) by claiming that the search for such properties must ultimately be in vain in light of the extreme compositional variation exhibited by organisms over diachronic distances: their ability to persist over such distances, PO maintains, critically relies upon their capacity for continual change. Accordingly PO rejects (II) and the associated claim that ‘activity follows from being/identity’: it maintains that an organism’s ontogeny is not guided by its possession of a privileged set of properties….” Austin, Christopher J. 2020. “Organisms, activity, and being: on the substance of process ontology.” European Journal for Philosophy of Science. 10: 13. doi.org/10.1007/s13194-020-0278-0. p. 12.

“I have argued that the most plausible account of the identity of a life-cycle-process is a dispositional one, as the general features of this sort of account best align with the theoretical commitments of PO….

“Furthermore, it’s easy to see that adopting this sort of dispositional account rather straightforwardly requires the rejection of a fundamental postulate of PO – that ‘being follows from activity’. For according to that account the identity, or being of the four-dimensional property patterning of an organism doesn’t follow from the activity which produces that pattern: rather, because the identity of a life-cycle-process consists in its set of developmental propensities (rather than its actually exhibited or characteristically exhibited stages), and its autopoietic activity (in any particular instance) is itself an expression of those propensities, the activity of an organism must follow from its identity, or being….” Austin, Christopher J. 2020. “Organisms, activity, and being: on the substance of process ontology.” European Journal for Philosophy of Science. 10: 13. doi.org/10.1007/s13194-020-0278-0. p. 18.

“Reductionism conflates claims about the world (properties of organisms are determined by properties of their parts) with claims about scientific representations of the world (biological theories are derivable from physical theories). But the move from the first of these claims to the second is permissible only if there is a strong correspondence between the two, that is, if scientific representations are (or aim to be) simply complete descriptions of the phenomena. But science, or at least biological science, it is now widely believed, works mainly by generating models of real phenomena, and these models idealise or abstract from many details of the target that are judged of minor significance for the use to which the models are to be put. Thus, scientific models do not provide, or even aim to provide, the whole and complete truth about the world. Hence, even a successful a priori argument that the properties of a complex whole depend in some sense on the properties of its parts is insufficient to show that the best model of the whole is related in any particular way to the best models of its parts.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 5.

“Identity of things has always been understood as an all or nothing question, applying, when it does, to exactly all the things that happen to exist. Identity of processes is a much less determinate matter. Think of the iconic exemplar of a process, a river. Is the Mississippi system one river, or one river the Mississippi and a tributary, the Missouri? If the latter, then are the lesser tributaries, the Ohio, the Arkansas, and so on, also not part of the Mississippi?… …dividing interconnected processes into distinct individuals is seldom if ever a question fully determined by objective facts.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 17.

“… the distinction between an organism and its life history is exactly what a processual understanding of an organism denies. The organism just is its life history; and hence it is at best highly misleading to claim that it is wholly present at any one stage of its life cycle.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 19.

“My claim is that we cannot avoid a concept of continuant process (e.g. rivers, vortices) and given that we have one it is by far the most apt for describing living systems. Moreover, if the need for such a concept is admitted there must be something amiss with a conceptual framework that rules it out a priori.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 20.

“In the philosophical tradition from Aristotle onwards, some of the most commonly proposed examples of such naturally occurring kinds have been biological species, and perhaps taxa at higher levels, such as genera, families, etc…. … there are other candidates in biology. Some of these are clearly functional (predator, heart, etc.) and no one would expect these to be materially, or structurally homogeneous.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 21.

“These so-called pluralists have argued that there is no unique way of dividing the domain of biological organisms into distinct kinds, and that different legitimate divisions serve different purposes…. In my view pluralism is grounded not on the denial that there are any naturally occurring distinctions on which to ground discrete kinds, but on the belief that there are too many, and they may overlap and cross-cut. Hence, there is nothing to prevent one from being a pluralist and a realist, from believing that there are many ways of classifying phenomena, and that many or all of them may reflect real and important divisions in nature.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 26.

“By a lineage, I mean any ancestral/descendent sequence of populations or species. Species and populations as individuals, then, are parts of lineages, either temporal, spatial, or both….

“Lineages, on the other hand are much more circumscribed entities. The human lineage includes the ancestral population that founded Mammalia, but thereafter, at every division in the mammalian tree only one branch carries on in the direction that will eventually lead to humans. All other branches are not part of the lineage.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. pp. 33-4.

“To sum up, lineages are the evolutionary processes that lead to species. Populations are spatial or temporal parts of species, up to and including, in some cases, the full spatial and temporal extent of the species…. Species, then, are the terminal twigs of the divergent tree-like evolutionary flow. But strictly speaking the terminal twigs are individual organisms.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 35.

“Biological individual is a broader category than organism. My liver, a cell in my liver, or a pride of lions are biological and are individuals. By their being individuals I mean at least that there is some integration of their parts and some differentiation from other entities that are not parts of them…. More than merely integration, an individual should be expected to do something, to interact as a whole with other parts of the world.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 38.

“Just as for my promiscuous realism about kinds, the point is not that there are no boundaries suitable for delineating individuals, but that there are too many.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 39.

“All individuals, I have said, do, or are at least capable of doing, something. So organisms, I suppose, are distinguished among biological individuals by what they do.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 39.

“We have seen compelling reasons to believe that biofilms are integrated individuals and Hullian interactors….

“Holobionts, consisting of an MDCL [monogenomic differentiated cell line – a multicellular stripped of its microbes and symbionts] and all associated microbes, seem even more clearly an integrated individual and an interactor….

“Given the promiscuous individualism I have already endorsed I have no objection in principle to the possibility that holobionts and biofilms are inteactors, while MDCLs and individual microbes are units of selection.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. pp. 41-2.

“Godfrey-Smith contrasts reproduction with reconstruction as different explanations of recurring structure. The MDCL reproduces, whereas the holobiont is reconstructed. But given that successful reproduction always in fact results in a holobiont, there is a strong case for adopting a broader conception of reproduction. One natural move would be to see the recruitment of symbionts as just part of development, an input like food, required to reach a healthy adult outcome. The trouble with this is that it assumes an asymmetric focus on the eukaryote ‘host’, and it would surely be desirable to have an account that accommodated symbiotic associations that lack such a focal host, like biofilms.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 43; reference: Godfrey-Smith, P. 2015. “Reproduction, Symbiosis and the Eukaryotic Cell.” PNAS 112(33): 10120-5.

“… it has generally been understood that the interaction between enzyme and substrate is more dynamic, and that the interaction between the two molecules reshapes both of them, an idea that has become known as the ‘induced fit’ model…

“But modern scientific understanding of the enzyme does not see its activity as separable even in principle from the entity. First, the enzyme does not exist as a unique rigid structure prior to its encounter with the substrate, but rather as an ensemble of structures (‘conformers’) through which it constantly cycles, activity that is enabled by its coupling with its aqueous environment….

“Moreover, the transformation of the substrate is not a simple switch from one structure to another, but involves a sequence of intermediate states. Enzyme and substrate first form a metastable unity, the substrate selecting one enzyme conformer from the available ensemble; this complex then finds the more stable, lower energy state known as the Michaelis complex; and the latter, finally, is chemically transformed into the enzyme and the product. This may still sound like a series of activities occurring to a series of things. But the more fundamental reality is that the whole inventory of enzymes and other proteins in the cell exist always as dynamic ensembles of conformers of varying stability and abundance. The transformations and stabilisations of this inventory are not reducible to the activities of a set of discrete structures, but are the result of a constant negotiation between the proteins and populations of other molecules, crucially including the aqueous background.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. pp. 53-4.

“The sum total of the exons and introns, or more technically the sequence that comes between a start codon, a triplet that induces the transcription process to begin, and a stop codon, that makes it stop, is called an open reading frame (ORF). Is the ORF the gene, or just the set of exons?

“Matters become still more complex when we look more closely at what may happen after transcription of an ORF into RNA. As the introns are removed, the exons may be assembled in a variety of different ways, sometimes thousands of ways, producing different RNA sequences and ultimately distinct proteins (alternative splicing). Moreover, in some of these alternative splice products exons may be deleted as well as introns. Finally, there are cases of transplicing, in which transcripts from different ORFs are joined together. So an ORF may provide the information for a large number of proteins, and not all parts of it need provide the information for the same set….

“Partially overlapping sets of sequences will provide information for different sets of proteins.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 57.

“Life is a hierarchy of processes, and larger scale processes, lineages, both shape and are shaped by the smaller scale processes that constitute them.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 60.

“I do not think there is a determinate number of levels in nature or that all entities belong to a specific level. Is the circulatory system an organ, or a level intermediate between the organ and the organism comprising an assembly of organs (such as the heart and the arteries) and stuff (the blood)? Do such stuffs as blood or lymph belong in the hierarchy at all?” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 66.

“So life, I claim, is composed of a multitude of mutually sustaining processes at a range of spatial and temporal scales.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 66.

“Both organisms and lineages exist because they are stable, and their mutually conditioned stability is what evolution makes possible.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 68.

“Life has found a quite different [from machines made of parts], perhaps better, way of being stable. First, by regeneration and self-repair of parts, some organisms can live for very long times, some plants for thousands of years. But second, by virtue of the nested hierarchy of living systems, life itself is stable over billions of years. The human lineage, like all others, goes back several billion years. This stability is made possible by a hierarchy of processes – evolutionary, developmental, metabolic, and so on. Their contribution to stabilisation and, in the case of organisms, reproduction, looks inescapably teleological as it seems designed to maintain some element of the system or hierarchy. But this is just how stabilisation works in a world of process. So, ultimately, nothing but the survival of the stable is required to explain the emergence of a living world with all the extraordinary purposiveness of our own.” Dupré, John. 2021. The Metaphysics of Biology. Cambridge UP. p. 68.

“And that is what we have with the mutant Arabidopsis [a small plant, a weed, that is the equivalent of the fruit fly as model organism among plants]. A protein that is normally present and active is absent and therefore not active. The genetic approach allows you to break the system one gene at a time. So, if you take out the protein that makes the plant able to convert carlactone to carlactonoic acid, then you end up with a plant where almost all meristems activate to produce branches [to thus produce a bushy plant]….

“The most useful way of conceptualising what is going on, in my view, is to understand this Arabidopsis system as a series of dynamic, self-organising, feedback-driven systems, operating at different scales….

“At the cellular level: there is a compound derived from carlactonoic acid acting as a signal, that is decoded by a signal transduction pathway. Through the action of this pathway, the carlactonoic acid derivatives, called strigolactones, are adjusting the levels of a small family of proteins. These proteins, among other things, are regulating the allocation of yet another family of proteins onto the membranes of cells in the plant, and these proteins are catalysing the export of a different compound, called auxin, out of cells. The amount of auxin inside the cells (which is now changing because of the presence of this transporter protein on the membrane) itself depends on several things. And the amount of auxin, working through different signal tranduction pathways, is able to adjust the amount of carlactonoic acid and hence strigolactone. So, you can think of this cell-level network as a dynamic self-organising system of interacting molecules. This system is sensitive to both local and systemic inputs, and is therefore equilibrating, or shifting between equilibria, with different dynamics in different circumstances.

“At the meristem tissue level: shoot meristems at the tip of growing shoots build the plant, producing stem beneath them and leaves at their flanks. You can think of this meristem as a dynamic self-organising system of cells, which is also sensitive to local and systemic inputs….

“At the plant level: each growing meristem exports auxin, which is transported down the plant and influences the activity of other meristems in the shoot. These interactions are also continuous and dynamic, so that if you prune away the leading shoot, removing it as an auxin source, buds further down the stem activate to produce branches, which in turn export auxin into the rest of the plant and prevent more buds from activating….

“This gives stacks of regulatory networks, or architectures, that are operating at different scales. Those scales all link together. They are not really separate or distinct, but thinking about them in that way is instructive for understanding how the system works.” Leyser, Ottoline & Harris Wiseman. 2020. “Integrative Biology: Parts, Wholes, Levels and Systems.” pp. 17-32. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 24, 25, 26.

“‘Reduction is the idea … that physics is the theory of everything.’” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 38; subquote from: Nagel, Thomas. 1998. “Reductionism and antireductionism.” In: Bock G.R. & J.A. Goode (eds). The Limits of Reductionism in Biology. Novartis Foundation Symposium, 213. pp. 3-14. John Wiley and Sons. p. 3.

“The Vienna Circle never quite achieved its aims in full. Its leader, Moritz Schlick, was murdered by a student in 1936 and the Anschluss of Austria in 1938 sent many of its main members into exile. However, just in time, the ideas of the Vienna Circle had entered the English-speaking world through the publication of A.J. Ayer’s Language, Truth and Logic in 1936, probably the nearest thing to a bestseller that philosophy has ever seen. It is therefore unsurprising that in molecular biology, Francis Crick’s reductionism seems to be sung straight from the logical positivist hymn sheet: ‘The ultimate aim of the modern movement in biology is in fact to explain all biology in terms of physics and chemistry.’” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 38-9; subquote: Crick, Francis. 1966. Of Molecules and Men. Seattle: U of Washington Press. p. 10.

“In a simple physical system – an infinite class [many objects of same, simple type] – there are sufficiently few quantum states that they can be averaged. In a complex biological system – a finite class [complex molecules with many different possible states] – there are so many that no average may be obtained. There is therefore no causal connection between the microscopic and macroscopic worlds for biological objects.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 42.

“For Elsasser, biology was the science of the complex, and therefore is a superset of all the other sciences which deal with subject matter of greater regularity than the messy stuff of biology. Chemistry and physics are subsets of ‘biology’ (as Elsasser conceived it), activities that commence when we start to refine our area of study down to the molecular and atomic level – they are simply the areas of ‘biology’ where determinism and causality apply.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 42-3; reference: Elsasser, W.M. 1969. “Acausal phenomena in physics and biology: A case for reconstruction.” Am Sci. 57(4): 502-16.

“The centrepiece of Rosen’s critique of reductionism is the [M/R] system – standing for Metabolism/Repair. [M,R] is a small self-referential network of four components, three of which act functionally within the network. It may be interpreted as a biochemical pathway with four moieties and three steps, in which the each of the final three moieties are also catalysts for a unique step. This toy system was the subject of a mathematical demonstration that it was not possible to predict the properties of its entirety through an analysis of the properties of its individual components. [M,R] is therefore not reducible to its component parts and can only be understood as a whole.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 43-4; reference: Rosen, Robert. 1991. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Allen, T. & D. Roberts (eds.) Columbia UP.

“Rosen’s anti-reductionism was explanatory. Irreducibility is a property independent of the size of the thing that cannot be reduced. [M,R], he claims, simply cannot be explained using a reductionist approach.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 44-5.

“Break [M,R] down into its component individual steps and these are then in the domains of ‘physics’ or ‘chemistry’. However, what we can say mathematically about the behaviour of the component parts, cannot be subjected to any additive process that will allow us a complete mathematical description of the whole.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 45.

“Rosen also ventured that [M,R] could have a more general interpretation. As well as representing a single self-referential network, the component parts could be taken to represent sets of reactions in living things. For instance, the first step could represent not just one, but all, metabolic reactions, the second and third steps sets of other reactions necessary to ensure that metabolism can continue – hence the Metabolism/Repair name. Pursuing this set-oriented interpretation of [M,R], Aloisius Louie has described its components in terms of formal set algebra. Louie’s central result from this analysis is the identification [of?] the presence of an impredicative set within [M,R], meaning a set that is member of itself. Impredicative sets are non-computable on a Turing machine, which remains the basic conceptual architecture of all computers. By implication, no complex system and no biological system can therefore be fully functionally modelled in silico.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 45; reference: Louie, Aloisius. 2009. More that Life Itself: A Synthetic Continuation in Relational Biology. Frankfurt: Ontos Verlag.

“Neo-reductionism proposes that physics provides the description of the molecular order of a system – its micro-state – whereas ‘engineering’ explanations refer to supr-molecular configurations of that system – its macro-state….

“… neo-reductionism sees the universe as consisting of a micro-space, its objective atomic/quantum physical reality, and a macro-space, which is the configuration of larger order entities studied by all the other sciences, and which is supervenient on the micro-space. Interestingly, Elsasser had already outlined a similar concept as part of his anti-reductionist argument. His concept of variostability refers to the tendency of a macro-state of a system to remain coherent in the presence of micro-state variation.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 47-9; reference: Elsasser, W.M. 1998. Reflections on a Theory of Organisms: Holism in Biology. Johns Hopkins UP.

“Robert Rosen had stern words for reductionists on the subject of modelling, making a distinction between a true model and a mere simulation. Imagine an attempt to build a piece of software to represent a biochemical network. No matter how accurate the representation of the entities of the system may be, they are only in a model sensu stricto if the rules that connect them and govern their behaviour are also accurate representations of the laws of the natural world. Otherwise the software is a simulation. The entailment structure – the framework of rules that govern how bits of the system interact – of a true model faithfully represents the corresponding entailments of the thing being modelled. Failure to do so will generate a black box, a simulation which may be very good at predicting the output given a set of inputs, but which does not represent any true understanding of the system. Simulations are merely ad hoc black box predictors of the phenomenological behaviour of whatever they simulate.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 50.

“Should the relevant parts of chemistry be disproved, the reductional chain will be broken, and the biology will require to be re-reduced to the new physics or chemistry. Previous satisfactory reductions may suddenly become invalid in this way, and reduction must always therefore be considered to be provisional. However, just as a previous reductive chain may be broken by changes in the underlying theory, so may reduction become possible where before it was not. Anti-reductionist declarations must always be provisional too. Ernest Nagel points out that chemistry is only reducible to post-1925 physics, and thermodynamics is only reducible to post-1866 statistical mechanics. In both cases it was advances in the lower theory (physics) that enabled the reduction, not any new insight into chemistry or any improvement in reductionist method.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 51; reference: Nagel, Ernest. 1960. “The meaning of reductionism in the natural sciences.” In: Danto, A. and S. Morgenbesser (eds). Philosophy of Science. pp. 288-312. Cleveland: Meridian.

“Neo-reductionism avoids Rosen’s strictures regarding modelling and simulation, not by merely adopting the biological principle of reduction and/or conceding that reductions can remain provisional, but by replacing modelling with realisation. Neo-reductionism’s concept of a non-unique macro-space to micro-space supervenience relationship implies that it is more important to understand how micro-space variation affects that of macro-space than to model the macro-space on the micro-space. In other words, the question becomes how a macro-space is realised upwards from its underlying micro-space, rather than how to reduce/model downwards from macro-space to micro-space….

“Modelling a system is therefore less important than the question of whether the system behaves similarly to a known automaton, i.e. realisation.

“For neo-reductionism, systems biology is labouring under the weight of the modelling problem, whereas it ought to be recasting itself in terms of the realisation problem. The modelling problem founders both on the sheer scale of the data… and also potentially on the hidden problems of self-referential systems – if Rosen is correct, it cannot counter explanatory anti-reductionist arguments either. Even leaving Rosen aside, it is evident that the modelling problem is the problem of data increasing faster than the conclusions we can draw from it – a problem of where to end. The realisation problem, by contrast, is one of where to start.” Gatherer, Derek. 2020. “Modelling versus Realisation: Rival Philosophies of Computational Theory in Systems Biology.” pp. 33-57. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 51-3.

“Secularised biology has tended to encourage metaphysical materialism, ontological atomism (in which organisms are seen as assemblies of parts), theoretical reductionism, and an abiding hope that we can use genetic engineering to cure ‘inborn errors of metabolism’ and devise bio-enhancements that will put humans, or at least some of them, in the driver’s seat of evolutionary advance, an ambition often figured as humans taking God’s place.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 93.

“Fisher’s ‘fundamental principle of natural selection’, together with several other ways in which gene frequencies can shift in populations – in particular, genetic drift, or chance fixation of genes in small populations, and gene flow from one population to another by migration – constitutes the probabilistic heart of the Modern Evolutionary Synthesis…. The Synthesis treats evolution as change in gene frequencies in Mendelian populations: populations open to genetic exchange at the reproductive instants that tie one generation to another. Organisms develop, the Synthesis says, but don’t evolve; populations evolve but don’t develop…. The benefits of understanding the dynamic relationship between environment, organism, and gene from the level of statistically and probabilistically describable populations outweighed any direct connection between development and evolution.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 96; reference: Fisher, R.A. 1930. The Genetic Theory of Natural Selection. Oxford UP.

“Emphasising unity disguised differences … between two long-lived research projects to which the Synthesis quickly gave rise.

“One of these projects, ‘population ecology’, was devoted to proving that traits previously used as species markers because they were assumed to be adaptively neutral (and hence stable enough to construct typological classifications) are actually adaptations that reflect the exigencies of particular environmental circumstances. By contrast, what I will call the ‘speciation project’ used the reform of systematics it shared with population ecologists to explore how Mendelian populations evolve genetic barriers to reproducing, how new species radiate biogeographically, and how higher taxa evolve.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 97.

“Adaptationism has roots in suggestions by a group of religious thinkers at Oxford University in the early 20th century that adaptation by natural selection updates rather than contests Paley’s argument from design…. …natural selection is a law of nature that serves as vicar for God’s creative act, a view still asserted by many religious evolutionists.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 98.

“As adherents to the Synthesis, speciationists did not invoke development as an explanation of evolution, but neither did they entirely lose sight of the fact that natural selection has evolutionary import only when organisms are viewed developmentally. The dynamic responsiveness of genomes to environmental change over trans-generational time can be adaptive only if it is mediated by ontogeny in each generation. ‘The organism is not specified by its genes’, writes Lewontin, ‘but is a unique outcome of an ontogenetic process that is contingent on the sequence of environments in which it occurs’. When genes are viewed as resources for development, the influence of one gene is always relative to the changing influence of others, so much so that Lewontin regarded the entire genome as the least unit of selection (on genes as developmental resources).” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 101; subquote: Lewontin, R.C. 1974. “Organism and environment.” In: Plotkin, H. (ed.) Learning, Development and Culture: Essays in Evolutionary Epistemology. pp. 151-170. NY: John Wiley and Sons. p. 20.

“To be sure, speciationists are adherents of the Modern Synthesis. They do not regard development as evolution in miniature. But that doesn’t mean that they do not see organisms as ecologically embedded developmental systems.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 102.

“The perception of substantial solidity that Aristotle was the first to stress and to contrast with non-substantial artefacts arises from misdescribed differences between the timescales of processes that unfold at different rates at different hierarchical levels of organic structuration. ‘A cell persists far longer than any of its molecular constituents’. Similarly, an organism is longer lived than any of its cells, whose metabolic turnover is much more rapid. In turn, a species lasts longer than an organism, but not as long as the clade to which it belongs.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 103; subquote: Dupre, J. & Nicholson, D.J. 2018. “Toward a processual philosophy of biology.” In: Nicholson, D.J. & J. Dupre (eds). Everything Flows. Oxford UP. p. 13.

“Hence natural selection is conceived as design without a designer, a conceit that, as I have already remarked, is complicit enough with the intelligent design creationism it opposes to have provoked ardent protestations of atheism from defenders like Dawkins.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 105.

“… genocentric versions of Darwinism draw heavily on the molecular revolution in genetics that got underway in the 1950s. But it is equally true that genocentrism gave molecular biology an evolutionary theory. It needed one. Molecular biology came out of biochemistry. Its adepts had little awareness of the Modern Synthesis, the background of which is natural history, and to the extent that they knew about it they were typically indifferent or hostile to it.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 105.

“Reformulating the study of evolution in terms of process ontology will, I believe, liberate the submerged developmentalism of speciationists. It will also lead to better interpretations of what we know about adaptation by freeing it from design thinking, which in seeing organisms as passive things rather than active processes misses development as the locus of evolution.” Depew, David J. 2020. “Organisms, Development, and Evolution: Invitation to a New Understanding.” pp. 91-115. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 111.

“Next, we should note that the processes studied within each of these historically-oriented disciplines have their origins in other, related scientific fields. Cosmology depends on the physics of fluids, energetic reactions and gravity; geology depends on various aspects of materials science; archaeology depends on diverse scientific theories in chemistry, biology, ecology, sociology and so on. So, what does the study of evolution depend on? Where do the various strands of evolutionary science find their home? We suggest that the scientific habitat for the web of evolutionary studies is the field of ecology….

“The environment is the context within which natural selection takes place, giving direction to the selective forces. Which animals happen to meet each other, which seeds land in proximity, which hapless individuals are washed or blown away – such random happenstances as these play a part in the overall course of evolutionary change. And ecology, as we have seen, is the science that seeks order in the juxtapositions and encounters, the accidents and serendipity, as they occur to living organisms.” Gunton, Richard & Francis Gilbert. 2020. “The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense Except in the Light of Ecology’.” pp. 189-211. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. pp. 202, 203.

“Ecology is the crucial context for thinking about evolution because the characteristics of living organisms can only be interpreted in the context of their lives in some environment or other.” Gunton, Richard & Francis Gilbert. 2020. “The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense Except in the Light of Ecology’.” pp. 189-211. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 204.

“Evolutionary ecology is the study of how natural selection actually happens. It examines patterns in birth, reproduction and death rates: how it is that organisms do better or worse in the struggle for existence in terms of their heritable traits.” Gunton, Richard & Francis Gilbert. 2020. “The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense Except in the Light of Ecology’.” pp. 189-211. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 206.

“Traits, moreover, are in general the features of organisms that must be referred to in any account of ecological interactions concerning individuals.” Gunton, Richard & Francis Gilbert. 2020. “The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense Except in the Light of Ecology’.” pp. 189-211. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 208.

“To Dobzhansky’s famous adage, therefore, we should add that nothing in evolution makes sense except in the light of ecology, and in particular the ecology of species’ traits. Ecology, in turn, makes no sense apart from an understanding of the organismal and cellular fields of biology that account for the structures and functions of organisms which are manifested as traits.” Gunton, Richard & Francis Gilbert. 2020. “The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense Except in the Light of Ecology’.” pp. 189-211. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 209.

“[Corners of a three-way, circular interdependence] Laws of ecology, functional context: selection on traits. Relationships of evolution, historical context: origins of traits. Structures of biology, structural context: production of traits.” Gunton, Richard & Francis Gilbert. 2020. “The Reintegration of Biology, or ‘Nothing in Evolution Makes Sense Except in the Light of Ecology’.” pp. 189-211. In Rethinking Biology: Public Understandings. Reiss, Michael J., Fraser Watts & Harris Wiseman. (eds). World Scientific. p. 209.

“More succinctly, metabolism-first approaches are cast in term of physics (e.g., matter, energy, forces), and genetics-first cast in terms of the copying of information. These physical and informational perspectives are traditionally treated as two parallel, but distinct, narratives for describing living systems. A challenge in unifying these approaches is that the concept of information–which relies on the existence of counterfactuals–is not easily reconciled with describing physical systems, whose dynamics are typically described by an initial state and deterministic laws. The counterfactual nature of information is evident when one considers that for a message to carry information, a different message must also be possible.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. pp. 424-5.

“Within this proposed framework [where the emergence of top-down information flow represents an evolutionary transition in information], the debate between genetics-first and metabolism-first scenarios takes on a new dimension: both may be unified under a common information-based descriptive paradigm, where genetics may be thought of in terms of digital information processing and metabolism roughly as a form of analog information processing.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 425.

“Collapsing genetic information and catalytic function to the same molecule introduces a paradox. If genotype (genetic information) and phenotype (catalytic function) are encoded in the same molecule, there is an inherent chemical trade-off between genotypic (selection for replication) and phenotypic (selection for function) selection. For example, well-folded RNA sequences are likely to be poor templates for copying, conversely poorly folded RNA sequences are unlikely to be good ribozymes (catalytic RNAs). This trade-off imposes a physical limit on the information content of primitive genomes. This physical constraint imposed on information content should be viewed in contrast with the more widely discussed informational limits of early replicators, defined by Eigen’s ‘error threshold’ as the maximum amount of genomic information that can be reliably propagated from generation to generation for a fixed mutation rate. Both the informational limit(s) on physical systems and the physical limit(s) on informational systems are important factors shaping biological evolution.

“Modern life has overcome the chemical limitations imposed on template-based replication through the decoupling of selection for replication from selection for function. In effect, this amounts to physically separating information propagation (replication) from the processing of that information (function). Life achieves this decoupling by utilizing two species of biopolymer that play different biochemical roles: DNA stores genetic information and proteins execute the majority of catalytic and structural functions.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 426.

“Trivial replicators are constrained by strict physical limits imposed on their capacity to generate copies, such as the chemical trade-off between templating ability and catalytic function imposed on an RNA genome encoding RNA catalysts. In contrast, non-trivial replicators – also commonly referred to as reproducers–have in some sense transcended many of these constraints due to the explicit use of programs, symbolic logic and codes to mediate self-reproduction. Non-trivial replicators require constructors, defined as entities that can cause some change in a physical system while retaining the ability to cause it again. Examples of constructors include heat engines and chemical catalysts.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 427.

“Szathmary and Maynard Smith, for example, have offered a classification scheme that distinguishes the complexity of replicators based on hereditary potential. They identify limited heredity replicators as those where the number of types is smaller than, or roughly equal to, the number of individuals in a realistic physical system (i.e., short oligonucleotides). Alternatively, unlimited heredity replicators are identified as those where the number of types far exceeds the number of individuals that could possibly exist in any realistic system (i.e., genes and genomes of extant life). By definition, only unlimited heredity replicators allow the potential for unlimited growth in complexity: unlimited heredity replicators occupy a vast state-space (much larger than anything physically achievable)….” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 427.

“The limited/unlimited heredity classification scheme distinguishes replicators based on the total number of all possible states of the chemical substrate, whereas the trivial/non-trivial classification scheme distinguishes replicators based on the number of physically accessible states due to the presence of constructors. Living systems are members of the class of non-trivial replicators with virtual constructors, and are capable of unlimited heredity.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 428.

“ Trivial Non-trivial [reproducers]
“Limited heredity short oligonucleotides such physical constructors such as
as non-enzymatic template catalysts and autocatalytic
replicators, crystals sets
“Unlimited heredity monomolecular genes and virtual constructors such as
genomes such as would exist the cellular operating system
in RNA-world riboorganisms of extant life and von
Neumann automata”
Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 428.

“A relatively simple example of top-down causation is the three-dimensional folding of an RNA molecule. The global constraint imposed by the network of structural interactions between residues causes the molecule to acquire a specific three-dimensional conformation.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 429.

“In top-down causation by information control, a higher hierarchal level influences lower level entities to achieve a specific functional outcome (goal) through the use of feedback control loops. Feedback control depends on the flow of information through the system, where information on the system’s current state is evaluated relative to a particular functional outcome. Top-down causation by information control thereby presents a framework for understanding how information–an abstraction–can play a causally efficacious role in biological systems.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 430.

“It is important to note that while information is abstract, in the sense that it involves one entity symbolically representing another, it is nonetheless physical and only exists when physically instantiated (it therefore holds similar ontological status to energy).” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 430.

“Convergent evolution thus provides a clear example of top-down causation via adaptive selection, where causal influences run from macroscopic environmental context to microscopic biochemical structure.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 430.

“Top-down causation operates through functional equivalence classes. Functional equivalence occurs when a given ‘higher-level’ state leads to the same high-level outcome, independent of which ‘lower-level’ state instantiates it. Equivalence classes are defined in terms of their function, not their particular physical instantiation: operations are considered (functionally) equivalent (i.e., in the same equivalence class) if they produce the same outcome for different lower-level mechanisms. Functional equivalence classes therefore represent the physical manifestations of virtual constructors. Functional equivalence is evident, for example, in the case of convergent evolution presented above, where convergence occurs because natural selection optimizes a functionally equivalent outcome (in this case, echolocation).” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. pp. 430-1.

“Life may be defined as a self-reproducing system that functions via top-down causation by adaptive selection and information control.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 431.

“Hallmarks of Life[:]
“Global organization
“Information as a causal agency
“Top-down causation
“Analog and digital information processing
“Laws and states co-evolve
“Logical structure of a universal constructor
“Dual hardware and software roles of genetic material
“Non-trivial replication
“Physical separation of instructions (algorithms) from the mechanism that implements them.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 432.

“The prominent role of top-down causation in extant life suggests that many of the transitions in the complexity of chemical reaction networks leading to life’s emergence may be characterizable as transitions in informational and causal architecture.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 433.

“The notion of functional equivalence is closely related to that of biological modularity, where module is a separable functional unit within a biological network. Modules may be replaced by other members of their functional equivalence class without affecting the global network structure.” Walker, Sara I. 2014. “Top-Down Causation and the Rise of Information in the Emergence of Life.” Information. 5:424-439. doi:10.3390/info5030424. p. 435.

“Five essentially different classes of top-down influence can be identified, and their existence demonstrated by many real-world examples. They are: algorithmic top-down causation; top-down causation via non-adaptive information control, top-down causation via adaptive selection, top-down causation via adaptive information control and intelligent top-down causation (the effect of the human mind on the physical world).” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 126.

“An equivalence class identifies all lower level states that correspond to the same higher level state. For example, billions of different micro-states will correspond to the same higher level state of a gas, as characterized by its temperature, pressure and density…. … numerous different molecular configurations give the same functional state of a neuron in a human brain.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 128.

“Algorithmic top-down causation occurs when high-level variables have causal power over lower level dynamics through system structuring, so that the outcome depends uniquely on the higher level structural, boundary conditions and initial conditions. The lower level variables determine the outcome in an algorithmic way from the initial and boundary conditions (for example, the software loaded in a computer) as a consequence of the structural relations (for example, the wiring in a computer or interconnections of neurons); changing these conditions leads to different lower level events and dynamical outcomes. Provided the lower level interactions mesh together in a coherent way, the constrained operation of lower level forces, operating in a law-like/algorithmic way, leads to reliable higher level behaviour whose outcome depends on the nature of the constrains and initial conditions….

“An excellent example–indeed the present day canonical one–is digital computers; the low-level gates and transistors act in accord with the data and program loaded (word processor, music program, image processing program, etc.), which is a high-level concept whose structure and function cannot be explained in lower level terms. The hardware and software are each hierarchically structured in a symbiotic way so as to allow this higher level functionality.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. pp. 128-9.

“top-down causation via non-adaptive information control.

“In non-adaptive information control, higher level entities influence lower level entities, so as to attain specific, fixed goals through the existence of feedback control loops, whereby information on the difference between the system’s actual state and desired state is used to lessen this discrepancy. Unlike the previous case, the outcome is not determined by the boundary or initial conditions; rather it is determined by the goals, indeed the whole purpose of such systems is to make initial conditions irrelevant. A different outcome will occur if the goal is changed. Thus, the nature of causality is quite different than the previous case, when feedback control systems are guided by goals, which are higher level entities….

“An excellent example is a thermostat….” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 129.

“top-down causation via adaptive selection.

“Adaptive processes take place when many entities interact, for example the cells in a body or the individuals in a population, and variation takes place in the properties of these entities, followed by selection of preferred entities that are better suited to their environment or context. Higher level environments provide niches that are either favourable or unfavourable to particular kinds of lower level entities; those variations that are better suited to the niche are preserved and the others decay away. Criteria of suitability in terms of fitting the niche can be thought of as fitness criteria guiding adaptive selection…. A different lower level structure will result if the higher level context is changed.

“Thus, this is top-down causation from the context to the system. An equivalence class of lower level variables will be favoured by a particular niche structure in association with specific fitness criteria; if the top-level conditions change, the outcome will change. Unlike feedback control, this process does not attain pre-selected internal goals by a specific set of mechanisms or systems; rather it creates systems that favour the meta-goals embodied in the fitness criteria. This is an adaptive process rather than a control process….

“Darwinian evolution is a specific example….” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 129.

“A key feature of the biological world is that similar processes of adaptive selection take place not only on evolutionary time scales, but also on developmental and functional timescales….” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 130.

“top-down causation via adaptive information control.

“Adaptive information control takes place when there is adaptive selection of goals in a feedback control system, thus combining both feedback control and adaptive selection. The goals of the feedback control system are irreducible higher level variables determining the outcome, but are not fixed as in the case of non-adaptive feedback control; they can be adaptively changed in response to experience and information received. The overall process is guided by fitness criteria for selection of goals….

“The classical example is associative learning in animals, such as Pavlovian conditioning: an animal responds to a stimulus such as a sound, which is taken as a sign of something else and causes physical reactions implemented by motor neurons. The training is causally effective by top-down action from the brain to cells in muscles. The fitness criterion is avoidance of negative stimuli; change of the associated goals (through a change in the environment) results in change of behaviour.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 130.

“intelligent top-down causation (i.e. the effect of the human mind on the physical world).

“Intelligent top-down causation is the special case of feedback control with adaptive choice of goals where the selection of goals involves the use of symbolic representation to investigate the outcome of goal choices. Here, a symbolic system is a set of structured patterns realized in time or space, that is arbitrarily chosen by an individual or group to represent objects, states and relationships….

“Example: aircraft design. Plans for a jumbo jet aircraft result in billions of atoms being deployed to create the aircraft in accordance with those plans. This is a non-trivial example: it costs a great deal of money to employ experts in aerodynamics, structures, materials, fuels, lubrication, controls, etc., to design and then to manufacture the aircraft in accordance with those plans….

“Example: the value of money….

“Example: roles, expectations and values.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. pp. 130, 131.

“The last three classes of top-down causation are all examples of complex adaptive systems.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 131.

“Adaptive selection can accumulate structure and information by selecting a subset of entities from a set of many variants….

“This is an analogue of Maxwell’s demon… Darwinian selection in effect envisages a macro demon who acts down to the molecular level to select a specific sequence encoding desirable genetic information from an ensemble of nucleic acids. This again enables a local violation of the second law.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 132.

“The key point about causality in real-world contexts, then, is that simultaneous multiple causality (interlevel, as well as within each level) is always in operation in complex systems. Claiming that any specific single cause is the only causation in action is fundamentally misleading, as it ignores the complex nature of the real causal web.” Ellis, George. 2011. “Top-down causation and emergence: some comments on mechanisms.” Interface Focus. 2:126-140. doi:10.1098/rsfs.2011.0062. p. 133.

“Although an integrated theory of the various instances of SO [self-organization] has yet to be built, commonalities among the models and empirical examples that have been explored indicate that the potential for emergence of SO dynamical structures exists wherever there are sufficiently concentrated spatial gradients in free energy. This potential is called a voltage when dealing with electrical energy, but the same concept applies to free energy in any form. The function of the SO system is to channel the flow of energy across the gradient, thus reducing the steepness of the gradient. The structure and function of the SO system is both created and sustained by extracting work from the free energy differences as energy flows through the channel provided by the SO system. Thus, for example, the plasma channel of a lightning strike is created by the pressure to relieve dielectric stress on the atmosphere, formed through charge transport in convective storms.” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. p. 1788.

“Specific heat is the property that makes a spinning earth into a heat engine, transferring energy not only across spectral bands but also from the sunny to the dark side.” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. p. 1789.

“The transduction of sunlight not only makes photosynthetic life possible, but also it appears to have stabilized its core chemistry even in the face of major shocks to planetary ecosystems, such as those resulting in recurring mass extinctions. This universally known but underemphasized fact suggests that photosynthesizing life is a statistically favoured component of the biosphere, or that a high-flux channel for light transduction is a favoured endpoint, towards which perturbed ecosystems recover.” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. p. 1789.

“… NS [natural selection] maximizes fitness whereas SO maximizes (for example in certain ecologies) the rate of energy flow across a gradient. However, these criteria overlap far more than is superficially apparent. For example, both fitness and the channelling of energy flow require consumption of energy and the extraction of work to create structure and function. It is entirely consistent with both theory and observations in ecology and evolution that NS would generally result in more effective energy processing at any level of biological organization (the cell, multicellular organism, population, ecosystem), so it seems plausible that the maximization criteria of SO and NS are at least highly complementary.” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. p. 1789.

“Salthe has suggested that nonliving SO systems, like atmospheric convection cells and vortices, also tend to exhibit birth, senescence and death, but reproduction is a less critical aspect of these systems in which birth through spontaneous generation is more common; therefore, persistence of the phenomenon of weather is not as dependent on reproduction as the phenomenon of life…. In comparison, the ability of weather structures to increase in complexity and efficiency is very limited….” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. p. 1790; reference: Salthe, S.N. 1993. Development and Evolution: Complexity and Change in Biology. MIT Press.

“Each species plays a particular role in a functioning ecosystem, and evolution is constrained by NS to maintain the coordination of the system as a whole. For example, the study of food web architectures shows that NS in coevolutionary setting prevents the evolution of communities composed entirely of predatory species, and a flourishing community of primary producers inevitably attracts or generates grazers, then predators and so on. Thus, NS is a mechanism that coordinates the coevolution of populations so as to promote homeostasis and efficient energy processing at the ecosystem level. The dynamical maintenance of ecosystem structure allows ecosystems themselves to adjust adaptively to changes in their environments, such as would occur through global climate change. This could be described as the adaptability of an ecosystem, because it does not involve competition among ecosystems. Ultimately, NS in the context of coevolutionary systems serves as a mechanism that coordinates the internal dynamics of ecosystems in a way that maximizes the capture and processing of solar energy.” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. pp. 1790-1.

“We submit the conjecture that NS is no more and no less than any other thermodynamic process and that all emergent processes (e.g. convection) are the equivalent of cryptic (some more cryptic to our eyes than others) thermodynamic games resulting in the higher order processing of fuel (gradients).” Hoelzer, G.A., E. Smith & J.W. Pepper. 2006. “On the logical relationship between natural selection and self-organization.” Journal of Evolutionary Biology. 19:1785-1794. doi:10.1111/j.1420-9101.2006.01177.x. p. 1792.

“An example [of evolutionary transitions with a change in the way information is stored] is the origin of epigenetic regulation, whereby heritable states of gene activation lead to a potentially exponential increase in the amount of information that may be transmitted from generation to generation (since a set of N genes, existing in two states – on or off – via epigenetic rearrangements, can have 2N distinct states). Such a vast jump in the potential information content of single cells is believed to have led to a dramatic selective advantage in unicellular populations capable of epigenetic regulation and inheritance. The reasoning is straightforward: epigenetic factors permit a single cell line with a given genotype to express many different phenotypes on which natural selection might act, thereby providing a competitive advantage through diversification. Importantly, this innovation was crucial to the later emergence of multicellularity by permitting differentiation of many cell types from a single genomic inventory.” Walker, Sara Imari, Luis Cisneros & Paul C.W. Davies. 2012. “Evolutionary Transitions and Top-Down Causation.” Artificial Life. 13:283-290. doi.org/10.7551/978-0-262-31050-5-ch038. p. 283.

“Because of their high degree of interconnection, systems of interacting proteins act as neural networks trained by evolution to respond appropriately to patterns of extracellular stimuli.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 307.

“In principle, any protein that transforms an input signal into an output signal could act as a computational or information-carrying element. Thus an enzyme in a biochemical pathway ‘reads’ the concentration of its substrate and produces a corresponding level of product…. Simple enzymes and receptors generate a monotonic relationship between input and output, which saturates as the concentration of substrate or ligand rises. A more abrupt and switch-like performance is shown by many proteins, typically those composed of multiple subunits, where interactions between subunits cause the rate of enzyme reaction or ligand binding to rise steeply in sigmoidal fashion over a limited range of concentration.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 307.

“The action of a protein kinase may also be made more complex if it works back on itself to phosphorylate its own amino acids. Proteins that show this intramolecular feedback sometimes appears [sic] to act as an irreversible switch….” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 307.

“These phosphorylated tyrosines are subsequently recognized by other proteins in the cytoplasm which bind to the sequence containing the modified tyrosine and hence change their own activity. In this way, information that the cell has encountered a specific hormone or growth factor is distributed along multiple divergent paths.

“Phosphorylation also provides the basis of integration whereby a single protein combines multiple inputs to produce a single output in a manner analogous to the integration by a nerve cell of multiple synaptic inputs.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 307.

“Living cells contain an enormous diversity of protein structures and the signals they carry are not limited to the binding of molecules or covalent modifications. Thus many proteins take as their ‘input’ contact with a macromolecule such as another protein or a molecule of DNA or RNA. Proteins are also known that respond specifically to light, to temperature, mechanical forces or voltage. The ‘output’ of a protein is just as diverse, and may be the formation of a macromolecular structure, the generation of a physical movement or production of light. Each input/output relationship is kinetically distinct, usually non-linear, and often extremely rapid.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 308.

“Two of the most common responses of living cells to external stimuli are amplification and adaptation. Amplification enables a cell to transform faint and ephemeral stimuli into substantive biochemical changes: adaptation enables it to measure relative rather than absolute changes and hence respond over a wide range of input stimuli.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 311.

“The imprint of the environment on the concentration and activity of many thousands of molecules of the cell is in effect a memory trace. In contrast to the permanent information encoded in DNA, however, it is a ‘random access memory’ containing ever-changing information about the cell’s surroundings.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 312.

“Because proteins also integrate inputs and produce outputs it seems inescapable that the highly interconnected network of protein-based pathways in living cells will share some of the properties of neural nets…. Responses of this protein-based neural network may be expected to be robust and resistant to damage. The training of the network, which in the case of a computer-based network is achieved through the presentation of a training set of examples, would, in the case of living cells, be achieved by a darwinian process of random change and selection….

“Curiously, in one respect the mathematical formalism of artificial neural networks is a more accurate approximation for networks of protein molecules than for networks of real neurons. The processing of electrical signals by a nerve cell is considerably more complex than the static sigmoidal nonlinearity of individual allosteric proteins. Many other features of biochemical signalling pathways, however, have no counterpart in most conventional computer-based neural networks. Thus the architecture of the cytoplasmic network lacks well-defined boundaries, and individual units are not all equivalent in performance. The timescales of interactions between ‘units’ also varies enormously.

“Arguably, the most important defining characteristic of protein-based neural networks is that they are governed by diffusive processes.” Bray, Dennis. 1995. “Protein molecules as computational elements in living cells.” Nature. 376:307-312. p. 312.

“Whereas weather is a diffuse phenomenon primarily involving mass transport and physical state change, life creates transport channels in the chemical domain, employing the more concentrated energy flows associated with molecular re-arrangements.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 52.

“All self-sufficient ecosystems are by definition autotrophic, while only some organisms are.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 52.

“Within core metabolism, we recognize two major categories of function, Anabolism comprises the set of reactions that build organic compounds, while catabolism is the breaking down of organic compounds for energy or materials. Anabolism is essentially a reductive process, meaning that it consumes energy-rich electrons to create molecular bonds.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 53.

“Catabolism is associated with organization into ecosystems, in which heterotrophs consume other organisms or products thereof, and break down their organic molecules for energy or biologically available nitrogen or carbon. Catabolic reactions appear to function as support for anabolism, providing the same inputs as those used by reductive autotrophs but not changing the essential anabolic reaction network.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 53.

“Organisms that are photoautotrophic, obtaining energy from sunlight, have also come to store organic molecules and to access them catabolically.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 53.

“Only the anabolic core of intermediary metabolism is truly universal, existing in the same form in all ecosystems. Catabolic strategies vary among ecosystems and can be almost absent in communities of chemo-autotrophs.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 53.

“The anabolic network is dense, and leaves no energetic waste products. Said another way, core metabolism converts all carbon from a fully oxidized abiotic input (CO2), either into its most reduced form (methane), or into constituents of biomass such as the fatty acids, sugars, amino acids, nucleotides, and cofactors, which then provide the platform for further metabolism. This feature would also be expected of a network that was driven into existence by pressures to transfer electrons from high-energy to low-energy bonds, and to return phosphate from a high-energy polymer state to low-energy orthophosphate.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 54.

“The creation of energy channels by means of phase transition provides a way to understand how the core biochemistry of life can have been stable throughout the age of the earth: a state of the geosphere that includes life becomes more likely than a purely abiotic state. The nonliving earth would have been metastable under conditions of continuous geochemical free energy production. Its ‘collapse’ to greater stability was the emergence of life.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 56.

“… life is among other things a transport phenomenon.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 56.

“We have already noted that the inelastic absorption of light by photosynthetic organisms provides a channel–independent of other physical processes–for the transduction of light energy between the visible and thermal infrared bands. An elementary calculation shows that absorption in place of elastic scattering increases heat-transporting capacity by a factor of ~109 for each atom acting as an absorber. In other words, every atom effectively rendered capable of photo-absorption by organosynthesis becomes a billion times more efficient as a transporter of energy from sunlight to black-body radiation than the same atom in an abiotic state. The enhancement of this energy capacity is mitigated by the large volume of biomass apparently required to create each photosynthetic absorption site.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 57.

“This point of view [evolution of life by phases of collapse by irreversible chemical transitions] emphasizes that life is a confederacy–of chemical constituents, pathways, and functions–and that the modular form of its emergence continues to be reflected in its modern organization. The essentially thermodynamic succession of a biogeosphere through increasingly stable states also explains why metabolism seems to show a clear and deterministic progression, while species and their ecologies appear to have been subject to continual waves of extinction.” Morowitz, Harold & Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity. 13(1):51-9. doi:10.1002/cplx.20191. p. 57.

“The niche has not and cannot – at least as it has been characterized thus far – do the substantive, foundational work it is claimed to do in ecology. The conceptual content tethered to the term ‘niche’ is just too problematically disjoint and amorphous to play that role.” Justus, James. 2021. The Philosophy of Ecology: An Introduction. Cambridge UP. p. 15.

“… the ecologist Frederic Clements is best known for claiming to find functional integration within biological communities that resembled the physiological integration within individual organisms, and which justified conceptualizing communities as a kind of superorganism with analogous homeostatic properties.” Justus, James. 2021. The Philosophy of Ecology: An Introduction. Cambridge UP. p. 58; reference: Clements, Frederic. 1916. Plant Succession: An Analysis of the Development of Vegetation. Washington, DC: Carnegie Institute of Washington.

“The advantage of diversification in the inhabitants of the same region is, in fact, the same as that of the physiological division of labor in the organs of the same individual body….” Darwin, Charles. 1859. The Origin of Species. p. 115. In: Justus, James. 2021. The Philosophy of Ecology: An Introduction. Cambridge UP. p. 58.

“In particular, I argue that the concepts of resistance, resilience, and tolerance jointly provide an adequate definition of ecological stability. Roughly speaking, a community exhibits these concepts to a high degree if it does the following: changes little after being perturbed (resistance), returns rapidly to a reference state or dynamic after being perturbed (resilience), and will return to that reference state or dynamic after most perturbations (tolerance).” Justus, James. 2021. The Philosophy of Ecology: An Introduction. Cambridge UP. p. 62.

“Specifically, biodiversity realism is indefensible…. … but the common poison pill is the motley, disunified assortment of things that are supposed to comprise biodiversity:

“‘Multidimensional biosdiversity includes not only the number of different species (species richness) and their relative abundance, but also genetic diversity, phenotypic diversity, differences in evolutionary history such as phylogenetic diversity, diversity at community and ecosystem levels (e.g. ecosystem diversity, functional diversity, and trophic network diversity), and differences in the diversity represented between areas, among other things.’” Justus, James. 2021. The Philosophy of Ecology: An Introduction. Cambridge UP. pp. 127-8; subquote: Santana, C. (forthcoming).

“Gaia fails as a model for understanding nature, because it treats the biosphere as if it were selected for its macroscopic properties…. Self-organized criticality [attractor such as cone with specific height angle formed by dropping sand], on the other hand, does not assume any macroscopic optimality; Bak simply views the SOC state as an attractor of a dynamic system. Still, the concept of SOC ignores selection among system components, and the diversity and modularity that are crucial to robustness. Some other perspective is needed, perhaps incorporating features of both views.” Levin, Simon A. 2005. “Self-organization and the Emergence of Complexity in Ecological Systems.” BioScience. 55(12):1075-79. p. 1076; reference: Bak, Per & K. Chan. 1991. “Self-organized criticality.” Scientific American. 264:46-54.

“Yet with the Earth as a laboratory containing millions of extant and evolving species, the number and variety of plausible ecological studies is functionally inexhaustible.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. p. 158.

“We view ecological systems as dissipative, self-organizing, historically derived, nonlinear systems that are typically far from equilibrium…. Structure and organization are hierarchical spanning many levels of organization linked by direct and indirect interactions and accompanied by positive and negative feedbacks…. Within and between these levels, self-organization and the dynamical constraints and opportunities imposed by nonlinearity couple with natural selection, and constrain system development to a finite range of structures and behaviors or attractor basins.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. p. 164.

“Ecological attractor basins typically contain multiple local attractors, producing the alternative states commonly observed.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. p. 164.

“This leads us to suggest that attractor mechanics, the dynamics of dynamics, is the key to a deeper ecological understanding…. Yet an essential element is missing, a developmental complement to natural selection and self-organization. We offer that this element is deeply hidden in the fundamental nature of attractors and is manifest as emergence.

“We are cognizant of the pitfalls that accompany assertions that some property or structure is emergent. However, we have additional insight from direct experimentation that we believe points the way to an explanation of emergence… For example, vastly different ecological communities can be generated rom a finite species pool, as a function of colonization sequence and sensitive dependence to initial conditions….

“Are these behaviors the result of emergent properties and the emergence of structure? We believe so because the structures ultimately produced by assembly, and the dynamical differences that developed, could not be recreated using only those species present in the final community state.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. pp. 165-7.

“We … suggest that asymptotic behavior is seldom realized in the real world because nature happens. Invasion, disturbance, evolution, species movement, and fluctuating resources to name a few, variously eliminate, reshape, and replace attractors altogether.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. p. 168.

“Ecological communities can sometimes be assembled that cannot be reconstructed from their constituent parts. This Humpty Dumpty effect is a direct result of historical contingency driven by system development in the face of coupling and decoupling. The presence of one or more transient species, or their dynamics, is required to generate the final community state. The mechanics are simple. The presence of transient species at specific times during development actualizes new regions of state space while eliminating others. The result is a modification of the attractor and its equilibria….

“In direct analogy, our experiments have shown that the same fixed species pool that created the Humpty Dumpty effect also contains routes to fully reconstructible community solutions. These systems are not emergent in any sense, and their nature can be fully exposed by reductionistic methodologies. On theoretical grounds it follows two communities comprised of the same species can exist, where one exhibits emergence while the other does not. This duality suggests that emergence can be something more than a system-level property as defined by the elements that compose the system.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. p. 176.

“We began this paper based upon conjectures we have developed to explain the intriguing behavior of the assembly experiments discussed above. These experiments have shown that (1) the attractor space is richly varied and complex, (2) a portion of this space is deterministic, while a portion is indeterministic, (3) attractors can dynamically break, after which may be no link, trajectory or solution from the original attractor or parent to the new or child attractor. The Humpty Dumpty effect is real. The only explanatory recourse remaining is to conclude that hard emergence exists [“a complete mechanistic decoupling between the property and the elements of the system, a phenomenon captured by the common phrase ‘the whole is more than the sum of the parts.’” pp. 161-2], and that its source is in the creation, evolution, destruction, and interaction of dynamical attractors.” Drake, James A., Michael M. Fuller, Craig R. Zimmermann & Javier G.P. Gamarra. 2006. “Emergence in ecological systems.” In: From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. N. Rooney et al. (eds). Springer. pp. 157-184. pp. 178-9.

“We use the term living system to include any energy-matter-fluxing life form, or aggregate of life forms, so it includes the smallest living organism up to the entire biosphere. It does not assume a priori an organism-centered, perspective on ecological systems….” O’Connor, Mary I., Matthew W. Pennell, Florian Altermatt, Blake Matthews, Carlos J. Melian & Andrew Gonzalez. 2019. “Principles of Ecology Revisited: Integrating Information and Ecological Theories for a More Unified Science.” Frontiers in Ecology and Evolution. 7:219. doi:10.3389/fevo.2019.00219. p. 3.

“Five principles that integrate information in ecological understanding….

“Principle 1: Information is a fundamental feature of living systems, and therefore also of all ecological systems….

“Principle 2: Syntactic and semiotic information interact in feedbacks, with energetic processes and material cycles, to influence structure, function and organization in ecological systems….

“Principle 3: Information processing requires energy and materials, therefore supply of energy and materials and thermodynamic constraints can limit information processing….

“Principle 4: Information processing allows components of living systems to measure the environment and their own state and to measure the relationship between their state and past and expected environments….

“Principle 5: Information processing systems are linked within and across scales of biological organization. Strong positive feedbacks in information processing can define or reinforce levels of organization–from a cell to an individual to symbioses all the way to an ecosystem and the biosphere.” O’Connor, Mary I., Matthew W. Pennell, Florian Altermatt, Blake Matthews, Carlos J. Melian & Andrew Gonzalez. 2019. “Principles of Ecology Revisited: Integrating Information and Ecological Theories for a More Unified Science.” Frontiers in Ecology and Evolution. 7:219. doi:10.3389/fevo.2019.00219. p. 3.

“On the other hand, information influences dynamics in ways not driven by individual organisms or mediated by communication; some forms of information stored in biological structures have energetic value, decay, and constrain future possible states of a system.” O’Connor, Mary I., Matthew W. Pennell, Florian Altermatt, Blake Matthews, Carlos J. Melian & Andrew Gonzalez. 2019. “Principles of Ecology Revisited: Integrating Information and Ecological Theories for a More Unified Science.” Frontiers in Ecology and Evolution. 7:219. doi:10.3389/fevo.2019.00219. p. 5.

“Information[:] The reduction in uncertainty associated with the difference between two states of a system…. Also called potential information, intrinsic information, physical information and syntactic information.” O’Connor, Mary I., Matthew W. Pennell, Florian Altermatt, Blake Matthews, Carlos J. Melian & Andrew Gonzalez. 2019. “Principles of Ecology Revisited: Integrating Information and Ecological Theories for a More Unified Science.” Frontiers in Ecology and Evolution. 7:219. doi:10.3389/fevo.2019.00219. p. 6.

“There are two distinct uses of the term ‘entropy’ in the context of information–one associated with information theory, and another associated with thermodynamics.” O’Connor, Mary I., Matthew W. Pennell, Florian Altermatt, Blake Matthews, Carlos J. Melian & Andrew Gonzalez. 2019. “Principles of Ecology Revisited: Integrating Information and Ecological Theories for a More Unified Science.” Frontiers in Ecology and Evolution. 7:219. doi:10.3389/fevo.2019.00219. p. 8.

“From the perspective of life as non-equilibrium thermodynamic systems, ecosystems are considered holarchic systems that grow and accumulate information and organization over time; evolution is one mode of information accumulation, but not the only mode.” O’Connor, Mary I., Matthew W. Pennell, Florian Altermatt, Blake Matthews, Carlos J. Melian & Andrew Gonzalez. 2019. “Principles of Ecology Revisited: Integrating Information and Ecological Theories for a More Unified Science.” Frontiers in Ecology and Evolution. 7:219. doi:10.3389/fevo.2019.00219. p. 15.

“Functionality, however, is not a local property of a molecule. For example, the functionality of expressed RNA and protein sequences is clearly context-dependent….” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 2.

“One is therefore left to conclude that the most important features of biological information (i.e. functionality) are decisively non-local, subject to informational control and feedback, so that the dynamical rules will generally change with time in a manner that is both a function of the current state and the history of the organism.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 2.

“… a common source of confusion stems from the fact that molecules play three distinct roles: structural, informational and chemical.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 2.

“In analogue chemical systems, information is contained in a continuously variable composition of an assembly of molecules rather than in a discrete string of digital bits. ‘Metabolism-first’ scenarios for the origin of life fall within this analogue framework, positing that early life was based on autocatalytic metabolic cycles that would have been constructed in a manner akin to how analogue computer systems are cabled together to execute a specific problem-solving task…. The heritable information in this case typically consists of the compositional ratios of the molecules in the organized assemblies.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 3.

“Taking all of these factors into account, it is clear that analogue-only systems are not capable of adaptation in the same way as living systems are. Modern life is a hybrid: digital memory and digital switches enable control over many (non-interfering) analogue states, and therefore enable adaptability to changing environmental conditions with the same basic toolkit.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 3.

“By the above considerations, it seems that digital or analogue alone is insufficient to provide a satisfactory account of the origin of life–not just on technical grounds, but for deep conceptual reasons. The former suffers from difficulties of prebiotic synthesis and due to fundamental limitations on how information can be processed in such scenarios (being trivial rather than non-trivial…); whereas the latter suffers from issues of reprogrammability, control and potentially long-term evolvability.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 3.

“To avoid an infinite regress, in which the blueprint of a self-replicating UC [universal constructor] contains the blueprint which contains the blueprint… ad infinitum, von Neumann proposed that in the biological case the blueprint must play a dual role: it should not only contain instructions such as an algorithm, to make a certain kind of machine (e.g. the UC) but should also be blindly copied as a mere physical structure, without reference to the instructions its contains, and thus reference itself only indirectly. This dual hardware/software role mirrors precisely that played by DNA, where genes act both passively as physical structures to be copied, and are actively read-out as a source of algorithmic instructions. To implement this dualistic role, von Neumann appended a ‘supervisory unit’ to his automata whose task is to supervise which of these two roles that blueprint must play at a given time, thereby ensuring that the blueprint is treated both as an algorithm to be read-out and as a structure to be copied, depending on the context. In this manner, the organization of a von Neumann automaton ensures that instructions remain logically differentiated from their physical representation. To be functional over successive generations, a complete self-replicating automaton must therefore consist of three components: an UC, a (instructional) blueprint and a supervisory unit….

“… we can now identify that all known life functions in a manner akin to von Neumann automata, where DNA provides an (partial) algorithm, ribosomes act as the core of the UC and DNA polymerases (along with a suite of other molecular machinery) play the role of a supervisory unit.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. pp. 4-5.

“In spite of the striking similarities between an UC and modern life, there are some important differences. DNA does not contain a blueprint for building the entire cell, but instead contains only small pars of a much larger biological algorithm, which may be roughly described as the distributed ‘top-down’ control of an organism. The algorithm for building an organism is therefore not only stored in a linear digital sequence (tape), but also in the current state of the entire system (e.g. epigenetic factors such as the level of gene expression, post-translational modifications of proteins, methylation patterns, chromatin architecture, nucleosome distribution, cellular phenotype and environmental context). The algorithm itself is therefore highly delocalized, distributed inextricably throughout the very physical system whose dynamics it encodes.” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 5.

“Algorithmic information theory can make the foregoing distinction [between trival and non-trivial replicators] precise. The algorithmic information of a system or structure is defined to be the Shannon information contained in the shortest algorithm that can specify the system or structure as its output. For example, a trivial replicator, such as a crystal, is one that may be specified by an algorithm containing far fewer bits than the system it describes. In contrast, a non-trivial replicator is algorithmically incompressible and requires an algorithm, or instruction set, of complexity comparable to the system it describes (or creates).” Walker, Sara I. & Paul C.W. Davies. 2013. “The algorithmic origins of life.” Journal of the Royal Society Interface. 10.20120869. doi:org/10.1098/rsif.2012.0869. p. 5.

“Not all differences make a difference. A distinction needs to be made between the vast amount of information that is implicit in the detailed configuration of matter and the tiny fraction that makes it into a mechanism for making a difference. For clarity in the present discussion we will refer to the former as latent information. This term includes all the aspects needed to describe how configurations of matter differ from the lowest energy arrangement possible, in which there are not correlations or significant inhomogeneities.

“This distinction focuses attention on the characteristics of the mechanism that acquires the information, in particular its role in determining what latent information is acquired, which in turn must depend on the design of that mechanism, in other words on the information that already exists and is instantiated in the mechanism.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 65.

“Entropy, the physical variable that quantifies both disorder (and its converse, structure) in thermodynamics and uncertainty (and its converse, information) in information theory is well defined and calculable for a given configuration.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 66.

“The point is, inhomogeneities in the distribution of matter and energy amount to local departures from the lowest energy and least structured state, and therefore represent metastable accumulations of free energy, which can do work if released under certain conditions and redistributed within the wider system into configurations with the same total energy (since energy is conserved) but lower free energy (less inhomogeneity) overall.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 67.

“But if that free energy [energy coming slowly to Earth’s surface from its core] is trapped in some kind of potential well, as in chemical bonds, then dissipating it first requires some work to be done to provide the additional energy needed initially to overcome the potential barrier in order to release the trapped energy. As is well known, chemical energy can be released through providing the initial energy in the form of heat, and then the process can continue by virtue of the energy released. But another way to release chemical energy is by coupling to a complex scaffold of self-organising and self-maintaining chemical interactions that can lower the potential barrier – which is exactly what occurs at the core of all life!” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 67-8.

“The famous second law, that entropy can be created but not destroyed, is a constraint on which processes are actually possible, since conservation of energy is necessary but not sufficient.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 69.

“So self-assembly is an equilibrium-seeking process that releases energy (an exergonic process…. The energy released is dissipated as heat and, as required by the second law, thereby produces an amount of entropy equivalent to the increase in latent information that the self-assembly creates.

“Self-organisation, on the other hand, is a nonequilibrium process, characterised by a stable pattern of coordination in the interactions between the elements of the system and requiring a continual input of energy (an endergonic process) as well as the material resources needed to keep it going. In this case, the stability of the structure produced stems from the dynamics of the interactions, which require a continuous flux of energy to maintain them, rather than the statics of falling to the lowest energy state. If the energy flux decreased sufficiently, the self-organised order decays. So both self-assembly and self-organisation spontaneously produce structure, and therefore latent information – but self-organisation has the additional requirement of external energy….” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 70-1.

“An equivalent way of describing the outcome of autocatalysis is to say that it creates constraints on the phase space available to the system. What we mean by this is that as the available precursors get drawn into the cycle to produce more of the autocatalytic set molecules, the system is constrained to occupy only that region of its phase space that corresponds to high concentrations of those molecules, and is unable to access the more numerous configurations that correspond to other distributions of species and concentrations.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 74.

“Deacon coined the term ‘autocell’ to describe a hypothetical system in which a RAF [reflexively autocatalytic food-generated] set is able to generate its own containment through one of its products being a molecule that can spontaneously aggregate and grow into large regular structures by self-assembly….

“… we observe that the linking of the two processes implies a qualitative increase in latent information, which can justifiably be labelled as emergent since it is not possessed by systems displaying either process alone. RAF sets create more structure in molecular composition, self-assembly creates more structure in spatial configuration; and these are both examples of quantitative increases – more of the same kind of information. However, the linking of the processes creates a new kind of regularity – cycles, and coordination of the processes in time…..

“The simple fact of a RAF set arising in which one of the members is able to self-assemble in this way creates an intrinsic relationship between the two processes (Deacon calls it reciprocal linkage), and inherent in that relationship is the emergence of function, and therefore purpose, again features that are signatures of living systems.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 76-7; reference: Deacon, Terrence. 2006. “Reciprocal linkage between self-organizing processes is sufficient for self-reproduction and evolvability.” Biological Theory. 1(2):136-149.

“The forms of information we have so far identified as arising in the autocell model are mostly due to amplification and proliferation of the far-from-equilibrium patterns of concentration of chemical species, and of spatial patterns, and therefore still fall into the overall category of latent information as we have defined it here. But we have also noted some interesting and novel informational structures: temporal patterns; the embryonic emergence of individuation, purpose, and function; and population-level information about frequencies of variants.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 78-9.

“Noting that the core features of evolvability – replication with heredity, variation, and selection – mean that the copies are similar to the originals, but can also have some differences, and those differences make a difference to whether the copies will themselves be copied, we immediately recognise Bateson’s hallmark of information….

“… the difference that made a difference represents more than just information about the system that gets copied, it also represents something about the factors in the environment that contributed to the system’s success in getting copied….

“The second angle is that the differences that made the difference to whether a copy got copied again are part of what gets copied, so the information that those differences constituted is getting transmitted from one generation to the next. Transmission of information as information, that is, coupled to a mechanism for making a difference, is action not only at a spatial distance, but also at a temporal distance once the ability to store the information for later use arises….

“So once evolvability gets traction, in principle we have the seeds of information that carries meaning and of information transmission – two necessary and momentous steps towards life– yet so subtle at this stage that they could easily be dismissed.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 81-2.

“Evolution is an information generating and transmitting process, but the path to greater evolvability (faster accumulation of more useful information) is a precarious balancing act between two abysses. On one side, Eigen’s error paradox threatens to rapidly extinguish any nascent protolife if the rate of error (or introduction of differences from the original) is too high, for the simple reason that whatever latent information exists gets randomised by errors faster than it can propagate and accumulate. On the other hand, evolvability requires the introduction of differences (or copying errors) in order to discover better ways to persist and replicate. Maximising the error rate to accelerate exploration of new possibilities, while remaining just below the error threshold that terminates the process in a dead end, is a very fine balance.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 82.

“Robustness to parasitic mutants is achieved by confining the emerging protolife systems in enclosures or on surfaces of suitable substrates, so that any mutants that do arise are isolated and cannot spread to neighbouring systems. Ultimately they commit suicide by killing off the system they are confined to. Alternately they may mutate further to become ‘domesticated’ by the system, by evolving features that are useful to the system and reducing their harmful properties. Could this be the original ‘cooperate or die!’ storyline? Yet again the solution can be seen as an information one, since confinement implies constraints, which reduces the number of available microstates, and therefore the entropy.

“The diversity necessary for ongoing open-ended evolution is also maintained by a cooperative strategy, in this case overcoming the competitive exclusion problem when replicators depend on the same food source, by recruiting previously untapped food sources in the environment for the autocatalytic cycles, through evolution of new catalysts that can exploit them. The benefits of this strategy are twofold. It accesses new resources of energy and materials to accelerate growth, and it initiates functional specialisation in the autocatalytic networks, since such catalysts would essentially be primitive metabolic enzymes, a novel role that is differentiated from the more generalised roles of participants in RAF sets. What makes this a cooperative strategy is that, first, specialisation of functions means that replicators and metabolic enzymes are playing different but mutually supportive roles, and, second, specialisation of food sources means they are no longer in competition. We discern in this scenario the earliest shades of the decoupling of metabolism and reproduction, ultimately leading to coded replication, the first instance of genuinely semantic information, about which we will have more to say shortly.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 84.

“In particular we have seen that evolution is essentially an informational process; that it generates, accumulates, and transmits information; that it has to avoid a number of informational pitfalls; and that in doing so, it creates new forms of latent information – hierarchical structure, constraints, functional specialisation and cooperative relationships, and, ultimately, semantic information with all its future ramifications for causality.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 85.

“When replication is just based on catalyltic activity in a RAF set, the reaction rate depends on the extent to which the physical form (shape and affinities) of the catalyst correlates with those of the substrates. So there is a great deal of variability in rates for different reactants and catalysts, as well as some likelihood of variations in which of the possible reactions actually happen, resulting in a range of similar but not identical products. The specificity of such reactions is therefore not high, and efficiency is correspondingly lower. With template replication, however, because highly efficient specific enzymes have evolved for each of the twenty or so amino acids that living systems use, the replication rate, efficiency, and accuracy or specificity are high and essentially independent of the actual sequence on the template.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 90.

“Here is what is interesting about that [DNA to messenger RNA to proteins] with regard to our questions. In the first stage, there is unbounded variety in the possible sequences on the DNA, and furthermore, it is easy for mutations to generate further variations there. Similarly the third stage consisting of the protein products also has unbounded possible variety. But the middle stage is well defined, highly conserved, and operates with high fidelity. This constrained middle stage is the neutral and efficient interface translating huge variety in possible sequences on the genetic material, into huge variety in the possible products.

“This is an example of another well-known motif in the architecture of complex systems, the so-called bow tie, which can take into account a great diversity of inputs, process them with much smaller diversity in the protocols to elaborate these inputs, and produce wide diversity of outputs.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 91.

“We found that the degree of complexity that can be reached is limited until coded replication arises to decouple heredity – the business of information transmission from one generation to the next – from metabolism and the business of living. And once that happened, the consequences of digital coding have reinforced and amplified the adaptive power of evolution, which in turn has produced the mechanisms that create yet more complex structural and functional information and elicit semantic information from the latent information in the environment.” Grisogono, Anne-Marie. 2017. “(How) Did Information Emerge?” pp. 61-96. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 93.

“Whereas our understanding of energy can be reduced ultimately to symmetry principles, information is derived from its antithesis, symmetry breaking. Stored information records which of several alternative adaptive configurations have been selected historically.” Krakauer, David. 2017. “Cryptographic Nature.” pp. 157-173. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 157.

“… a comparison with the distinction in developmental biology between permissive and instructive interactions, reveals that ‘information’ is a way to talk about specificity.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 366.

“Biological specificity, we suggest, is simply causal specificity in biological systems. Since we have already argued that ‘information’ is a way to talk about biological specificity, we conclude that causal relationships are ‘informational’ simply when they are highly specific.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 366-7.

“Interaction between neighboring cells or tissues in development can lead to further differentiation in one, the responder, as a result of its interaction with the other, the inducer. Developmental biologists, commonly distinguish between ‘instructive’ (or active, explicit, directive) induction, on the one hand, and ‘permissive’ (or passive implicit), on the other.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 370.

“When the action system is largely responsible for the specificity of the interaction through the transfer of a specific message, to which the reaction system responds by entering into a particular pathway of differentiation, we speak of an instructive action. When, on the other hand, the specificity of a reaction is largely due to the state of the competence of the reaction system, so that even rather unspecific messages can serve as signals to open up new developmental pathways, we speak of a permissive action.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 370.

“A number of different ways to distinguish types of causes have been suggested, and two of these – stability and specificity – are particularly relevant to understanding biological information. Stability refers to whether an intervention continues to hold across a range of background conditions, and we will not pursue it here. Specificity refers to the fine-grained control that an intervention might have, controlling a gradient of change, rather than a simple on-off switch, for example.

“The intuitive idea is that interventions on a highly specific causal variable C can be used to produce any one of a large number of values of an effect variable, E, providing what Woodward terms ‘fine-grained influence’ over the effect variable.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 372; reference: Woodward, J. 2010. “Causation in biology: stability, specificity, and the choice of levels of explanation.” Biology & Philosophy. 25(3):287-318. p. 302.

“… the more specific the relationship between a cause variable and an effect variable, the more information we will have about the effect after we perform an intervention on the cause.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 373.

“Any two variables that satisfy the interventionist criterion of causation will show some degree of mutual information between interventions and effects. This criterion is sometimes called ‘minimal invariance’ – there are at least two values of C such that a manipulation of C from one value to the other changes the value of E. If the relationship C -> E is minimally invariant, that is, invariant under at least one intervention on C, then C has some specificity for E, that is, I(Ĉ;E) > 0 [I= mutual information of intervention by doing C for effect on E]…. Relationships with a large range of invariance have high specificity according to our measure.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 373-4.

“Sarkar needs to distinguish these two [copying strands of DNA to its complementary strand versus the relationship of DNA to a protein] because the relationship between DNA and RNA is not arbitrary – it is dictated by the laws of chemistry. Only the relationship between RNA and protein is arbitrary, because it depends on the available t-RNAs. Many different t-RNAs are available, and substituting these would lead to different genetic codes.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 376; reference: Sarkar, S. 1996. “Decoding ‘coding’: information and DNA.” BioScience. 46(11):857-864.

“There is just one type of informational specificity, and what distinguishes it from conformational specificity is its independence from the medium in which it is expressed or the mechanism by which it is transferred. Hence if arbitrariness should be regarded as an important condition for informational language in biology, it should be for the reason of this medium independence in general, rather than the coding relationship between RNA and amino acids in particular.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 376.

“The mutual information between the specificity of the environmental signal for the regulatory factor, on the one hand, and the specificity of the regulatory factors for a certain gene via its regulatory sequence, on the other hand, are chemically arbitrary and subject to the convention of an intervening allosteric biomolecule.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 378.

“Signalling occurs inside the organism, and the evolution of a signalling system allows it to optimally map the different environments to the appropriate behaviour. Signalling arose because the modular structure – the separation of transducer and effector – created a coordination problem. For the organism to respond adaptively, it needed to coordinate these parts, and a signalling system provided the solution.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 379.

“If a cause makes a specific difference to the linear sequence of a biomolecule, it contains Crick information for that molecule. This definition embodies the essential idea of Crick’s sequence hypothesis, without in principle limiting the location of information to nucleic acid sequences, as Crick does.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 379-380.

“The discrepancy between the number of coding sequences and the number of gene products leads to the insight that the informational specificity in coding regions of DNA must be amplified by other biomolecules in order to specify the whole range of products. ‘Precise determination’ implies a one-to-one relationship, and if we focus on coding sequences alone, we find a one-to-many relationship between sequence and product.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 380.

“So we conclude that while genes are seen as a key source of specificity, in biology causes are not regarded as informative merely because they are genetic, but whenever they are highly specific.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 382.

“Biological specificity is simply causal specificity in biological systems. Causal specificity is a degree property of causal relationships – the more specific a relationship, the more apt it is for the exercise of fine-grained control over the effect.” Stotz, Karola & Paul E. Griffiths. 2017. “Biological Information, Causality, and Specificity.” pp. 366-390. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 387.

“More formally, an ontological level (in biology) has associated with it an organisational structure with the properties of a complex system, especially the property that new phenomena emerge within it.” Farnsworth, Keith D., Larissa Albantakis & Tancredi Caruso. 2017. “Unifying concepts of biological function from molecules to ecosystems.” Oikos. 126(10):1367-1376. p. 1368.

“A biological function is a process enacted by a biological system A at ontological level n which influences one or more processes of a system B at level n+1, of which A is a component part.” Farnsworth, Keith D., Larissa Albantakis & Tancredi Caruso. 2017. “Unifying concepts of biological function from molecules to ecosystems.” Oikos. 126(10):1367-1376. p. 1369.

“The FEC [functional equivalence class] consists of all operations (behaviours or processes) having the effect in question and this is context-dependent because an effect always depends on the nature of both the subject and the object.” Farnsworth, Keith D., Larissa Albantakis & Tancredi Caruso. 2017. “Unifying concepts of biological function from molecules to ecosystems.” Oikos. 126(10):1367-1376. p. 1369.

“Most broadly, a community that can be viewed as a Kantian whole is consistent with a general definition of life: ‘A system can be said to be living if it is able to transform external matter and energy into an internal process of self-maintenance and production of its own components’.” Farnsworth, Keith D., Larissa Albantakis & Tancredi Caruso. 2017. “Unifying concepts of biological function from molecules to ecosystems.” Oikos. 126(10):1367-1376. p. 1371; subquote: Luisi, P. 2003. p. 52.

“By this definition [of living system above], all biological function ultimately amounts to production of living cells and this is readily quantified by biomass. Accordingly, we can regard biomass production as a ‘master function’, meaning that all functions may be quantified by their contribution to it…. The idea of a master function removes the need for a teleological account of function: it is the de-facto end point of the causal chains to which all other biological functions belong, in the proximal as opposed to ultimate sense of Mayr’s dichotomy.” Farnsworth, Keith D., Larissa Albantakis & Tancredi Caruso. 2017. “Unifying concepts of biological function from molecules to ecosystems.” Oikos. 126(10):1367-1376. p. 1371.

“In principle, ascribing a relative genealogical identity to a group of organisms requires estimating their genealogy and their connection to a common ancestor. However, in systematics, the common ancestor is not directly accessible and cannot be an empirical reference.” Montevil, Mael & Matteo Mossio. 2020. “The Identify of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions.” Frontiers in Physiology. 11(611):1-14. doi:10.3389/fphys.2020.00611. p. 4.

“Biological organisms are understood as natural systems realizing a dual causal regime. On the one hand, they are thermodynamically open systems: they are traversed by a flow of energy and matter that enables them to maintain themselves over time in conformity with the second principle of thermodynamic. On the other hand, biological organisms control the thermodynamic flow through the action of structures that, at specific time scales, exert constraints on the ongoing processes and transformations. In particular, organisms are constituted by a set of constraints that (1) are generative–they canalize target processes in such a way to maintain the conditions of existence of other constraints and (2) are dependent–their existence relies on the action of other constraints.

“The set of constitutive constraints that are both generative and dependent realize mutual dependence, which is usually referred to as closure. One of the conceptual strengths of the organizational perspective is that it provides an account for the concept of biological function, defined as the effect produced by a constraint subject to closure.” Montevil, Mael & Matteo Mossio. 2020. “The Identify of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions.” Frontiers in Physiology. 11(611):1-14. doi:10.3389/fphys.2020.00611. p. 6.

“In short, we suggest that individual organisms belong to the same identity class when they share the same specific organization of functional constraints and they are the offspring of the same close common ancestor.” Montevil, Mael & Matteo Mossio. 2020. “The Identify of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions.” Frontiers in Physiology. 11(611):1-14. doi:10.3389/fphys.2020.00611. p. 13.

“Because of their inherent tendency to vary, individual organisms that meet the criteria of an identity class at some moment may contravene these criteria as time passes, and their offspring will presumably do the same after some generations. Therefore, organisms’ identity is not only hybrid but also bounded….” Montevil, Mael & Matteo Mossio. 2020. “The Identify of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions.” Frontiers in Physiology. 11(611):1-14. doi:10.3389/fphys.2020.00611. p. 13.

“We review previous ideas [about origin of life] and synthesize them in four central hypotheses: (i) Multiple microenvironments contributed to the building blocks of life, and these niches were not necessarily inhabitable by the first organisms; (ii) Mineral catalysts were the backbone of prebiotic reaction networks that led to modern metabolism; (iii) Multiple local and global transport processes were essential for linking reactions occurring in separate locations; (iv) Global diversity and local selection of reactants and products provided mechanisms for the generation of most of the diverse building blocks necessary for life.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 101.

“Hypothesis 4: Global diversity and local scarcity of reactants and products were keys to prebiotic chemistry. Each unique environmental setting in the Hadean would have favored the production of a few important compounds, and mixing processes on large and small scales allowed the products of each setting to interact with each other. Thus, on a global scale, the great variety of ingredients required for life could be generated and combined in biochemically more productive ways than it would be possible in a primordial soup at one location.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor?” Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 102.

“… some argue that encapsulating membranes must have been an early feature of life, while others argue that it would have been a much later development. The latter point of view suggests that the earliest stages of life’s formation may have involved encapsulation through inorganic micro-compartments such as fluid inclusions, vesicles, porous sediments and hydrothermal chimneys or sea-ice brine pockets. If inorganic micro-compartments served as concentration points for prebiotic molecules, then it is possible that lipid membranes only became important at later stages in the origin and evolution of biochemicals. However, it is also conceivable that non-biological lipid membranes played a more active role by transporting prebiotic compounds between different environmental settings.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 105.

“The age and extent of oceans on Earth are unknown, but Hadean zircons provide geochemical evidence for liquid water near the Earth’s surface since 4.4 Ga. Geological evidence for life extends back to 3.5 billion years, possibly 3.8 Ga; hence the origin of life most likely happened in the early Archean (3.5-3.8 Ga) or Hadean (3.8-4.5 Ga) eon.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 106.

“The Hadean atmosphere could also have hosted particulate matter with catalytic surfaces…. Marine aerosols, volcanic ash, and dust particles could have acted as a continually recycled population of reaction chambers and catalytic surfaces, experiencing variable degrees of radiation, temperature and water activity during vertical and horizontal atmospheric transport. In particular, dehydration of amino acids during atmospheric transport has been suggested as a mechanism for activation and polymerization. Additionally, amphiphiles including stearic and oleic acids have been shown to form exterior films on marine aerosols that could have served as proto-membranes in prebiotic chemistry.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 106.

“Hence, non-marine water bodies including lakes, pore waters in vesicular volcanic rocks or in sediments, and groundwater contained in subsurface aquifers were almost certainly available to host prebiotic reactions that required salt-free conditions.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 108.

“The location of beaches at the interface between land, seawater, and air may have given them a prominent role in the origin of life, because it would have allowed them to concentrate and process a huge variety of reactants transported by rivers, the ocean, and the atmosphere. Furthermore, beaches have four characteristics advantageous for prebiotic organic synthesis: accumulation of heavy detrital minerals, evaporation-concentration cycles, a gradient in water activity, and high porosity.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 108.

“In an abiotic Hadean ocean, sea-ice would have captured volatiles and organics produced on the seafloor or in the atmosphere and encapsulated them for reaction with other chemical species.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 109.

“The sea-surface microlayer (SSML) describes the interface between the ocean and the atmosphere and is operationally defined as the upper 1000 μm of the ocean. The SSML is rich in organic and inorganic materials collected from both the atmosphere and ocean, held in place by buoyancy, electostatic attraction, physical or chemical adsorption, and surface tension.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 109.

“On the modern Earth, clay minerals with a high affinity for adsorption are responsible for 80% of organic net export from the surface ocean to the deep ocean. On the prebiotic Earth, this mechanism probably provided an efficient shuttle of monomers and polymers to deep marine sediments.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 110.

“Today, known hydrothermal vent systems can be broadly classified into magma-driven, basalt-hosted systems and serpentinization-driven, peridotite-hosted systems.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 110.

“Moreover, the region for potential catalysis and polymerization in the deep subsurface is extensive, as evidenced by the presence of crypto-endolythic microbial communities supported by serpentinization by-products at depth. Thus, the potential reaction space for prebiotic chemistry within the ocean crust is vast, hydrologically dynamic, and interconnected globally.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 112.

“In contrast, we argue that the diversity of settings in the Hadean would have allowed different reactions to occur in different settings, and each setting would have provided constrained parameters to nurture sparse reaction networks that could conceivably generate specific modules of modern biochemistry. Thus, life was not a highly improbable outcome of a single experiment in an organic soup, but instead a gradual emergence from successful interactions among globally distributed, simultaneously forming reaction products.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 112.

“Envisioning the origin of life in a global context is advantageous because it makes prebiotic chemistry more plausible and because the global context is an inescapable reality.” Stueken, E.E., R.E. Anderson, J.S. Bowman, W.J. Brazelton, J. Colangelo-Lillis, A.D. Goldman, S.M. Som & J.A.. Baross. 2013. “Did life originate from a global chemical reactor? Geobiology. 11:101-126. doi: 10.111/gbi.12025. p. 119.

“Perhaps the major reason why boundary conditions are usually glossed over is that the specifications are implicitly assumed to be anything that an investigator chooses them to be…. In the statement of most problems, the investigator chooses boundary constraints that are of a regular and ordered nature. These are the low-lying fruit that we retain as exemplars. Nothing, however, can prohibit boundary conditions that involve chance.” Ulanowicz, Robert E. 2014. “Reckoning the nonexistent: Putting the science right.” Ecological Modelling. 293:22-30. doi:10.1016/j.ecolmodel.2014.03.014. p. 28.

“Furthermore, physicist Walter Elsasser has argued that combined chance events are usually unique…. I have called such unique chance events ‘radical’, and they fully pervade the complex systems of ecology and the social sciences….

“Regarding false absolutes, it appears that Monod’s strict dichotomy between chance and necessity is not possible. In between blind chance and strict determinism lies a continuum of events characterized by the degree to which the arbitrary is constrained by the order with which it is fused. At one end of this spectrum, blind, unconstrained chance occurs in a directionless environment. Once there are constraints of any sort, however, (like the imbalance of loaded dice) the resulting conditional probabilities will differ from those calculated for blind chance. Going even further, Popper in his last book, A World of Propensities, pointed out how conditional probabilities can grow progressively so constrained that a few outcomes dominate, although occasionally other ‘interferences’ might still occur. Popper labeled such dominant outcomes ‘propensities’, and stressed how they are more general than laws, which he considered to be determinate only in a vacuum or under artificial conditions. Whence, it is possible to describe an entire spectrum of phenomena that legitimately can be classified as contingencies – starting with radical, novel chance, and running the gamut from blind chance to conditional chance to propensities and even to intentionalities.” Ulanowicz, Robert E. 2014. “Reckoning the nonexistent: Putting the science right.” Ecological Modelling. 293:22-30. doi:10.1016/j.ecolmodel.2014.03.014. p. 28; references: Elsasser, Walter M. 1969. “Acausal phenomena in physics and biology: a case for reconstruction.” Am. Sci. 57:502-516; Popper, K.R. 1990. A World of Propensities. Bristol: Thoemmes.

“One concludes that the reversible laws of physics guide but never of themselves detemine ecological dynamics. Rather, outcomes are the result of the interaction between opposing sets of contingencies. On one hand are the autocatalytic relationships that arise through mutually reinforcing contingencies, build constraints, and maximize power. That drive is opposed by entropic, chance, irreversible, equitable and inefficient contingencies that degrade constraints. It is contingencies, not physical laws, that have initiated all patterns of form and activities that we encounter.” Ulanowicz, Robert E. 2014. “Reckoning the nonexistent: Putting the science right.” Ecological Modelling. 293:22-30. doi:10.1016/j.ecolmodel.2014.03.014. p. 29.

“‘In principle, then, a causal circuit will generate a non random response to a random event….’” Bateson, Gregory. quoted in: Ulanowicz, Robert E. 2009. “The dual nature of ecosystem dynamics.” Ecological Modelling. 220:1886-1892. doi:10.1016/j.ecolmodel.2009.04.015. p. 1888; subquote: Bateson, G. 1972. Steps to an Ecology of Mind. NY: Ballantine Books.

“If the combination of ‘non-random’ and ‘indeterminate’ seems confusing and somewhat contradictory, perhaps the example of Polya’s Urn will help to clarify the distinctions. The process described by Gyorgy Polya begins with a collection of red and blue balls and an urn containing one red ball and one blue ball. The urn is shaken and a ball is blindly drawn from it. If that ball is the blue one, a blue ball from the collection is added to it and both are returned to the urn. The urn is shaken and another draw is made. If a ball drawn is red, it is replaced along with another red ball into the urn, etc. A first question arises as to whether a long sequence of such draws and additions would cause the ratio of red to blue balls to converge to a limit. It is rather easy to demonstrate that after, say, 1000 draws, the ratio converges to some constant, say 0.54681. That is, the ratio becomes progressively non-random as the number of draws grows.

“The fact that the system very rarely converges to 0.5000 prompts one to inquire what would happen if the urn were emptied and the starting configuration recreated? Would the subsequent series of draws converge to the same limit as the first? It is easy to demonstrate that it will not. After 1000 draws the second might approach a limit in the vicinity of 0.19732. The Polya process clearly is indeterminate. One eventually discovers that the ratio of balls is progressively constrained by the particular series of draws that have already occurred. It gradually becomes clear that the limiting ratio for any long sequence of draws and replacements can be any real fraction between zero and one.” Ulanowicz, Robert E. 2009. “The dual nature of ecosystem dynamics.” Ecological Modelling. 220:1886-1892. doi:10.1016/j.ecolmodel.2009.04.015. p. 1888.

“Finally, it is noteworthy that information has bee defined by Tribus and McIrvine as ‘anything that causes a change in probability assignment.’” Ulanowicz, Robert E. 2009. “The dual nature of ecosystem dynamics.” Ecological Modelling. 220:1886-1892. doi:10.1016/j.ecolmodel.2009.04.015. p. 1890; reference: Tribus, M. & E.C. McIrvine. 1971. “Energy and information.” Sci Am. 225(3):179-188.

“As such, TDC [top-down causation] by information control and adaptive selection are at the root of what characterizes living systems on the Earth.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 27.

“In the literature, the metabolic regulatory network is often distinguished from the genetic regulatory network but it is clearly the interplay between the two that forms the controlling informational instances of the cell. The metabolite pools act as intracellular molecular signals that link the metabolic network to the genetic network through genetic regulations. Despite their apparent daunting complexity, these biological networks are themselves very modular in their overall organization, with subdomains and network motifs being easily distinguishable.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 27.

“Two functions can be linked to one another by informational relationships resulting from sharing, exchanging information or action on one another to form a functional cyclic network….

“Because of their cyclic organization, these [functional cyclic] networks can also be seen as informational networks with inbuilt informational links acting as feedback control loops. As such, an informational link can be broadly defined as any type of physical and/or chemical interaction existing between two functions. This link has both a functional and informational meaning in contrast to random molecular interactions that are part of the noise.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 28.

“While there are different kinds of information, it can generally be defined as that which brings about a reduction of uncertainty or indeterminacy.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 28.

“Therefore, a master function creates the functional constraints and boundaries within which the lower functions can evolve, diversify and eventually become more complex. It is important to realize here that it is the COS [cellular operating system and distinguished from the cellular metabolism] that operates the reproduction and replication of the cell. The various molecular components of the COS can interact, recombine and diversify to lead to further complexification and differentiation, offering new capabilities and potentialities. Thus, the COS does constitute, in the philosophical sense the system formal cause. This characterizes a top-down causal effect by the whole system (defined by master functions) on the molecular parts (defined by the functions of lower levels that operate the master functions). Considering the master functions of a cell, the functional constraints are informational constraints. Each sub-function that has evolved within the master function is constantly selected for the quality of its information. Therefore, it is the master function that ultimately ‘decides’ whether the information will be kept or not.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 29.

“At the molecular level, functional convergence is likely more common than it was initially thought to be.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 34.

“In conclusion, TDC [top-down causation] by information control and adaptative selection are at the root of converging forces that shape the evolution of living biosystems from the simplest to the most complex levels. Living systems could therefore be defined as self-reproducing systems that function via TDC by information control and adaptive selection.” Jaeger, Luc & Erin R. Calkins. 2012. “Downward causation by information control in micro-organisms.” Interface Focus. 2:26-41. doi:10.1098/rsfs.2011.0045. p. 37.

“… [because fixed laws of physics implies that no initial conditions of the universe could be precise enough to allow any probability of paths to a universe containing life as we do] based on fixed laws that govern microstate evolution, we may well need to fine-tune not only the initial state but also the laws themselves in order to specify the particular ordering of states observed (constraining the universe to a unique past and future). Expressed more succinctly, if one insists on attributing the pathway from mundane chemistry to life as the outcome of fixed dynamical laws, then those laws must be selected with extraordinary care and precision, which is tantamount to intelligent design: it states that ‘life’ is ‘written into’ the laws of physics ab initio. There is no evidence at all that the actual known laws of physics possess this almost miraculous property.

“The way to escape from this conundrum – that ‘you can’t get anywhere from here’ – is clear: we must abandon the notion of fixed laws when it comes to living and conscious systems.” Walker, Sara I. & Paul C.W. Davies. 2017. “The ‘Hard Problem’ of Life.” pp. 19-37. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 30.

“A better idea is to assume that there exist conditions under which the dynamical rules are a function of the states (and therefore are in some sense an emergent property). Indeed, this seems consistent with what we know of life, where the manner in which biological systems evolve through time is clearly a function of their current state…. “State-dependent laws are a hallmark of self-referential systems such as life and mind.” Walker, Sara I. & Paul C.W. Davies. 2017. “The ‘Hard Problem’ of Life.” pp. 19-37. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 31.

“When we externally describe a system, we articulate the counterfactual possibilities and assign a quantity of ‘information’ to them. However, in order for these counterfactual possibilities to be physically realized, the information specifying them must be contained within the system and contribute to specifying which dynamical path through state space is taken. This should be a local property, yielding an effective description that is state dependent.” Walker, Sara I. & Paul C.W. Davies. 2017. “The ‘Hard Problem’ of Life.” pp. 19-37. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 32.

“In particular, we posit that the manner in which biological systems implement state-dependent dynamics is by utilizing information encoded locally in the current state of the system, that is, by attributing causal efficacy to information.” Walker, Sara I. & Paul C.W. Davies. 2017. “The ‘Hard Problem’ of Life.” pp. 19-37. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 33.

“It is widely recognized that coarse-graining plays a foundational role in how biological systems are structured, by defining the biologically relevant macrovariables. However, it is not clear how those macrostates arise, if they are objective or subjective or whether they are in fact a fundamental aspect of biological organization – intrinsic to the dynamics (i.e., such that macrostates are causal) rather than merely a useful phenomenonological descriptor. A framework in which coarse-grained information-encoding macrostates are causal holds promise for resolving many of the problems discussed herein. This is the key aspect of the hard problem of life.” Walker, Sara I. & Paul C.W. Davies. 2017. “The ‘Hard Problem’ of Life.” pp. 19-37. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. pp. 33-4.

“Here we have attempted to identify a core feature of life that won’t similarly be solved based on current paradigms – namely, that life seems distinct from other physical systems in how information affects the world (i.e., that macrostates are causal).” Walker, Sara I. & Paul C.W. Davies. 2017. “The ‘Hard Problem’ of Life.” pp. 19-37. In: Walker, Sara, P.C.W. Davies & George Ellis (eds). From Matter to Life: Information and Causality. Cambridge UP. p. 34.

“In the conventional narrative competition plays the central role in evolution. The origins of competition, however, derive from centripetality and its eliciting mutualism. Place two autocatalytic systems within a finite resource field and eventually their centripetalities will intersect. That is, competition cannot happen without centripetal drives at work the next level down. It is mutualism that is primary and competition plays a derivative, secondary role. Ulanowicz, Robert E. 2016. “Process Ecology: Philosophy Passes into Praxis.” Process Studies. 45(2):199-222. doi: 10.5840/process201645215. p. 210.

“In the preceding development of the transactional scenario for ecosystem development, three fundamental axioms were assumed:

“i) Contingency–Systems are continually being impacted by arbitrary events that cannot be framed in lawful fashion in closed form.
“Essentially, this axiom posits chance as an ontological reality. It’s not that such chance events actually break any laws; it’s that the laws as such are insufficient for determination and the accompanying and necessary boundary statements are impredicate.

“ii) Feedback–Processes, via interaction with other processes, are capable of influencing themselves.
“This is a radical assumption. It specifically violates closure and the Aristotelian prohibition against circular reasoning. It permits mereology in general and opens the way for autocatalysis and its associated behaviors, which are fundamental to the behaviors of living systems.

“iii) History–Systems differ from one another according to their histories, some of which is recorded in their material configurations.
“This assumption accepts what Darwin assumed about the natural world. History cannot be formulated wholly in terms of reversible laws.

“Of particular note, each of these statements is the antithesis of one of the fundamental assumptions that guided Enlightenment physics: Chance is the opposite of determinism; feedback violates closure and history negates reversibility. Atomism and universality simply have no counterparts in the revised metaphysics. In a world where relationships are primary, atomism either doesn’t exist or serves no useful function. Agency in the new scheme takes the form of configurations of processes that are not universal, but rather contingent and circumscribed in both time and space.

“Also of importance, assumptions a thru e [metaphysical assumptions of physics: closure, atomism, reversibility, determinism, universality or that the laws of nature apply always and everywhere with respect to time and space] undergird a collection of simplified, homogeneous, weakly-interacting models that portray the dynamics of systems that are prone to decay and fall apart. For example, the ideal gas model formed the basis for the conclusion that the ultimate fate of the universe is ‘heat death,’ or a rarefied collection of low-frequency photons. Assumptions i thru iii, to the contrary, support a dynamic that builds up organized activities and structures. Both dynamics are active aspects of nature and are in tension with one another in dialectic fashion–the Yin and Yang of existence.” Ulanowicz, Robert E. 2016. “Process Ecology: Philosophy Passes into Praxis.” Process Studies. 45(2):199-222. doi: 10.5840/process201645215. pp. 218-9.

“Our uncertainty about the origin of life can be summed up succinctly as our ignorance in calculating the probability, ℘life, for matter to transition from the non-living to living state.” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. p. 2.

“Another problematic aspect is the assumption that Darwinian evolution invariably leads to greater complexity. A now classic example in the molecular evolution literature is Spiegelman’s monster, a 4500 nucleotides RNA virus evolved in vitro, which through competitive selection on replication evolved to be as short as 218 bases (the ‘monster’). Spiegelman’s monster is an example of ‘compression selection’, whereby information is lost from a genome when it is no longer relevant to its fitness. This occurs, for example, when a replicator’s environment becomes more simple. A trend of increasing complexity requires complex, information-rich environments, not just the capacity for self-replication.” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. pp. 7-8.

“One cannot formulate a question related to life’s origins without assuming something about life, so the issue of defining life ultimately cannot be avoided (although one need not acknowledge it explicitly or make it a focus of research).” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. p. 10.

“Self-replication is a statistically irreversible process: a single cell can replicate to produce two daughter cells, but we do not observe the reverse situation in which two ‘daughter’ cell[s] spontaneously convert into one. In equilibrium thermodynamics, irreversibility is accompanied by an increase in entropy. It follows that self-replication might also produce an increase in entropy.” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. p. 11.

“During the emergence of life, a process driving increasing complexity with time was necessary. Darwinian evolution does not satisfactorily fill this void if taken alone (e.g. in the absence of feedback between environment and nascent life…), as it can lead to both simpler or more complex systems depending on the context of selection. In fact, a challenge with the majority of replication-based scenarios for the origin of life is that they either stall-out at a stage of relatively low complexity, or evolve toward states of lower complexity with time, specifically because information-rich environments are not included in the discussion.” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. p. 15.

“It is an open problem whether true universal constructors can in principle exist. Approximations are known to exist–for example, the logical architecture of the cell has been equated to that of a UC on numerous occasions. Our current state as a technologically advanced civilization is an even better approximation to a UC, as there are certainly many possible transformations that technological civilizations enable in physical reality, which seem impossible in the absence of technology.” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. p. 16.

“A more general and less strict concept than that of universal construction, is the idea of programmable constructors. Programmable constructors do not necessarily operate on a universality class of objects, but through interaction with other physical systems can be ‘programmed’ to perform specific physical transformations. In physics the idea of a ‘program’ is itself not well-defined. For purposes of discussion herein, we may consider these as inputs to a particular physical system or device that produce different outputs. The distinction between copying and programmable construction forms the core of distinguishing between trivial and non-trivial replication–that is between copying and construction, respectively.” Walker, Sara I. 2017. “Origins of life: a problem for physics, a key issues review.” Reports on Progress in Physics. 80:092601. doi: 10.1088/1361-6633/aa7804. p. 16.

“Coevolutionary models of two interacting species suggest that mutualisms often favour the evolution of trait complementarity, in which there is a high degree of trait matching between interacting partners. Examples include the match between nectar concentration and pollinator’s preferences, and seed size and body mass of frugivores. Moreover, trait convergence, in which trait similarity emerges as a response to similar selective pressures, is often observed in mutualisms, such as Muellerian mimicry rings, colour patterns in cleaning fishes, and patterns of fruit design in unrelated plant species. Complementarity and convergence have been identified as potential factors that may shape the organization of large mutualistic networks.” Guimaraes, Paulo R., Pedro Jordano & John N. Thompson. 2011. “Evolution and coevolution in mutualistic networks.” Ecol. Lett. 14:877:885. p. 877.

“… species that interact with super-generalists are more likely to evolve in response to them, whereas super-generalists will seldom respond to an evolutionary shift in one of their many partners.” Guimaraes, Paulo R., Pedro Jordano & John N. Thompson. 2011. “Evolution and coevolution in mutualistic networks.” Ecol. Lett. 14:877:885. p. 881.

“In species-rich networks, coevolutionary and non-coevolutionary changes are intrinsically interwoven, with coevolutionary events generating non-coevolutionary events through a complex set of cascading effects. Therefore, the importance of coevolution in shaping traits in large species-rich networks cannot be assessed simply by determining the relative proportion of current selection that involves reciprocal selection between pairs of species. By generating cascading effects and speeding up the overall rate of evolutionary change, coevolution generates additional non-coevolutionary events. Hence, as networks develop, coevolution may appear to be increasingly rare within species-rich mutualisms specifically because it fuels further non-reciprocal, evolutionary events.” Guimaraes, Paulo R., Pedro Jordano & John N. Thompson. 2011. “Evolution and coevolution in mutualistic networks.” Ecol. Lett. 14:877:885. p. 882.

“Third, our results highlight that not all species are equally important for the evolutionary dynamics of multispecific interactions. Rather, a small proportion of species, the super-generalists, may play a central role in organizing evolution and coevolution in species-rich assemblages, driving them toward high complementarity, and above all, convergence.” Guimaraes, Paulo R., Pedro Jordano & John N. Thompson. 2011. “Evolution and coevolution in mutualistic networks.” Ecol. Lett. 14:877:885. p. 884.

“Even if we do not regard LUCA itself as a community, there is no corresponding difficulty in thinking that the first living organisms were formed from a community of interacting self-organizing systems capable of passing material between one another and sustaining one another….

“Closely related to this is the question of ecosystems: in what sense are individual organisms individuals, if they depend on other individuals, even if only as food, in order to survive?…

“The definition becomes even more difficult when we consider obligate symbionts.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2021. “The essence of life revisited: how theories can shed light on it.” Theory in Biosciences. doi: 10.1007/s12064-021-00342-w. pp. 9, 10.

“A macroscopic and easily visible example [why chirality would or would not evolve as with amino acids] is found in snails and their predators in the Ryukyu Islands, in the far south of Japan. All snails are asymmetric, with shells that coil either clockwise or anticlockwise. Mating between individuals with opposite chirality is very difficult, giving an obvious selective advantage to snails with the majority clockwise chirality. However, in the Ryukyu Islands the minority of anticlockwise snails appears to be maintained, raising the question of the advantage of belonging to the minority. This seems to be explained by the fact that the principal predator, the snake Pareas iwasakii, has an asymmetric jaw adapted to extracting clockwise individuals from their shells, thus providing a survival advantage to anticlockwise snails. Notice that both snails and snakes must have evolved as communities, not as individuals.” Cornish-Bowden, Athel & Maria Luz Cardenas. 2021. “The essence of life revisited: how theories can shed light on it.” Theory in Biosciences. doi: 10.1007/s12064-021-00342-w. p. 11.

“One of the most significant empirical generalizations of biochemistry is that a small group of universal cofactors or coenzymes are key to the catalytic function of a majority of enzymes. As early as 1976 Harold White noted that at least 52% of catalogued enzymes require a cofactor…. The cofactors and their accompanying proteins constitute holoenzymes, which are the complete functional units of cell metbolism. It is striking that cofactors are identical throughout the biosphere, despite constant evolutionary variation in the much larger protein components of the holoenzymes.” Morowitz, Harold J., Vijayasarathy Srinivasan & Eric Smith. 2006. “The Swiss Army Knife of Biological Catalysis.” Complexity. 11(3). doi: 10.1002/cplx.20112. p. 9; reference: White, H. 1976. J. Mol. Evol. 7:101-104.

“In general cofactors are (1) high-potential carriers of groups to be transferred, (2) molecules that alter the configurations of substrates, and (3) members of couples in oxidized and reduced states.” Morowitz, Harold J., Vijayasarathy Srinivasan & Eric Smith. 2006. “The Swiss Army Knife of Biological Catalysis.” Complexity. 11(3). doi: 10.1002/cplx.20112. p. 9.

“Among the necessary organic cofactors, pyridoxal phosphate (PLP) seems to be somewhat different from the rest. It is a small, relatively simple molecule that might have occurred in the prebiotic reaction mixture….

“The core of the PLP molecule is a fully conjugated nitrogen heterocycle. This planar ring has six groups hexagonally arrayed on it: phosphate, aldehyde, alcohol, methyl, unbonded electron pair from nitrogen, and hydrogen. It is a compact toolkit of organic functional groups; indeed it resembles a completely opened Swiss army knife of tools to carry out organic reactions. Given this chemical diversity, it is perhaps not surprising that … lists 40 enzymatic reaction types for which PLP is a cofactor.” Morowitz, Harold J., Vijayasarathy Srinivasan & Eric Smith. 2006. “The Swiss Army Knife of Biological Catalysis.” Complexity. 11(3). doi: 10.1002/cplx.20112. p. 10.

“All of biomass is itself composed of <500 small molecules and polymers thereof, most of which participate in many reactions in the metabolic chart. This fact alone constitutes a form of universality, although less restrictive than that of the anabolic core. The most tractable and to us the most natural interpretation of this empirical regularity is that the metabolites were selected through a process of ergodic sampling of common reactions among small, C, H, and O molecules, rather than by infinitesimally sparse sampling of nucleic acid polymers or proteins catalyzing those reactions.” Smith, Eric & Harold J. Morowitz. 2004. “Universality in intermediary metabolism.” PNAS. 101(36):13168-13173. doi: 10.1073/pnas.0404922101. p. 13169.

“Investigations of how it is possible to generate the complex structures of life tend to have a teleological character that they deny to the process itself. They underutilize a necessary premise for any statistical interpretation of either emergence or universality: A chemical origin of life must have been due to thermodynamic forces away from the abiotic state.” Smith, Eric & Harold J. Morowitz. 2004. “Universality in intermediary metabolism.” PNAS. 101(36):13168-13173. doi: 10.1073/pnas.0404922101. p. 13169.

“We look for the emergence of life in a dynamical generalization of the statistical principles of energy distribution, although not necessarily a thermally near-equilibrium state. Just as the equilibrium Gibbs distribution at given temperature and chemical potentials describes a spectrum of molecular species, so we anticipate that an energetically stressed environment should be populated by a distribution of reaction currents, of which rTCA [reductive tricarboxylic acid cycle] is a plausible core for the reasons given above.

“In such networks, topology, rate kinetics, and the free-energetic stability of molecules together determine the favored pathways.” Smith, Eric & Harold J. Morowitz. 2004. “Universality in intermediary metabolism.” PNAS. 101(36):13168-13173. doi: 10.1073/pnas.0404922101. p. 13172.

“Such a [free energy landscape with hills and valleys of local energy minima] might describe a space of possible chemical species and reactions, for example. The free energy landscape has two important classes of fixed points for the small-scale dynamics: attracting fixed points and saddle points, which are attracting in all by one direction but repelling in the final direction. In the common thermodynamic limit, the system spends almost all its time in small neighborhoods of the attracting fixed points, so almost all other details of the landscape can be ignored. However, the conditional distribution for histories, conditioned on the existence of some transition, are dominated by small neighborhoods of the saddle points, and by most-likely paths that connect them to the attracting fixed points, making a heteroclinic network. The relative heights of the saddle points above the attracting fixed points determine the rates of transition. If transitions through each saddle are allowed to come into detailed balance, so that currents in both directions are equalized for every transition, the relative heights of the attracting fixed points determine their occupation probabilities.

“The entropy function for an equilibrium process on such a landscape, which presumes a sufficiently long waiting time that reaction rates have all come into detailed balance, depends only on neighborhoods of the attracting fixed points. The entropy function for a process that is out of equilibrium on the same landscape will generally depend on neighborhoods of the saddle points as well.

“The increase in the number of properties that must be specified to describe rates makes the non-equilibrium entropy a more complicated function than the equilibrium entropy, and one that can depend on currents through the saddle points as well as on time-reversal-invariant properties such as total matter and energy contents. More importantly, the system could be driven out of equilibrium by placing sources and sinks at several different points on the landscape, so the network topology as well as the properties of saddle points may affect the non-equilibrium entropy. Whole domains of configuration space may be cut off, because the reaction rates make them unreachable between the time that matter or energy enter as a particular source and the time they exit through some drain. The properties of rates in such an ensemble are collectively termed its kinetics; the opening or closing of large domains in configuration space is a key consequence of the evolved control over kinetics in living systems.

“For some problems, the additional knowledge and constraint imposed by kinetics can be incorporated by fairly straightforward extensions of equilibrium entropy functions, while for others one must shift the entire ensemble description from considering sets of states to considering sets of histories, leading to an entropy function of qualitatively different structure.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. pp. 199-200.

“More formally, we could say that the conditional probability for histories of the Earth and everything in it, conditioned on the presence of refrigerators, is strongly dominated by histories in which technological humans were the agents of their invention and production. This is a very fancy version of the result shown in the last section for free-energy landscapes: the conditional probability for histories of a system over a free energy landscape, conditioned on the existence of one or more transitions, is dominated by small neighborhoods of the saddle points through which those transitions are most accessible.

“The parable of refrigerators emphasizes that the emergence of life requires a thermodynamics of processes, and that these processes can be richly and hierarchically structured. The role of human intelligence in the parable probably makes it hopeless to formalize. Fortunately, for biology in contrast to human technology, there is evidence that the number of levels that must be considered to reconstruct the emergence of the biosphere is not intractably large, for the lowest levels of emergence of chemical order, many details of biological organization appear to be secondary.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. pp. 203-4.

“At every level of biological organization, specific ordered states – molecules, cells, species, ecosystems – turn over rapidly compared to the persistence time of the patterns they instantiate and maintain.

“The contrast with persistence in equilibrium systems, such as fossil minerals, is categorical. The pattern that is distinctive of quartz is a particular crystallographic unit-cell structure. The realization of the crystalline form in matter persists because the physical piece of quartz is robust against disruption. Yet all known quartz minerals on Earth have been reworked geologically since the age of the original core metabolism, which has been maintained by steadily overturning populations of small molecules and cells.

“The systematic dependence of durable patterns on ephemeral entities may be the most distinctive difference between biological order (or non-equilibrium order more generally) and equilibrium order.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. pp. 206-7.

“The chemical characterization of the living state begins with a comparison of the Earth without, and Earth with, a biosphere as an integral part of its dynamics and energetics. Consider the space of possible chemical species and chemical reactions, given the elemental composition of our planet. Of particular interest are the organic and organometallic compounds involving covalent bonds to C, H, O, N, P, and S, and transition metals, which have either bond free-energies or reaction transition-state energies ΔG (relative to the chemicals in an equilibrium ensemble) much larger than (say, 50-100 times) the thermal activation energy kBT. Absent a biosphere, terrestrial atoms would never (or almost-never) access this part of the chemical possibility-graph, because the Arrhenius factor …. suppresses reaction rates and fluctuation probabilities from an equilibrium ensemble.

“Compare this case to the Earth with a biosphere. Most of the chemical graph remains unoccupied by terrestrial atoms, but a small subset – the part that can be built by phosphate dehydration or physical assembly from abvout 125 particular small core metabolites – has a continuous current of gigatons of carbon (and comparable amounts of O, N, and H) per year flowing through it. The biosphere is the collection of processes that concentrate a subset of geochemical electron-potential (redox) energy or electromagnetic (solar flux) energy and cause/enable it to flow through the chemicals and reactions of this very distinctive subgraph of organometallic chemistry. Some forms of organization that mediate this flow are simply harnessed from near-equilibrium geochemical ensembles (the water solvent, phase-separated mixtures, or metal-sulfide centers resembling minerals, are well-known examples). Other forms of organization, however, would never be sampled in an equilibrium ensemble, if dynamics cannot adequately maintain and renew them, they cannot persist. The highly selected forms of order that can be self-maintained (as a system) and that contribute to the access of a unique chemical and energetic space define the nature of the living state.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. pp. 212-3.

“Darwinian evolution is the Markov process created by the emergence of individuality.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. p. 214.

“In the deep past when the whole genome was much less a unit of transmission due to horizontal gene transfer, evolution more closely resembled bulk-non-equilibrium thermodynamics with loosely coupled components and fewer barriers to independent optimization.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. p. 214.

“Beneath the organizational level of individuals and communities, and the adaptive dynamics of Darwinian selection, life is distinguished from non-life by a sparse and universal chemistry that appears to be associated with the biosphere as a whole, or at least the self-contained ecosystem level of aggregation. All biosynthetic fluxes pass through this core network, and multiple levels of feedback (physiological, evolutionary, ecological) contribute jointly to its maintenance.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” In: Complexity and the Arrow of Time. Lineweaver, Charles H., Paul C.W. Davies & Michael Ruse (eds). pp. 191-223. Cambridge UP. pp. 215-6.

“It is widely assumed that to hold the idea that life began by deterministic processes on the surface of the earth is, of necessity, an antireligious point of view. This is certainly not the case, as this view is acceptable to Buddhists, Taoists, liberal Protestants, Reform Jews, Roman Catholics, and pantheists. Indeed, the idea of life as necessary would seem at the very minimum, to presuppose that the universe is infused with something like a creative intelligence.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 4.

“When we speak of the origin of life, we are referring generally to the rise of organisms–discrete entities–in terms of the first definition [that life is a property of individual organisms rather than a property of planets]. It is well to remember, however, that this can take place only within a global ecological system.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 6.

“Undoubtedly there should also be a real and general biology, but we can only just begin to glimpse it. A true biology in its full sense would be the study of the nature and activity of all highly organized chemical systems wherever they were to be found–on this planet, on others in the solar system, in other solar systems, in other galaxies–and at all times, future and past.” Bernal, J.D. 1965. In: Theoretical and Mathematical Biology. Waterman, T. & H.J. Morowitz (eds). Blaisdell; quoted in: Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 16.

“In the last twenty or more years the molecular biologist has discovered that he or she could usually confine investigations to a noise-independent physical realm, even in cases where the particular system under investigation, an interesting mutant, may have been the result of noise. The great success of molecular biology suggested that all of biology could be understood from the principles applicable to the noise-independent realms of physics and chemistry.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 19.

“The development of the genetic system at the molecular level is interpreted as introducing a fundamental discontinuity in the history of life. In a genetic system, a single molecular event–that is, a mutation–can radically alter the system, thus deviating from the statistical domain of pregenetic biology. The transition is from thermal noise independence to noise dependence, from the realm of traditional physical laws to the realm of local extremum and strategy laws. The transition from physics to history involves a mixture of the two. This discontinuity emerges as the source of the unity and diversity characteristic of present-day life on Earth.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 19.

“The constructs that have proved useful to science are a small subset of all possible constructs, and we therefore recognize that the historical development of science has placed a set of methodological requirements on useful constructs…. These requirements are (1) logical fertility, (2) multiple connections, (3) permanence and stability, (4) extensibility, (5) causality, and (6) simplicity and elegance.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 22.

“At the molecular level, information can be stored in two ways, either in molecular structure, characterized by the specification of covalent or secondary bonds, or in dynamic processes such as the flow of intermediates or the conduction of electrical impulses….

“We can classically describe a molecular system in a multidimensional p, q space where the q’s are coordinates and the p’s are momenta. When we take the system to temperatures near absolute zero, we obliterate any information about the original configuration in a p space and confine the system to a very tiny subvolume in this space. Raising the temperature involves a randomization in momentum space. Since the rewarmed system is biologically functional, the information must be stored in coordinates in q space.

“This generalization may seem at odds with the assertion that energy flow is necessary to maintain order. Biological information is stored in molecules, which are unstable over long periods at ordinary temperatures; they are constantly undergoing thermal degradation. Near absolute zero these degradative processes cease and the information-storing structures are indefinitely stable. Thus, although information storage is structural, at most temperatures energy flow is required to restore structures as fast as they are being degraded, or to otherwise compensate for the degradation. Some instability in the form of mutations is necessary for evolution to take place.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 52-3.

“Sustained life is a property of an ecological system rather than a single organism or species.

“A one-species ecological system is never found. The carbon cycle requires at least one primary producer and a method of returning carbon to the CO2 pool. A system of only herbivores would eventually die of starvation.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 54.

“Theory in thermal physics is treated by three related disciplines: thermodynamics, statistical mechanics, and kinetic theory. The three offer different insights, and it is often necessary to examine problems in one or more of these various approaches. Thermodynamics and statistical mechanics rely heavily on the notion of equilibrium, which may occur by placing a system in a rigid adiabatic container (no flow of matter or energy), or by placing a system in a rigid container immersed in an infinite isothermal reservoir and allowing it to age for a long time.

“The question of how long is long enough is part of the science of kinetics….” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 69.

“Similarly, pressure, volume, and mole number have meaning independent of thermodynamics….

“With the concepts of temperature and entropy, which are thermodynamic to the core, there are no rigorous analogs from other disciplines. Strictly speaking, temperature and entropy are undefined away from equilibrium.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 72.

“At true thermodynamic equilibrium all parameters are time independent and all flows (that is, of matter, energy, and electrical charge) vanish. Steady states have time-independent parameters but non-zero flows. The formalism of thermodynamics often is but should not be uncritically carried over to steady states.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 73.

“Pagels states the algorithmic definition of complexity of a number as ‘the length of the minimal program required to compute it’….

“In general, for any system the complexity is the length of the most efficiently coded array of symbols that describes the appropriate molecular detail.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 74, 75; reference: Pagels, H. 1988. Dreams of Reason. Simon and Schuster.

“1. The system: An enclosure container containing C, H, N, O atoms in contact with an isothermal reservoir at a temperature above that of limitingly slow reaction rates and below that at which normal covalent bonds become unstable….

“For normal aqueous systems, a more likely range is 273 K < T < 373 K…

“2. Energy flow: Energy enters the system in quanta large enough to excite electronic transitions and exits the system in quanta corresponding to vibrational, rotational, and translational energies…..

“3. The principle of complexity: The systems described in (1), subject to energy flow of the kind described in (2), move to energies above the ground state by storing energy in chemical bonds. The steady states or quasi-steady states have chemical complexities that increase with the energy flow to a certain point.

“There is thus the interesting result that systems undergoing energy fluxes from high quantum sources to low quantum sinks undergo an increase in complexity. This principle of complexification follows strictly from the physical chemical properties of such systems and in no way demands biological organization….

“The cycling theorem of Morowitz, provides a different but related theoretical structure. It asserts that for chemical systems subject to the energy flow constraints outlined in (2) above, the steady state will be characterized by chemical cycles from low-energy compounds to higher energy compounds and back again.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 83-4.

“Thus, the gap between the approach from above and the approach from below must be filled by an evolutionary path from the ur-organism to the universal ancestor…. This epoch may have been characterized by a rich ecosystem with the most varied types of chemistry. When the universal ancestor finally evolved, it outcompeted the rest of ur-life, leaving many niches for the radiation of its descendents.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 88.

“A molecular self-replicating entity is a self-replicating entity that uses soluble molecules for its component parts. The use of the word soluble requires some statement concerning the solvent, which is generally considered to be water. The definition, however, can be generalized to indicate that the component parts are distributed in the environment in a homogeneous phase. Homogeneous phase is used here in a strictly thermodynamic sense….

“Viruses represent a difficult case since the environment for virus synthesis is complex, requiring the interior of a cell. By analogy consider bacterial cells that grow in a simple medium of inorganic salts and glucose. A single mutation can lead to a cell that requires tryptophan for growth. Tryptophan added to the medium restores the self-replication property of the system. Information in the cell has been replaced by information in the environment. Thus cells can have a variable degree of fastidiousness with respect to their nutrient requirements. A qualitative change occurs, however, at the level of viruses and replicative organelles such as mitochondria, where the host cell is considerably more than a nutrient environment and supplies replicative machinery that cannot be regarded as being in a homogeneous phase. Anything that is describable in terms of thermodynamic parameters, such as temperature, pH, and composition, may be regarded as environment.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 99, 100.

“Consider next a model system closed to the flow of matter and in contact with an infinite isothermal reservoir…. For homogeneous systems, the complete phenomenological description consists of specifying all concentrations and reaction rates. In terms of the graph, it can be taken to represent a network; concentration values can be assigned to the points (which roughly correspond to a voltage assignment in electrical network theory) and flow values to the lines (which correspond to currents in electrical network theory). The input of electronic energy in the chemical case is analogous to the introduction of voltage sources in the electrical case.

“Next, consider a constant flux of excitation energy into the model system. This can be in the form of photons, ionizing radiation, high-temperature thermal sources, spark discharge, or any other source that causes electronic transitions from lower-lying to higher energy states. Under constant energy flux, new values of concentrations and flows emerge. The system will age and eventually form a steady state where the time derivatives of the concentrations vanish. For this condition, Kirchhoff’s current law (for electric circuits) holds at every point in the chemical network. This balance requires that the final flows of material generated by the electronic transitions return to the points in the network where they originated. Thus, the steady state is necessarily characterized by cyclic flows of material around loops in the reaction network. As the material flows around these cycles, the input energy flows out as heat into the isothermal reservoir. Material cycling is seen to be a general feature of chemical networks kept at a far-from-equilibrium steady state by the constant influx of energy in a form capable of electronic excitation. The relation of the model system to a planetary surface is clear. Such a surface is more or less closed to the flow of matter and is exposed to a time-averaged constant flux of solar radiation. Outer space serves as an isothermal reservoir for the flow of heat, which is transferred in the form of infrared radiation. Global ecology is thus an example of a general principle. Cycling is not uniquely biological; rather, the ecological example is a special case of a more general principle….

“The equilibrium state is thus a power attractor in the molecular space we are using to describe the network.

“The attractor nature exhibited by the equilibrium distribution is a property of the network, not just a property of the equilibrium state. Therefore, during the dynamic states, the low-lying configurations also act as attractors, directing flows in the network toward those points. Dynamic states of the system in which low-lying molecules are not pumped up to higher states will tend to disappear as the high-energy material drains into the sinks established by the atttractors. For steady states to be maintained in the network, the energetically pumped cycles must involve the low-lying states as inputs. Thus, in the biosphere it is necessary that photosynthetic processes operate on molecules such as water and carbon dioxide. Again, this is not a uniquely biological result but follows from the analysis of chemical networks.

“This extension of the cycling theorem demonstrates that the previously stated features of global ecology have their origin in the general properties of networks of reacting molecules. The importance of this fact is that it imbeds global ecology deeply into its underlying physics.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 118-9, 120.

“To deal with a tangible case [of complexity vs organization] consider an ensemble of systems made up in the following way. First a culture of cells of mycoplasma or cyanobacteria or any bacteria is grown. We will assume that in any clone all cells are effectively identical. Each cell is isolated in a constant volume container of the volume of the cell and each container is placed in a constant temperature reservoir at the growth temperature of the cells….

“The initial ensemble is an unstable far-from-equilibrium collection of highly complex systems. If allowed to decay for a very, very long time, the ensemble would become an equilibrium one, and on average an amount of energy ΔH would have flowed from each container to the reservoir. In addition to the initial ensemble and the equilibrium ensemble, construct a third ensemble by radiating the equilibrium ensemble with gamma rays until the amount of energy in minus the amount of energy out for each member of the ensemble averages ΔH….

“The thermal fluctuation case [third ensemble] is an example of a system of low complexity with a high information measure.

“Complexity for the equilibrium system is low because the ensemble is dominated by a few small molecules in high concentration. The complexity of members of the other ensembles will be high since the living case can be described in the limit as a single, large molecular structure. The gamma-ray-pumped system will be characterized as a large and extremely varied collection of molecules. The description of the two high-energy systems will require a finely detailed atomic specification, hence the complexity will be a number of the order of the number of atoms for both cases.

“In spite of having comparable complexities, the living ensemble and the gamma-ray-pumped ensemble have radically different levels of organization. An organized system, as contrasted to an ordinary complex system, is a complex system that can be defined by a reduced description, a set of rules or statements much smaller than the complexity that specifies the system by focusing on the process by which it come to be. I therefore define organization as the complexity of the system minus the complexity of the reduced description. Implied in this is a new feature, one that is dynamic rather than static.

“Complexity applies to a snapshot of a system, a measure at some instant in time. Organization deals with how the system came to be.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 123-7.

“The signature principle states that because of historical continuity prebiotic processes should leave a signature in contemporary biochemistry….

“Reconsider the metabolic chart and note that it is characterized by a high degree of connectivity. One could not, for example, have major discontinuities in carbohydrate metabolism without substantial alterations in amino acid and lipid metabolism. The more highly connected a substance is the more difficult it is to remove it from the network and the more difficult it would have been to add it once the network was in place. All of this makes the study of current-day biochemistry a rich mine of information about pre-biochemistry. This analysis has not been pursued with sufficient vigor, and there is much to be uncovered in this area. The signature principle is the basis of my contention that metabolism recapitulates biogenesis.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 154, 155.

“The principle of the limited munificence of nature or the ‘no-free-lunch’ construct says that the biosphere cannot require the other geospheres continuously to supply molecules more complex than the thermodynamically lowest lying combinations of available atoms.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 155.

“The environment thus provides the components to form closed vesicles of approximately spherical shape…. Dissolved in the membrane interior will be nonpolar molecules that may have a nonsymmetrical radial distribution owing to the curvature of the membrane and any outside–inside difference that may develop.

“Among the dissolved molecules will be chromophores–molecules that absorb visible or near ultraviolet light from the solar spectrum. One of the properties of chromophores is that excited electronic states have an electrical dipole moment different from the ground state….

“Once an electrical potential can be maintained continuously by light flux the state is set for

“1. oxidation-reduction reactions if electrons can be carried or conducted across the membrane
“2. acid-base driven reactions if protons can be carried or conducted across the membrane
“3. a coupling of the two types of reactions because both are driven by the same electrical potential
“4. a coupling through reactions of the form
“AH2 -> <- A + 2H+ + 2 electrons

“Thus the foundations of bioenergetics are implicit in the earliest vesicles that formed spontaneously. These may be regarded as true protocells.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. pp. 174-5.

“Two characteristic features of life are strongly dependent on the chemical features that emerge when nitrogen enters the system: catalysis and information storage.” Morowitz, Harold J. 1992. Beginnings of Cellular Life. Yale UP. p. 177.

“By ‘relativity principle’ in this context, I mean distancing ourselves in our theories from specific absolute standpoints for which there can be no a priori justification. From Copernicus and Galileo through to Poincaré and Einstein, the reach of this general principle of relativity has been progressively extended by removing various absolute standpoints in turn.” Noble, Denis. 2012. “A theory of biological relativity: no privileged level of causation.” Interface Focus. 2:55-64. doi: 10.1098/rsfs.2011.0067. p. 55.

“It is hard to think of an a priori reason why one level in a biological system should be privileged over other levels when it comes to causation. That would run counter to the relativity principle.” Noble, Denis. 2012. “A theory of biological relativity: no privileged level of causation.” Interface Focus. 2:55-64. doi: 10.1098/rsfs.2011.0067. p. 56.

“To think that the genome completely determines the organism is almost as absurd as thinking that the pipes in a large cathedral organ determine what the organist plays.” Noble, Denis. 2012. “A theory of biological relativity: no privileged level of causation.” Interface Focus. 2:55-64. doi: 10.1098/rsfs.2011.0067. p. 57.

“Microbes are able to exchange genes, communicate between cells (quorum sensing), translocate collectively over surfaces (swarming motility), and form biofilms–spatially-extended multicellular colonies with coordinated division of labor, cellular differentiation and cooperative defense against antagonists.” Goldenfeld, Nigel & Carl Woese. 2010. “Life is physics: evolution as a collective phenomenon far from equilibrium.” Annual Review of Condensed Matter Physics. 2:375-399. doi: 10.1146/annurev-conmatphys-062910-140509. p. 375.

“What would biology look like as a science if we sought to anticipate the types of evolutionary processes available to the suite of genetic operators now known?…

“Maybe this sounds far-fetched, but in fact this methodology has already been used to good effect in biology. One example we have in mind is the groundbreaking discovery of the class of molecules known as topoisomerases, whose existence was fist recognized theoretically, leading to their eventual discovery. The topoisomerases area a class of enzymes that are able to perform the miracle of passing one strand of DNA through another, by breaking and then reforming them. The end result of this process is that DNA can be uncoiled through a process of successive topological changes, allowing transcription and replication to occur. Without the topoisomerases, this would be essentially impossible on the timescale relevant to cellular processes.” Goldenfeld, Nigel & Carl Woese. 2010. “Life is physics: evolution as a collective phenomenon far from equilibrium.” Annual Review of Condensed Matter Physics. 2:375-399. doi: 10.1146/annurev-conmatphys-062910-140509. p. 380.

“In the natural development of the sciences, issues of complexity are sensibly postponed until they can no longer be avoided. Physics was able to delay serious consideration of collective effects for nearly three hundred years, and only in the last thirty years or so has it confronted complex collective phenomena involving multiple scales of space and time, unpredictable dynamics and large fluctuations. Its track record of success is mixed.

“Biology was not so lucky: at its outset, complex phenomena were encountered, but tools were lacking to cope with the difficulty. Rather than abiding by ignorance, a language-culture was developed to explain away the conceptual difficulties using guesswork solutions such as ‘natural selection.’” Goldenfeld, Nigel & Carl Woese. 2010. “Life is physics: evolution as a collective phenomenon far from equilibrium.” Annual Review of Condensed Matter Physics. 2:375-399. doi: 10.1146/annurev-conmatphys-062910-140509. p. 391.

“The two paradigms dominating biological theory are the machine-like functioning of componentry, and the Darwinian framework for understanding the stochastic dynamics of death and reproduction. The representation of biological processes as machines is often by way of models, which represent control flow and causation, and for which the goal is to conceptually or quantitatively reproduce typical observed behaviors…. Energy naturally appears in these contexts as an input, as a quantitative constraint, or as a medium of control. However, models constructed for the purpose of illustrating causality often diminish the importance of the incursion of error at all levels of organization and the consequent energetic costs of systemic error correction, and so are not suited to composition into a system-level description of either emergence or stability. At the other extreme, Darwinian selection is a purely informational theory, concerned with emergence and stabilization through statistical processes. Yet, for lack of a comprehensive theory of individual function, models of the dynamics resulting from selection inevitably take for granted the platform of physiology, growth, development, and reproduction, decoupling the problem of information input from energetic constraints on the mechanisms by which it occurs.

“In the absence of traditional biological paradigms that link energy flow and the restriction of states of order, how are we to understand at an aggregate level what the biosphere is doing as it constructs and maintains itself, and what limits may exist to how well or how far it can do this?….

“[NOTE] The point is that the very concept of control, intended to capture the rich causality of living processes, presumes the ability of one component to restrict variation in another, while Darwinian dynamics arise when prior variation cannot be suppressed, but only evaluated after it occurs by the selective environment.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. pp. 185-6.

“The featurelessness of the few sources of energy powering life ensures that all sources of biological information are effectively compared against one another by the biosphere itself, through its partitioning of energy flow.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 186.

“A key observation in these papers will be that the optimal efficiency in using energy to reject entropy is attained by reversible transformations.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 186.

“Persistence is a system as well as a molecular property, and the energy cost of ensuring persistence should somehow be counted as the cost of making the information ‘in the gene’ continuously available during a sequence of biosynthetic events….

“Energy is continuously consumed to ensure persistence at the level of the cell or organism, by correcting errors of structure or function that occur in all components.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. pp. 189-190.

“Equilibrium is special because it is the condition with highest entropy, hence least information, of all conditions compatible with the values taken by its state variables. In an equilibrium system, there is no ‘hidden information’ that can influence its future dynamics beyond the influence from the state variables.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 190.

“Reversible transformations are those that cause the system to pass only through (or arbitrarily close to) states of equilibrium at all times. Reversible transformations can never create or destroy information; they can at most redistribute it among components of a system.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 190.

“The distinctive feature of biological systems, which can make models difficult to compose but limiting behaviors tractable, is the machine-like nature of biological control. The essence of mechanical control is the separation of timescales between the processes of change in the controlled system and those in its controller. The problem of assigning informatic costs to persistence … is the problem of explaining the stability of a controller which is itself composed of stochastic components. However, when it arises, this kind of persistence is what makes possible the approximation of reversible transformations…. The substrate on which a reversible machine acts may be kept near its equilibrium as long as the relaxation of its components is fast compared to the timescales on which the machine moves, fails, or requires replacement.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 191.

“The separation of timescales between catalyzed and uncatalyzed reactions kinetically isolates particular reaction sequences and couples these to sources of energy, while leaving most mechanisms for decay slow and decoupled.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 191.

“The idea that, with the correct entropy measure, the biosphere might be recognized as the most disordered state compatible with its boundary conditions–and therefore the most stable–is not inconsistent with the use of reversible transformations and equilibrium entropy measures to characterize its informational state.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 192.

“The distinguishing feature of the bound developed in this and the next two papers is that the limit on the amount of information that can be put into a biological system is determined by the cumulative work done on the system and by its temperature as an energy scale, but not on the time taken to do the work, on thermal effects of degradation, or on any other ‘material’ aspect of the system or its transformations. This dependence of information solely on work and energy scale is a necessary consequence of any bound derived from reversible transformations.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 192.

“The second-law reasoning behind Eq (1) [dW = dQ = -kBTdS ≡ kBTd∮, where W = work, Q = heat, and d∮ = an increase in information] is this: The entropy of a driven system can only be reduced by some amount –dS if the entropy difference is ‘exported’ to the environment in the form of heat. Yet to reject entropy -dS as heat to a bath at tempeature T requires an amount of energy dQ = -kTdS, by definition of temperature, as the energy-per-unit-entropy in a heat flow. Furthermore, for all of this amount of energy to have been available to carry away entropy as heat, it must have come to the system in some entropy-free form, in other words as work in an amount dW = dQ carried on some non-stochastic degree of freedom.” Smith, Eric. 2008. “Thermodynamics of natural selection I: Energy flow and the limits on organization.” Journal of Theoretical Biology. 252:185-197. doi: 10.1016/j.jtbi.2008.02.010. p. 193.

“… life consists of subsystems, which are partly integrated and partly autonomous, and are brought together in cooperative assemblies to form living wholes. We characterize life as a ‘confederacy’ of different sources of order, many of which we argue have independent origins within different domains of chemical or physical processes, or planetary conditions.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 14.

“The universal feature of life to be explained is its capacity to preserve a distinctive, dynamical, chemical pattern in a planetary context, apparently indefinitely, and under the full range of planetary perturbations from microscopic fluctuations to astrophysical disturbances.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 19.

“We will argue that life emerged early and has persisted robustly because the origin of life was actually a transition away from a less stable planetary condition devoid of life, and into a more stable condition that includes a biosphere. In entropic terms, this transition was still a ‘collapse’ from an improbable to a more probable phase, but the stable phase in this case was the dynamically ordered living state.

“Even at equilibrium, the idea of a collapse into order is not new or radical in open systems that can undergo phase transitions: it happens every time rapidly cooled water vapor nucleates its preferred state of frost, or whenever a supersaturated cloud condenses into a downpour. The frost and the liquid raindrop are both, in entropic terms, more ordered than the phased from which they formed, though the energy loss that makes them more ordered accounts for an even larger amount of entropy as heat in the environment. Systems that undergo non-equilibrium phase transitions can collapse into order in ways even more intuitively like the emergence of life: this happens whenever a fracture suddenly forms and propagates in a stressed elastic solid, or a lightening strike forms across a gap in the atmosphere between a charged cloud and the ground.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 27.

“We argue that the pervasive role played by ordered phases is error buffering: in systems subject to errors in very many dimensions, cooperative effects can provide regression toward sufficiently low-dimensional spaces of variation that the residual errors can be managed within the limits of complexity of controllers and control signals. This buffering is only available, however, where cooperative effects are strong enough to cross thresholds to form ordered states. The capacity to self-buffer many dimensions of internal error is a form of autonomy….” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 31.

“… we propose that the origin of life was not so much the creation of an autonomous system to which complexity was added, as it was the gathering of dispersed and heterogeneous mechanisms of order formation in geochemistry, into a system where their progressive integration and interdependence gradually made them autonomous.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 36.

“Ecosystems must become ‘first-class citizens’ in biology, in some respects prior to and more fundamental than organisms.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 40.

“Short of the diversity of life, the world of mineralogy probably contains the richest family of related yet distinct structures produced by a few underlying generating mechanisms….

“More than 4500 mineral phases are known on Earth today, which combine in a bewildering variety of assemblages. The ab initio prediction of the favored assemblage in many conditions is still an unsolved problem…. The combination of determined elements, sensitive dependence on boundary conditions, and long memory also characterizes the biosphere.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. pp. 85, 86.

“… we believe that an Earth that had never been geologically active, or that had quenched too soon or formed a rigid lid, would never have generated a biosphere at all – despite the existence of solar free energy sources that by appearances could sustain life that had achieved sufficient complexity.

“It is essential that our planet is a restless planet….

“As important as the maintenance of dynamics in the Earth, which drives energy flows through its subsystems, is the fact that Earth is a chemical entity, that its unrest is carried in the forces and flows of chemical states and processes, and that the continuity with the biosphere occurs in specific domains of organometallic chemistry.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 106.

“Weathering accomplishes the oxidation of the lithosphere with transfer of reductants to the hydrosphere and ultimately the atmosphere, along with other alterations in mineral composition and phases.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 115.

“The co-presence of ions and molecules forming strong redox couples, which would never occur near equilibrium, is the joint product of all the above planetary forces: mantle stratification and convection, star-driven atmospheric oxidation, fracture-conducted melt concentration and hydrothermal alteration, and finally delivery by mixing into the hydrosphere. Each of these mechanisms has contributed in a particular way to the accumulation of a free energy behind a barrier. Jointly they culminate in the steady delivery of systems with moderate free energies of reaction ~0.1 eV, comparable to the energy of covalent bonds.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 126.

“However, it should be appreciated that Earth’s subsurface is extensive and diversified, with a long history, and that many kinds of environments are known to host chemotrophic life.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 142.

“Individual vent fields are transient on the timescales expected for macroevolution or possibly for the full transition from geochemistry to cellular life. Individual hydrothermal circulation systems are typically active on timescales ~<105 years.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 143.

“In particular high-temperature and highly reducing environments on Earth today, and more widely in the early Archean or the putative Hadean, an increasing fraction of biosynthetic reactions become exergonic.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 150.

“They [Amend and Shock] showed that for mixtures at 100̊ C, biosynthesis of 11 of the 20 amino acids is exergonic. In contrast, the biosynthesis of all 20 amino acids is strongly endergnic in mixtures that produce 18̊ C oxic seawter….

“The fact that primary biosynthesis is exergonic in mixed vent fluids may provide part of the explanation for the extraordinarily high primary productivity of vent environments. A similar calculation, adjusted to the much lower fO2 [fugacity of oxygen] in plausible models of a Hadean ocean component in mixed vent fluids, suggests that instead of only 11/20 amino acid pathways being exergonic, synthesis of most of the amino acids may have been exergonic on the early earth.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 154; reference: Amend, J.P. & E.L. Shock. 1998. “Energetics of amino acid synthesis in hydrothermal ecosystems.” Science. 281:1659-1662.

“The network architecture of metabolic reactions decomposes into modules and layers. Important motifs include autocatalytic loops either within or across hierarchical layers, repeated sequences of functional-group rearrangements, and distinctive and conserved dependence on certain catalysts – especially those involving metal reaction centers.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 170.

“The layer of life that converts material and energy from the abiotic geospheres into the biomass that carries out all living processes is metabolism. It is both the interface layer that anchors life within planetary processes, and the first level in the synthetic hierarchy of living matter.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 170.

“… information is a property of systems that are subject to limits on their variation. So far as the constituents of metabolism and their network relations are dictated by the composition and energetics of the Earth, the production of selected metabolites is the first and deepest source of limits on the forms the biosphere can take, or could ever have taken.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 171.

“The most diverse and most informative evidence that metabolism has a comprehensible and even rule-like order comes from the many ways it decomposes into quasi-independent subsystems and redundant elements.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 173.

“A different metaphor is suggested by the environments on Earth that generate reductants out of equilibrium with ambient carbon as well as environmental oxidants. It does not eliminate the role of machines, because even chemotrophic life uses chemical work to overcome locally endergonic steps in biosynthesis, but it removes the image of work as an all-encompassing barrier between thermodynamics and life. Chemotrophic organisms ‘capture’ free energy by the process of building biomass.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 188.

“Six pathways are now known to support autotrophic carbon fixation, which are in part genuinely different and independent. Yet the variations are mostly minor; all carbon fixation pathways show large overlaps of reaction sequences, and even larger homologies of reaction mechanisms and local-group chemistry. Where truly significant innovations have occurred, they appear to have been constrained to integrate within the same overall system, and therefore they feed their products back through a small standard set of precursors to anabolism and other key intermediates. For such cases, universality is not a property of any particular pathway, but must be recognized in the relations among pathways and the rules that have apparently governed the evolution of variants.

“To describe metabolic universality, one needs a multilevel representation, in order to see that some regularities exist at the level of metabolites, reactions, or pathway segments, while others exist as patterns of local group chemistry or limits on innovation imposed by a need to integrate within a self-maintaining system. We will introduce the idea of a universal covering network of autotrophic carbon fixation as the first level in such a description of regularities. The covering network … is the smallest network that contains all known carbon fixation pathways, together with the universal anabolic precursors and the branch pathways to the major CHO compounds: sugars, fatty acids, and isoprene alcohols….

“The three most striking features of the covering network are (1) that it is small, (2) that it is easy to define a relatively unambiguous boundary, and (3) that it has significant internal structure.” Smith, Eric & Harold Morowitz. 2016. The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere. Cambridge UP. p. 197.

“The fact that carbon fixation is not only simple, but that it is simple in this way – with explicit links to minerals and the periodic table – leads us to propose that the same set of constraints can have been both causes of limited evolutionary innovation in the world of modern cells, and yet common to the cellular world and back through pre-cellular life and protometabolism to prebiotic geochemistry. The plausible continuity from minerals to modern enzymes leads us to characterize the emergence of metabolism as an ‘enfoldi