2023 Citations

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

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Citations collected in 2023 (works listed above):

“Charles Darwin himself was well aware of the phenomenon of convergent evolution. In an attempt to explain to his readers how natural selection might produce convergent biological evolution, in On the Origin of Species Darwin wrote: ‘I am inclined to believe that in nearly the same way as two men have sometimes independently hit on the very same invention, so natural selection … has sometimes modified in very nearly the same manner two parts in two organic beings, which owe but little of their structure in common to inheritance from the same ancestor’….

“What Darwin did not realize was how powerful the selective effects of functional and developmental constraints are in limiting and directing the seemingly endless pathways open to evolutionary change, and in producing convergent evolution. It is due to the fact that the number of functional and developmental options open to natural selection are limited that life has repeatedly ‘independently hit on the very same invention,’ as he put it, both in the oceans as well as on land.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. xiii; subquotes: Darwin, Charles. 1859. The Origin of Species. pp. 193-4.

“Thus when we seek to analyze two convergent forms in nature–forms that look very similar but are present in organisms that did not inherit them from a common ancestor, forms that were independently evolved in the two organisms that possess them–we should ask the two questions: (1) how do the forms function? and (2) how do the forms grow?” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 5.

“Instead of spheres, other forms of filter-feeding marine animals include the plant-like sea ferns and sea fans. These octocorals have numerous tiny polyps that are arranged along the branches of their skeletons that filter small organisms and organic debris from seawater. A Pennatula octocoral colony looks astonishingly like a fern frond, having a cental stem axis with bilaterally symmetrical branches that bifurcate off the stem axis to the left and right at regular intervals along the stem.

“The similarity of a colony of marine animals to the frond of a fern, a land plant, becomes intelligible when we realize that the fern is also a filter feeder. Instead of food particles suspended in seawater, the fern is adapted to filter photons of light that are streaming from the sun from the air that surrounds the land plant….The frond branches of the fern are made chiefly of cellulose and the photon-capture structures are leaves, whereas the frond branches of the octocoral are made chiefly of calcium carbonate and the food-capture structures are polyps, but the filter-feeding function and branching-growth geometric development of the fronds is convergent in both sets of organisms–hence the convergence in form.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 10-11, 12.

“The early land plants that grew in three dimensions were small vertical stems with no leaves…. One solution to this classic area-volume problem [if plants were to grow to larger sizes] is to take the single stem and branch it into multiple stems, each with its own photosynthetic surface area… The second solution is to evolve specialized structures with large surfaces to absorb more photons–in essence, to evolve leaves. This is how the crown of the palm tree came to be.

“Larger plants require more water and nutrients, and on land the only source for these is in the soil below the vertical plant. Plants accordingly had to evolve solutions to the area-volume problem here as well, to evolve structures that would increase the surface area at the opposite end of the plant that could be used for absorption of water and nutrients–that is, to evolve roots….

“Roots were also a solution to a separate problem for large land plants–the force of wind… The end result of all these evolutionary processes was the land-plant tree that we are all familiar with.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 13-4.

“Allo-convergent evolution is the independent evolution of the same or very similar new trait from different precursor traits in different lineages. Iso-convergent evolution is the independent evolution of the same or very similar new trait from the same precursor trait in different lineages. Retro-convergent evolution is the independent re-evolution of the same or very similar trait to an ancestral trait in different lineages.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 21-2.

“SET:
“CONVERGENT EVOLUTION: The evolution of the same or very similar traits independently in different lineages of organisms.

“SUBSETS:
“1. Allo-convergent evolution: the independent evolution of the same or very similar new trait from different precursor traits in different lineages.
“2. Iso-convergent evolution: The independent evolution of the same or very similar new trait from the same precursor trait in different lineages.
“3. Retro-convergent evolution: The independent re-evolution of the same or very similar trait to an ancestral trait in different lineages.

“Subsets:
“3a. Retro-alloconvergent evolution: The independent re-evolution of the same or very similar trait to an ancestral trait from different precursor traits in different lineages.
“3b. Retro-isoconvergent evolution: The independent re-evolution of the same or very similar trait to an ancestral trait from the same precursor trait in different lineages.

“ECOLOGICAL NICHE CONVERGENCE: The evolution of the same or very similar mode of life, ecological role, or ecological niche independently in different lineages of organisms.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 22.

“A classic example of iso-convergence is the independent evolution of wings in bats, birds, and the extinct pterodactyls of the Mesozoic. A bat is a member of the clade of the mammals, a bird is a member of the clade of the dinosaurs, and a pterodactyl is a member of the clade of the pterosaurs–yet all three animals are members of the larger inclusive clade of the vertebrates. And the same precursor trait–the vertebrate forelimb–was independently modified to form wing structures iso-convergently in bats, birds, and pterodactyls.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 24.

“Ecological niche construction is best recognized by considering truly bizarre ways of making a living–ecological roles that are so strange that, at first glance, it would seem probable that only one species would have evolved such a restricted ecological pathway. And then to observe, astonishingly, that the ecological evolution of life on Earth is so constrained that multiple species have ecologically converged on that same odd pathway in their evolution. Prime examples of ecological niche convergence are the evolution of carnivorous plants, which has independently occurred in twelve different plant lineages, the evolution of parasitic plants, which has independently occurred in seven different plant lineages, and the evolution of a highly restricted form of insectivory–eating insects that bore into tree bark–which has independently evolved in seven different lineages of animals from avian-dinosaurian woodpeckers, finches, and honeycreepers, to marsupial mammals (striped possums), and to primate mammals (the Aye-aye). All of these animals have strikingly different morphologies but their way of making a living in nature, their ecological niche, is the same.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 29.

“Convergence arises because the evolutionary pathways available to life are not endless but instead are limited. If the number of possible evolutionary pathways was infinite then each species on Earth would be morphologically different from every other species, and each species would have its own unique ecological role or niche. Such an Earth does not exist. Instead, repeated evolutionary convergence on similar morphologies, niches, molecules, and even mental states is the norm for life on Earth.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 31.

“Many marine animals have evolved the ability to photosynthesize their own food, and some organisms that are anatomically animals can be primary producers in marine ecosystems. Marine animals accomplish this evolutionary feat in several ways–the most common is for the animal to evolve a symbiosis with another photosynthetic organism, most often species of algae. Here the animals are following a pathway convergent on that used by the algae themselves in the Paleoproterozoic, which formed symbioses with the aerobic-photosynthesizing cyanobacteria. The chloroplasts of modern multicellular plants are the descendants of ancient symbiotic cyanobacteria. Another pathway is for the animal to eat a photosynthetic organism, digest all of the organism except its chlorplasts, and then incorporate the chloroplasts into its own tissues–an evolutionary pathway used by the emerald-green slug Elysia chlorotica….” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 35.

“The evolution of photoautotrophic animals has occurred repeatedly, convergently, in widely separated animal lineages in Earth history–and not only in multicellular, unikontan animals but also in unicellular, bikontan organisms as well. All in all, the convergent evolution of photoautotrophy by heterotrophic organisms has occurred at least 57 times in independent lineages of marine life.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 36.

“Perhaps the most spectacular of the living photoautotrophic marine animals are the giant clams, species of the genus Tridacna in the cardiid subfamily Tridacninae…. The relationship between the giant clam and the dinophyte algae is a symbiotic one–the clams metabolize the complex hydrocarbons (food) and oxygen produced by their photosynthetic algal symbionts, and in return the algae metabolize the carbon dioxide and phosphate and nitrate wastes produced by the clams and produce more hydrocarbons and oxygen. In addition, the clams provide their algal symbionts protection from predation by grazing marine animals by holding them within their tissues….

“As a result of their photoautotrophic lifestyle, living Tridacna giant clams grow to be the largest bivalve molluscs ever to exist in Earth history. Individuals of the largest giant-clam species, Tridacna gigas, can weigh up to 260 kilograms and have shells 130 centimeters long, compared to an average large clam that has a shell about the size of your hand.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 36.

“The flatworm Symsagittifera roscoffensis has convergently evolved photoautotrophy in a symbiosis with the unicellular alga Platymonas convolutae, which invades the flatworm larvae soon after they hatch from their eggs in sandy, marginal-marine environments. The symbiosis becomes more well developed with time, such that the adult flatworms are gutless and cease to feed, depending entirely upon the photosynthetic algae for their nutritional requirements….” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 44.

“The emerald-green slug Elysia chlorotica is an intriguing sacoglossan gastropod that does not host photosynthetic algae or bacteria in its tissues. Rather, it eats the marine alga Vaucheria litorea and stores the alga’s photosynthetic chloroplasts in cells lining its digestive diverticular. The photosynthetic chloroplasts continue to function within the snail’s cells, and to provide the snail with energy and oxygen. The snail is able to keep the algal chloroplasts alive by providing them with essential algal proteins that the snail manufactures itself. The snail, an animal, is able to synthesize algal proteins because it has acquired the necessary algal nuclear genes by the process of horizontal gene transfer–a case of natural genetic engineering by the sacoglossan snails.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 44-5.

“Just as we have seen in the case of photoautotrophy, the convergent evolution of chemoautotrophy in marine organisms has occurred from simple unicellular, bikontan ciliophorans to complex multicellular animals like crabs and shrimp. All in all, the evolution of chemoautotrophy by heterotrophic organisms has occurred independently in at least 41 lineages of marine life. As with the photoautotrophic marine animals, the great majority of the chemoautotrophic marine animals are lophotrochozoans: five lineages of brachiopods (all extinct), seven lineages of annelid worms, and 20 lineages of molluscs (12 living and eight extinct).” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 58.

“Perhaps the most unusual type of animal imaginable is a sessile marine predator–a carnivore that does not actively hunt its prey, but rather waits for its prey to come to it. Yet even here the similarity of marine animals to land plants re-emerges in that sessile predators actually do exist on land, but they are plants rather than animals. These are the famous carnivorous plants–plants that actually trap, kill, and digest animals….” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 71.

“All the great reefal ecosystems that have existed through Phanerozoic time, such as the modern Australian Great Barrier Reef, were composed of millions of sessile, predatory flower animals. Only later in their evolutionary history did various groups of predatory cnidarians evolve some mobility, particularly the medusozoans with their mobile jellyfish stage of growth. Curiously, some of the normally filter-feeding sponges have independently evolved adaptations to converge on the ecological niche of sessile carnivory.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 71.

“A second example of ecological niche convergence on unusual types of carnivory in marine animals is suction feeding…. Suction feeding is almost impossible on dry land, in the thin air of Earth’s atmosphere…. In the oceans, however, suction feeding has convergently evolved in at least 20 independent lineages of swimming vertebrates….

“Last, in the clade of the pinniped carnivorans, suction feeding is used both by seals and walruses, and is suspected to be present in the third family of extant pinnipeds, the sea lions….

“A third example of ecological niche convergence on unusual types of carnivory that is found in marine animals is the niche of lure fishing, in which predatory animals do not pursue prey but instead lie in wait, most of their bodies motionless and camouflaged, and waggle a decoy lure to entice their prey to come close enough to them to be captured….

“Perhaps the most bizarre form of carnivory to have evolved in marine life is fishes that fish for other fish, complete with a fishing rod, fishing line, and fishing lure–sometimes even a light at the end of the fishing line to attract other fish in the dark. What is near unbelievable with this scenario is that these fishes are not tool makers–instead of constructing a fishing rod, line, and lure they grow these structures with their own body tissues. These are the aptly named anglerfishes–almost three hundred species possessing fishing rods that belong to the clade of the lophiiform fishes….

“The bizarre anglerfish are not unique. The giant-mouth catfishes have convergently evolved organic structures to also fish for other fish….

“One last example of ecological niche convergence on unusual types of carnivory in marine animals is the repeated evolution of zooplanktivory in disparate vertebrate lineages–carnivores possessing specialized adaptations to feed on tiny marine zooplankton. Since these animals eat tiny prey, one might assume that they themselves would be small–and that assumption would be wrong, as the zooplanktivorous baleen whales are larger than the largest dinosaur that ever existed. Of these peculiar planktivorous predatoers, Friedman has noted … ‘The repeated evolutionary convergence on suspension feeding at large body sizes in phylogenetically disparate vertebrate lineages implies that this ecological strategy represents an important trophic role that has persisted over geological timescales.’” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 71, 72, 78, 79, 80; subquote: Friedman, M. 2012. “Parallel Evolutionary Trajectories Underlie the Origin of Giant Suspension-Feeding Whales and Bony Fishes.” Proceedings of the Royal Society of London: Series B, Biological Sciences. 279:944-951. p. 944.

“In contrast to the algal-grazing fish vertebrates, the green turtle vertebrates can eat living plants…. Symbiotic bacteria and protozoa facilitate digestion. Thus perhaps the green turtles should be renamed the sea ruminants in recognition of the convergence of their digestive systems with those of the land-dwelling ruminants.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 87.

“In the oceans the agricultural cultivation of crops has independently evolved in five clades of animals–ray-finned vertebrates (damselfishes), annelid worms, and three separate clades of marine snails. The damselfish vertebrates cultivate crops of photosynthetic algae; thus they are more allo-convergent with human vertebrates, who cultivate photosynthetic plants, than with the three clades of land-dwelling insect agriculturalists, which all cultivate fungi. Damselfishes have evolved the most complex agricultural behaviors seen in marine animals–they weed their crops to remove unwanted algal competitors, defend their crop territories from other herbivores, and carefully graze their crops to stimulate the algae to remain in the rapid-growth, early-succession phase.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 89.

“The convergent evolution of agricultural behavior on land has produced ‘higher agriculture’ independently in ants, termites, and humans. In all three clades, similar agricultural behaviors include (1) preparing the substrate to be used for growing crops, (2) planting the crops, (3) monitoring the growth and potential disease status of the crops, (4) protecting the crops from disease, (5) protecting the crops from crop-eating species other than the farmers, (6) weeding invasive species out of the crops, (7) using chemical herbicides for weed control, (8) using microbes for biological pest control, (9) using microbial symbionts to procure nutrients for the crops, and (10) the sustainable harvesting of the crops for food. Marine agriculture, in contrast, is less complex and would be classified as ‘low-level’. In most cases the agricultural behaviors of substrate preparation, weeding, fertilizing, defense of the crop from other herbivores, and sustainable harvesting have been independently evolved in marine agricultural clades. As such, marine agriculture is more convergent on the simpler agricultural systems of the land-dwelling ambrosia beetles. Even so, from the perspective of theoretical morphology, the demonstrable convergent evolution of even simple agricultural behaviors in clades of animals in radically different environmental conditions–in the oceans and on dry land–is evidence that there are a limited number of ways to successfully cultivate crops, and that convergent behavior must necessarily result because independent lineages of animals have a limited number of farming options to discover.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 91-2.

“Things are very different in the oceans [for scavengers]. In addition to our normal concept of animals that are carrion eaters–animals that search for dead bodies to eat–in the oceans there exists a different group of scavenging animals known as detritus feeders…. Detritus-feeding coprophagy (the term literally means ‘feces eating’) would at first appear to be a poor method for food acquisition, as presumably most of the nutritive value of the original food has been extracted by the animal excreting the feces. However, once the fecal pellets have been colonized by microbial organisms, the microbial organisms themselves become the source of nutrition for the coprophagous detritus feeder….

“The early trilobite arthropods were detritus feeders….

“Most of these [modern] scattered and disparate detritus-feeding lineages are not convergent–in most cases they are simply continuing the ancient mode of feeding of their distant Cambrian ancestors.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 116-7.

“Much of the seafloor in modern oceans is composed of soupy muds and silts, and is unstable. However, this environmental condition is a relatively new phenomenon in earth’s history. When animals first evolved, some 780 million years ago, seafloors were covered by microbial mats and films that bound the fine-grained sediment together into firm biomat environments. The first Ediacaran and sponge-like animals flourished in these benthic biomat environments in the last 239 million years in the Proterozoic Eon, an interval of time that has been called the ‘Garden of Ediacara’. The garden of Ediacara came to end some 541 million years ago with the onset of the Phanerozoic Eon and the ‘Cambrian Explosion’ of evolutionary diversification in the bilaterian animals–and the extinction of the Ediacaran animals. Not only did the bilaterian animals rapidly diversify, they also radically altered the entire marine biosphere of Earth. New herbivorous animals evolved, much larger and voracious, and consumed the biomats of earth’s seafloors while newly evolved actively burrowing animals churned up the sediment of the sea bottoms. Some of these endobenthic, burrowing animals were searching for food but a great many also burrowed within the sediment to escape or hide from newly evolved predators–larger and more voracious carnivores that ate the newly evolved herbivores. Thus began the ecological coevolution of herbivores and carnivores, a trophic-interaction escalation that produced the first complex trophic pyramids and multi-tiered marine ecosystems.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 119-120.

“Adaptations for floating on the surface of soft substrata [of the ocean floor] are called ‘snowshoe adaptations’ and adaptations for floating in the layer of soft substrata are called ‘iceberg adaptations’.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 120.

“… four major types of rooted forms in marine animals: tap rooted, bunch rooted, mat rooted, and mangrove rooted….

“However, the direction of growth in tap-root-form marine animals is the reverse of growth seen in tap-rooted land plants. The tap root of a carrot grows downward, but the tap-root-form marine animals grow upward to escape smothering by accumulating sediments.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 129.

“A second attachment pathway [for marine organisms to hard surfaces where first pathway is weaker strategy of using roots] is to use cement. In almost every phylum of marine life that has evolved skeletons there are clades that have also evolved the capability of using that same biomineralization process to cement the organism to hard substrata….

“A third stability strategy is to bore into the hard substratum rather than try to attach to its surface area. This adaptive pathway is less common in marine animals than cementation and is accomplished by two separate means–mechanical boring or chemical boring.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 133.

“… plankton are small and drift with water currents, nekton are large and swim independent of water currents [but definitions here differ].” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 139.

“Eight lineages of snails have convergently evolved to invade the ecological niche of the plankton. The janthinid purple snails evolved a novel adaption to acquire flotation–they create a raft of mucus-covered air bubbles from which they hang, upside down, just below the surface of the ocean.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 144.

“In summary, no fewer than 41 independent lineages of marine organisms have separately evolved planktic adaptations and converged on the ecological niche of the plankton. The great majority of these evolutionary convergences occurred in the early Paleozoic in what has been named the ‘Paleozoic Plankton Revolution.’ Why did the Paleozoic plankton revolution occur? Signor and Vermeij have argued for three separate evolutionary triggers: to escape from benthic predators, to escape from unstable benthic substrates and bioturbating animals, and to utilize an increase of nutrients in the water column.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 151; reference: Signor, P.W. & G.J. Vermeij. 1994. “The Plankton and the Benthos: Origins and Early History of an Evolving Relationship.” Paleobiology. 20:297-319.

“Moving forward in time to the modern era we are confronted with another plankton question–how can so many species coexist in the plankton that are seemingly dependent upon the same limited number of resources? This question has been termed the ‘paradox of the plankton’ by Hutchinson, as this phenomenon appears to contradict the theory of competitive exclusion….

“In contrast, Rigby and Milson have argued for habitat instability as an abiotic mechanism to prevent competitive exclusion that resolves the paradox of the plankton. That is, ecologically similar planktic species can coexist because their pelagic habitat is so unstable that long-term competition and exclusion cannot come to completion.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 151-2; references: Hutchinson, G.E. 1961. “The Paradox of the Plankton.” American Naturalist. 95:137-145; Rigby, S. & C. Milsom [sic]. 1996. “Benthic Origins of Zooplankton: An Environmentally Determined Macroevolutionary Effect.” Geology. 24:52-54.

“Things are different in the dense waters of the oceans, where five independent lineages of animals have evolved jet-propulsion flying…. Instead [of jet fuel], jet-propelled animals have evolved two organic forms to generate internal pressure and the accelerated expulsion of seawater–squeeze-bottle forms and bellows forms. The squid and cuttlefish cephalopods are squeeze-bottle-form jets–they intake water into their internal mantle cavities, pressurize the water using their muscles, and eject a high-pressure jet of seawater out of their hyponome–a specialized organic nozzle with a narrow opening….

“The other organic form of jet propulsion in marine animals is the bellows form, evolved independently in the lineage of the bivalve molluscs and in the lineage of the extinct strophomenate brachiopods. In both cases the function of bivalve and brachiopod jet propulsion is to escape from predators. Clarkson notes that the ‘large scallop Pecten normally lies free on the sea floor, but it can swim by vigorous and repeated clapping of the valves [of its shell] together so as to expel water in successive jets on both sides of the ‘ears’.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 153, 155.

“On land, the vertebrate clade of animals iso-convergently evolved wings from their forelimbs three separate times–in the pterosaurian flying reptiles, the dinosaurian birds, the mammalian bats–and left the ground to fly into the skies….

“However, back in the oceans, marine animals have evolved winged forms as well, but in six independent lineages. Four of these lineages are vertebrates–one chondrichthyan and three osteichthyan–and two are independent lineages of gastropod molluscs. As in the case of the flying ommastrephid squid the question of whether fish can fly is removed when they are observed exiting the waters of the ocean and flying through the air.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 156.

“Specifically, Murphy et al. note that very small flying insects all fly in air with a Reynods number, or Re <= 100 and that all of these species use the Weis-Fogh ‘clap-and-fling’ flying mechanism–a behavior that appears to be obligate in these tiny insects.

“Seawater is much denser than air, yet in a balance of inertial and viscous forces within seawater that yields Re numbers similar in range (Re = 10-100) to those that tiny flying insects experience in air, Murphy et al. have found that the marine sea butterfly Limacina helicina and the sea angels Clione limacina and C. antarctica have convergently evolved the same clap-and-fling Weis-Fogh flying mechanism used by terrestrial flying insects. In summary, Murphy et al. point out, ‘It is highly surprising to find a zooplankter ‘mimicking’ insect flight as almost all zooplankton swim in this intermediate Reynolds number range (Re = 10-100) by using their appendages as paddles rather than wings.’” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 158; reference: Murphy, D.W., D. Adhikai, D.R. Webster & J. Yen. 2016. “underwater Flight by the Plankonic Sea Butterfly.” Journal of Experimental Biology. 219:535-543.

“At least seven major lineages of plants have independently evolved convergent Velcro-like forms to achieve dispersal of their seeds by having them hitchhike on other organisms–usually land animals….

“Things are different in the oceans. At sea it is usually animals that are hitchhiking on plants, rather than plants hitchhiking on animals like on land.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 172.

“Unlike the marine arthropods, the vertebrates evolved jointed appendages in the process of leaving the oceans and invading the landmasses of Earth. The marine arthropods had already accomplished that feat, having successfully invaded the land earlier in the Silurian.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 173.

“The convergent evolution of protective body armor has occurred in seemingly countless independent lineages of marine organisms…. This is in sharp contrast to animals that live on land, where protective body armor is rare….

“… over 30 lineages of marine animals have convergently evolved protective body armor. As soon as the oxygen content in marine waters arose to sufficient levels to allow the metabolic secretion of mineralized tissues, animals began to armor themselves in the earliest Cambrian, triggering the Cambrian Explosion in animal diversity and the beginning of the Phanerozoic Era….

“Most lineages of armored marine animals develop skeletal armor made of calcium carbonate…. Others evolved skeletal armor made of various calcium-phosphatre compounds, such as the hydroxyapatite bones of the vertebrates and the phosphatic shells of the linguliform brachiopods. Still others evolved skeletons made of silica… And last, the enormously diverse clade of the marine arthropods evolved organic skeletons made of horny and tough chitin, an amorphous polysaccharide, and not a mineral compound like silica or calcium carbonate.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 182-3.

“Land plants are sessile, they cannot run away from animals that threaten them, so at least 19 independent land plant lineages have convergently evolved sharp spines and thorns to defend themselves from herbivorous animals….

“In contrast, spinous defense is rare in land animals–porcupines, hedgehogs, and spiny echidnas come to mind…. Thus the actual number of mammalian lineages that have convergently evolved spinous defense is five.

“Things are different in the oceans, where at least ten lineages of marine animals have independently evolved spinous defensive structures.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 188.

“In contrast to the land animals, poisonous defense has convergently evolved in numerous independent land-plant lineages.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 191.

“At least 68 convergent lineages of land plants have evolved chemical defenses to defend themselves from herbivores–from poisonous leaves, stems, seeds, fruits, and bulbs, to the entire plant being poisonous.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 191.

“When the defensive organism is adapted to produce a specific poison for the purposes of defense, such that even a small amount of that defensive poison will cause serious harm to the attacking organism, then that poison is classified as a toxin. If the defensive organism has evolved an adaptation for deliberately transmitting its defensive poison into the attacking organism’s body–usually by biting or stinging–then the transmitted poison is classified as a venom.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 191.

“Many convergent venomous marine animals are themselves predators, and use their venom-delivery structures for both offensive, predatory, and defensive anti-predatory purposes. Interestingly, numerous venomous marine animals use two different types of venom for these two different uses….” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 194.

“In an interesting case of ecological niche convergence, the cone snails then evolved faster-acting and more potent venoms to defend themselves from attacking fish, eventually resulting in venoms so lethal that they killed the fish, thus ‘opportunistically offering the snail a new meal option. At least three different lineages of cone snails made the switch over to speedy prey.’” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 195; subquote: Wilcox, C. 2016. Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry. NY: Scientific American/ Farrar, Straus and Giroux. p. 155.

“Surprisingly, however, many of the fundamental organ systems evolved by marine animals have been carried on relatively unchanged in animals that are now living on land and breathing air. Even more surprising is the fact that many of these same organ systems evolved independently in different lineages of marine animals–they are convergent.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 199.

“The evolutionary transition from unicellular forms of life to multicellular forms occurred independently in the plants, animals, and fungi.

“At a closer glance, the evolution of multicellularity is rampantly convergent across the full spectrum of life on Earth. Multicellularity has evolved independently at least three separate times in the bacteria, once in the brown algae, once in the golden algae, twice in the red algae, twice in the green algae (one lineage of which produce the plants), once in the amoebocytes, three separate times in the fungi, and once in the choanozoa (which produced the animals).” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 200.

“In one of the most spectacular examples of iso-convergent evolution due to the co-option of ancestral gene regulatory networks, we now know that all animal eyes are produced by modifying the same conserved regulatory gene present in the animal genome–the Pax-6 gene–and that that modification has independently occurred in the evolution of eyes in some forty-nine separate lineages of animals.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 211.

“Terrestrial animals breathe air, not water. Two specialized structures have been evolved by land animals for gas exchange with air–tracheae and lungs. These two respiratory systems are very different, and represent a case of the divergent evolution of gas-exchange organic systems. However, both systems have been independently evolved more than once.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 220.

“Every single type of visual system, from the simplest photoreceptor cells to complex camera eyes, has been independently evolved by animals in the seas long before animal life existed on land. All in all, visual systems have been independently evolved in at least 46 separate lineages of animals living in the oceans of Earth.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 227.

“Only in water, with its high conductivity of electricity, is the development of functioning organic electroreceptive sensory structures possible. Even terrestrial animals that have convergently evolved electrosensory organs, like the duckbilled platypus Ornithorhychus anatinus and the Australian echidna Tachyglossus aculeatus, only use them in water (platypus) or wet soils to detect earthworms (echidna).

“At least six independent lineages of marine and freshwater fishes have evolved active electroreceptive organs, at least fourteen independent lineages have evolved passive electroreceptive organs….” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 229.

“In today’s oceans, endothermy is present in five separate lineages of living marine fishes, and was probably present in an unknown number of extinct lineages of fishes that we may never know about…. Unlike the evolution of endothermic metabolism in land animals, which is usually attributed to selective advantage of energetic lifestyles and the ability to sustain high activity levels, endothermy in marine animals has been argued to have been evolved in the process of niche expansion of these fish lineages into cold-water regions of the oceans.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 231.

“… it might seem that the possession of prehensile appendages is an adaption found only in the land animals. However, once we enter the oceans we find animals that evolved prehensile appendages long before any animal life existed on land at all. The ctenophores and cnidarians independently evolved tentacles that are used to grasp and manipulate prey animals, and did so over 600 million years ago….

“In the marine realm, prehensile tentacles have been best developed by the cephalopod molluscs–they independently have evolved tentacles that they use not only to grasp prey but also to grasp tools and build habitats.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. p. 235.

“… whereas [in contrast to natural selection only from the Modern Synthesis] in the twenty-first-century extended evolutionary synthesis much of evolutionary convergence is being argued to be produced by developmental constraints and developmental bias, not by natural selection…. … whereas [in contrast to the Modern Synthesis] in the twentieth-first-century, historically contingent evolution is being argued to be constrained to occur within a finite number of limited convergent pathways, and thus to be probabilistically predictable.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 237, 238.

“… life was confined to the oceans of the planet for over 3,500 million years. It is not easy living on dry land. Dehydration is a very serious problem for land-dwelling organisms. In contrast, life in the seas is surrounded at all times by water; dehydration is an unknown phenomenon. Land-dwelling organisms must deal with the crushing force of gravity whereas, for neutrally buoyant plankton and nekton in the dense waters of the oceans, gravity is an unknown phenomenon. Land-dwelling organisms must endure large fluctuations in temperatures that occur very rapidly–every twenty-four hours, as the sun rises to bring the heat of the day and sets to cool into the darkness of the night. In contrast, life in the oceans experiences very little variation in temperature and, in depths where temperature does vary, the temperature change is very gradual–gently rising and falling with the passing of the four seasons. Last, water is a very good radiation shield and marine organisms located just a few centimeters below the surface of the oceans are protected from ultraviolet radiation from the sun…. For most of the history of Earth that ozone shield did not exist at all, and that intense ultraviolet radiation flux present on the land was deadly.” McGhee, George R. 2019. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. MIT Press. pp. 239-240.

“Under Active Inference, perception and action are two complementary ways to fulfill the same imperative: minimization of free energy. Perception minimizes free energy (and surprise) by (Bayesian) belief updating or changing your mind, thus making your beliefs compatible with sensory observations. Instead, action minimizes free energy (and surprise) by changing the world to make it more compatible with your beliefs and goals…. Learning is yet another way to minimize free energy. However, it is not fundamentally different from perception; it simply operates at a slower timescale.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 9.

“… the Active Inference framework accommodates planning–or the selection of the optimal course of action (or policy) in the future. Optimality here is measured in relation to an expected free energy and is distinct from the notion of variational free energy considered above in the context of action and perception.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. pp. 9-10.

“The second notion of surprise is referred to as Bayesian surprise. This is a measure of how much we have to update our beliefs following an observation. In other words, Bayesian surprise quantifies the difference between a prior and a posterior probability.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 20.

“By acting on the world to change the way in which data are generated, we can ensure a model is fit for purpose by choosing those data that are least surprising under our model.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 24.

“Active Inference goes beyond the recognition that perception and action have the same (inferential) nature. It also assumes that both perception and action cooperate to realize a single objective–or optimize just one function–rather than having two distinct objectives, as more commonly assumed. In the Active Inference literature, this common objective has been described in various (informal and formal) ways, including the minimization of surprise, entropy, uncertainty, prediction error, or (variational) free energy.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. pp. 24-5.

“Technically, Active Inference agents come equipped with models that assign high marginal probabilities to the states they prefer to visit or the observations they prefer to obtain. For a fish, this means a high marginal likelihood for being in water. This implies that organisms implicitly expect the observations they sample to be within their comfort zone (e.g., physiological bounds).” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. pp. 26-7.

“Yet, exact Bayesian Inference supporting perception and action is computationally intractable in most cases…. Active Inference appeals to a variational approximation of Bayesian Inference that is tractable.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 27.

“… one can assume that updating what one knows (the prior) to accommodate the data entails a cognitive cost; hence, an explanation that diverges minimally from the prior is preferable.

“On this view, the complexity cost is just Bayesian surprise. In other words, the degree to which ‘I change my mind’ is quantified by the divergence between the prior and the posterior. This means every accurate explanation form my sensations incurs a complexity cost, and this cost scores the degree of Bayesian belief updating. Variational free energy, then, scores the difference between accuracy and complexity.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 29.

“… instead of minimizing the divergence, we want to select policies [courses of multi-step actions] that maximize the expected divergence–hence, information gain.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 34.

“When evaluating the free energy of outcomes, the outcomes are the consequences. However, when evaluating the expected free energy [by policies with actions to improve a model], the outcomes play the role of causes in the sense they are variables that are hidden in the future but explain decisions in the present.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 34.

“Variational free energy is at the core of Active Inference. It measures the fit between the internal generative model and (current and past) observations. By minimizing variational free energy, creatures maximize their model evidence. This ensures that the generative model becomes a good model of the environment and that the environment complies with the model.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 38.

“Expected states are preferred and include the organism’s conditions for survival (e.g., niche-specific goal states), whereas their opposite–surprising states–are dis-preferred. In this way, by fulfilling their expectations, Active Inference agents ensure their own survival. Given the important links between the notion of priors and the conditions that undergird an organism’s existence, we can also say that in Active Inference, the identity of an agent is isomorphic with its priors….

“Note that in this view, surprise (or sometimes surprisal) is a formal construct of information theory and not necessarily equivalent to a (folk) psychological construct. Roughly the more the organism’s state differs from the prior (which encodes the preferred states), the more it is surprising–hence Active Inference amounts to the idea that an organism (or its brain) has to actively minimize its surprise to stay alive.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 39.

“Technically, a blanket (b) is defined as follows:

“μ ⊥ x∣b ⇔ p(μ,x∣b) = p(μ∣b)p(x∣b)

“This says (in two different but equivalent ways) that a variable µ is conditionally independent of a variable x if b is known. In other words, if we know b, knowing x would give us no additional information about µ. A common example of this is a Markov chain, where the past causes the present causes the future. In this scenario, the past may only influence the future via the present. This means no additional information about the future is gained by finding out about the past (assuming we know the present).” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 43.

“… one can use a Markov blanket to separate an entire organism from the environment or nest multiple Markov blankets within one another. For example, brains, organisms, dyads, and communities can be conceived in terms of different Markov blankets that are nested within one another.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 44.

“The key point to notice here is that the internal states of an adaptive system bear a formal relation to external states. This is due to a kind of symmetry across the Markov blanket as both influence and are influenced by blanket states…. In other words, on average, the internal and external states acquire a kind of (generalized) synchrony–just as we might anticipate on attaching a pendulum to each end of a wooden beam. Over time, as they synchronize, each pendulum becomes predictive of the other through the vicarious influence of the beam.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 45.

“… any adaptive system engages in ‘self-evidencing’. Self-evidencing here means acting to garner sensory data consistent with (i.e., that affords evidence to) an internal model, hence maximizing model evidence.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 47.

“Ensuring that a small proportion of sensory states is occupied with high probability is equivalent to maintaining a particular entropy. This is a defining characteristic of self-organizing systems….

“From a physiologist’s perspective, surprise minimization formalizes the idea of homeostasis.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 48.

“In fields like optimal control, reinforcement learning, and economics, the optimization of behavior results from a value function of states…. Essentially, each state (or state-action pair) is assigned a value, which represents how good a state is for an agent to be in. The value of states (or state-action pairs) is usually learned by trial and error, by counting how many times–and after how much time–one obtains reward by starting from those states. Behavior consists in optimizing reward acquisition by reaching high-valued states, hence capitalizing on learning history.

“In contrast, in Active Inference, behavior is the result of inference and its optimization is a function of beliefs. This formulation unites notions of (prior) belief and preference. As discussed above, using the notion of expected free energy amounts to endowing the agent with an implicit prior belief that it will realize its preferences. Hence, the agent’s preference for a course of action becomes simply a belief about what it expects to do, and to encounter, in the future–or a belief about future trajectories of states that it will visit. This replaces the notion of value with the notion of (prior) belief. This is an apparently strange move, if one has a background in reinforcement learning (where value and belief are separated), or Bayesian statistics (where belief does not entail any value).” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 53.

“It is worth briefly outlining what we mean by drawing analogies between Hamiltonian physics and Active Inference. This is intended on three levels. The first is that the advance offered by Active Inference to the behavioral and life sciences is comparable to the advance Lagrangian and Hamiltonian formulations offered to Newton’s accounts of mechanics. While Newtonian mechanics were originally formulated in terms of differential equations–including Newton’s famous third law expressing the proportionality between acceleration and force–a complementary perspective on mechanics was offered by considering what is conserved by dynamical systems. Newtonian dynamics can then be derived from these conservation laws. These offer a perspective on which to base further theoretical advances, and they form the basis for parts of stochastic, relativistic, and quantum physics. Analogously, Active Inference reformulates the sorts of neuronal and behavioural dynamics that might previously have been built up from a series of differential equations by specifying the quantity–free energy–from which these dynamics may be derived. Just as different sorts of Hamiltonians lead to different types of physics, free energies based on different generative models lead to different neuronal and behavioral dynamics.

“The second point of connection between Hamiltonian physics and Active Inference arises from a more direct association between a Hamiltonian and probability measures. The idea here is to associate the conserved Hamiltonian with the energy of the system. Remember that the quantities we have referred to as energies so far have all had the form of a negative log probability. This reflects an interpretation of energy as simply a measure of the improbability of any given configuration of a system. On this view, conservation of energy and of probability are equivalent laws. As dissipative systems.–coupled to external states via a Markov blanket–move to states of low energy or high probability, we can directly associate the energy or Hamiltonian with surprise. As such, Active Inference is Hamiltonian physics applied to a certain kind of system (systems that feature a Markov blanket).” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. pp. 54-5.

“… Active Inference is in keeping with enactive theories of life and cognition, which emphasize the self-organization of behavior and autopoietic interactions with the environment, which ensure that living organisms remain within acceptable bounds. Active Inference provides a formal framework explaining how living organisms manage to resist the dispersion of their states by self-organizing a statistical structure–the Markov blanket–that affords reciprocal exchanges between organism and environment while also separating (and in a sense protecting the integrity of) the organisms’ states from external, environmental dynamics.” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 57.

“In the continuum between simpler and more complex creatures, Active Inference draws a line between those that minimize variational free energy and those that also minimize expected free energy [as the latter use ‘policies’ of multiple steps].” Parr, Thomas, Giovanni Pezzulo & Karl J. Friston. 2022. Active Inference: The Free Energy Principle in Mind, Brian, and Behavior. MIT Press. p. 58.

“Here are the core design principles that Ostrom derived for common-pool resource groups that enabled them to avoid the tragedy of the commons:

“1. Groups that functioned well had clearly defined boundaries, which means that they knew they were a group, what the group was about, and who was a member.

“2. They also had rules adapted to local conditions, which ensured that group members experienced proportional equivalence between benefits and costs.

“3. There were collective choice arrangements so that everybody affected by a decision had an opportunity to contribute to making that decision.

“4. There was monitoring, which means that lapses in agreed-upon behaviors could be detected; and this monitoring was preferably conducted by group members rather than external authorities.

“5. There were graduated sanctions, which means that lapses in agreed-upon behaviors were corrected, gently at first but with a capacity to escalate if necessary.

“6. There were conflict resolution mechanisms that quickly resolved differences in a way recognized as fair by all members.

“7. There was at least a minimal recognition of rights to organize, which gave group members the authority to manage their own affairs without external interference, the opposite of top-down regulation.

“8. Finally, in the case of larger common-pool resources, there was polycentric governance, which refers to groups of groups in multiple layers of nested enterprises, with each subgroup relating to other groups using principles 1 throough 7. In other words, successful common-pool resource groups had prosocial relations with other groups.” Atkins, Paul W.B., David Sloan Wilson & Steven C. Hayes. 2019. Prosocial: Using Evolutionary Science to Build Productive, Equitable, and Collaborative Groups. Oakland, CA: Context Press. p. 24; reference: Ostrom, Elinor.

“The word ‘commons’ derives from the Norman word commun. To commune is to participate, to share and enjoy fellowship. And in turn the word ‘commun’ draws upon the word munus, which means ‘a gift, service, or duty’ that in turn contributes to the word munificent, meaning ‘bountiful, liberal, generous,’ and the Latin munificare, meaning ‘to enrich.’ Thus the ‘commons’ literally refers to sharing gifts to enrich all. Sharing of gifts implies both the satisfaction of individual needs and a duty to the collective. David Bollier argues that it is more helpful to treat the commons as a verb rather than a noun; ‘commoning’ rather than ‘the commons.’ Commoning is the care the community feels for the resource and the community itself; it is the making and implementation of rules of access and use; and it is the social norms and customs that evolve to ease and resolve conflict, encourage cooperation, and punish free riders and shirkers.” Atkins, Paul W.B., David Sloan Wilson & Steven C. Hayes. 2019. Prosocial: Using Evolutionary Science to Build Productive, Equitable, and Collaborative Groups. Oakland, CA: Context Press. p. 30; reference: Bollier, David. 2014. Think like a commoner: A short introduction to the life of the commons. Gabriola Island, BC: New Society Publishers.

“[Ostrom’s principle #1 from above corresponds to] Shared identity and purpose … Function: defines group

“[Ostrom’s principle 2 from above corresponds to] Equitable distribution of contributions and benefits… Function: ensures effectiveness by balancing individual and collective interests

“[Ostrom’s principle 3 from above corresponds to] Fair and inclusive decision making… Function: ensures effectiveness by balancing individual and collective interests

“[Ostrom’s principle 4 from above corresponds to] Monitoring agreed behaviors… Function: ensures effectiveness by balancing individual and collective interests

“[Ostrom’s principle 5 from above corresponds to] Graduated responding to helpful and unhelpful behavior… Function: ensures effectiveness by balancing individual and collective interests

“[Ostrom’s principle 6 from above corresponds to] Fast and fair conflict resolution… Function: ensures effectiveness by balancing individual and collective interests

“[Ostrom’s principle 7 from above corresponds to] Authority to self-govern (according to principles 1 – 6)… Function: ensures effectiveness while supporting engagement

“[Ostrom’s principle 8 from above corresponds to] Collaborative relations with other groups (using principles 1 – 7)… Function: scale to entire systems.” Atkins, Paul W.B., David Sloan Wilson & Steven C. Hayes. 2019. Prosocial: Using Evolutionary Science to Build Productive, Equitable, and Collaborative Groups. Oakland, CA: Context Press. p. 36.

“The philosopher Jaegwon Kim, for example, argues persuasively that if there is complete causal closure at the microphysical (e.g. molecular) level then there is no room for additional causation from macro-levels. The feelings and thoughts we have as humans must then be an illusion, and to work it has to be assumed to be a very strong illusion.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. p. 278; reference: Kim, Jaegwon. 2000. Mind in a physical world. MIT Press.

“In this article we challenge two assumptions in the purely micro-level view. The first is the possibility of causal closure in living organisms, meaning that there is no room for any other influence, particularly that of intention; the second is the assumption that any stochasticity involved cannot itself be functional.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. p. 277.

“Specifically we distinguish between the dynamics of a system and the conditions under which those dynamics play out. Those conditions can then be seen as constraining the dynamics, just as the dimensions and elasticity of the container of a gas determine the pressure and temperature generated by the dynamics of the molecular movements.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. p. 279.

“The immune system achieves such guided responses throughout the life of an organism. The mutation rate in the variable part of the genome that forms the template for an immunoglobulin protein can be accelerated by many orders of magnitude in response to a new antigen challenge. So far as is known, these mutations occur stochastically, and what is modified is the speed at which they occur. However, the location in the genome is certainly not a matter of chance. The functionality, in this case, lies precisely in targeting the relevant part of the genome. The arrival of the antigen itself activates the hypermutation process, and the binding to a successful antibody triggers the proliferation of those cells that make it. Thus, the system targets the specific antigen.

“What this process achieves is that all the other sequences in the DNA array forming a template for the immunoglobulin protein are held sufficiently constant to maintain functionality. Even more remarkably, all the functionality in the rest of the genome is also maintained….

“By holding correct parts of the immunoglobulin sequence constant, the system finely tunes the rapid mutation to only a tiny part of the entire genome. Such tuning is one way in which organisms can dynamically respond to environmental change. Another way is that their biological networks buffer the organism from the majority of molecular changes at the genetic level. The robustness of the networks acts like a cloud overlying the DNA so that, under favourable environmental conditions, as much as 80% of the genome changes have negligible effects….

“The system harnesses the stochasticity. The immune system is the paradigm example of this harnessing.

“The system includes: (a) sensing the environmental challenge, i.e. the antigen invasion, (b) transmitting this signal to the nuclei of immune system cells to trigger hyper-mutation in just a tiny fraction of the genome, (c) then sensing of the correctness or otherwise of the outcome, followed by the ‘reproduce or die’ signal: cells that do not produce an antibody to the antigen do not reproduce. At this stage, natural selection occurs amongst the population of immune system cells. Thus, this is a complete, finely-tuned physiological feedback and guided search system rapidly generating an acquired characteristic in response to an environmental challenge, and inherited through the surviving population of cells. By all the usual criteria this is a teleological, i.e. goal-directed, process.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. pp. 283-4.

“Organisms are open systems at both micro- and macro-levels. Thus, there are not hard boundaries to causation between levels; or as Capra and Luisi express it:

‘In nature, there is no ‘above’ or ‘below’, and there are no hierarchies. There are only networks nesting within other networks.’

“‘Nesting’ is the key. Each level of function meshes with and so interacts with other levels. Molecular networks nest within cells, which in turn nest within cellular (tissue) networks, within organ network, and whole organism networks, then within their social networks, and also in interaction with other species (ecology). This meshwork is what we mean by open systems–while there may be causal distance, there is no causal isolation….

“Where we differ from Capra and Luisi is on the question of hierarchy. In systems with agency, there is a hierarchy of sorts. The decisions of the agent, the organism, influence function at other levels, even as function at other levels forms the integral being of the agent. The level at which agency can exist constrains all the other levels. However, an agent depends on the capacity to act, which in turn is constrained by functionality. In that sense, there is no privileged level of causality, all levels engage in the process of agency, of making decisions and acting on them…. It is not merely an ‘illusion’ but a potent level of organisation. Furthermore, the expression of our thoughts, our ideas, framing them in language and social interaction is a functional boundary.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. pp. 286-7; reference: Capra, F. & P.L. Luisi. 2014. The systems view of life: A unifying vision. Cambridge UP.

“Functional boundaries between organisational levels mean causation up and down are necessarily different, but they do not compete for primacy. They mesh together and are both enabling and creative. In setting boundaries, downward causation can be viewed more like a context, setting constraints, purpose and goals. It is then not too difficult to view reasons, ethics, laws and customs operating in this way. They are socio-biological processes influencing predisposiiton states in the organism. Thinking that we need to solve how upward and downward causation ‘compete’ with each other is a mistake. They mesh.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. pp. 288-9.

“With the macro-level contextual constraints of events at the micro-level, there is no causal closure. The process is ongonig and reiterative with an ebb and flow of predisposition states influencing decisions by the organism. This openness, or lack of causal closure, is a point that seems to be missing in the accounts of philosophers like Jaegwon Kim.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. p. 289.

“In his 1986 lecture to The Royal Society, Popper distinguished between what he called ‘active’ and ‘passive’ Darwinism. By ‘passive’ he meant a theory of evolution that attributes all change to natural selection, which is a passive filter for degrees of fitness for survival. This idea is also a central tenet of neo-Darwinism (The Modern Synthesis). In contrast, by ‘active’ he meant the directionality that organisms create as agents, and which was first identified by Charles Darwin through his work on sexual selection–through an active choice of mates for reproduction.

“The propositions in the current article contribute to understanding why Darwin was right to distinguish between natural selection and what he called artificial selection–the active, or purposeful selection of varieties of species by human agency. The distinction is valid of course only if we believe that agents exist and that we can identify them.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. p. 289; reference: Popper, Karl.

“List bases his arguments for free will on three propositions:

“1. The fact that, for any macro-level situation, there will be innumerable micro-level states that correspond to the same macro-level state.
“2. From this, he shows that the high-level state can branch (in making a choice) while any given lower-level state does not and (in a deterministic world) cannot branch.
“3. From these statements, he shows that all three of his criteria for free-will are then satisfied. These are intentional agency, the existence of alternative possibilities, and causal efficacy….

“We believe that our work provides strong support for (1).

“Nevertheless, we are not convinced that, on its own, (2) would answer most micro-level determinists since they could still argue that in any given case only one of the many possible lower level instantiations occurs. Which one occurs can be described by pure biochemistry. Thus, they would argue that since on any given occasion, only one of them occurs then the particular high-level state cannot branch either. One way of viewing our contribution to the debate is to show that it is not necessary to assume that only one lower-level state occurs in any given timeline. Thus events at the macro-level harness those at a micro-level in generating possible alternative actions. Our case is based precisely on the organism’s ability to anticipate many options simultaneously. It is the subsequent selection of one or more of these that is the choice process. The organism is then able to apply an ongoing creative logic to the choice of action, which in turn continuously moulds or modifies micro-level processes….

“By adding the harnessing of stochasticity as an active ingredient to List’s set of propositions, it enables many micro-level states to be available to an organism in making choices. The argument for ‘free will’, or as we would have it ‘free agency’, become more tenable, and all the consequences of List’s third proposition then follow.” Noble, Raymond & Denis Noble. 2021. “Can Reasons and Values Influence Action: How Might Intentional Agency Work Physiologically?” Journal for General Philosophy of Science. 52:277-295. doi: 10.1007/s10838-020-09525-3. p. 289-290; reference: List, C. 2019. Why free will is real. Harvard UP.

“A recent symposium on evolution and cancer featured the revolutionary idea that cancer is best studied as the stochastic development of a new species within the tissues of the organism, which readily explains the rapid radiation of genomic forms in late-stage metastatic cancer, and why aggressive treatment often provokes further rapid mutation in response to the stress on the cancer ‘species.’” Noble, Denis. 2021. “Function Forms from the Symmetry Between Order and Disorder.” Function. 2(1):zqaa037. doi: 10.1093/function/zqaa037. p. 1; reference for symposium: cancerevolution.org.

“… we propose that the following phenomena configure the cytoplasmic macromolecules to perform their biochemical and physiological functions. (i) Negatively charged macromolecules and their complexes mutually repel through the ‘screened electrostatic forces’ of classical physical chemistry to retain their individuality. (ii) The high crowding of cytoplasmic macromolecules shapes the remaining cytosol into a system of electrolyte pools and pathways. (iii) The charges on the surfaces of these pathways act as switches, which control the cytoplasmic transport of ions. (iv) The pools have unequal ‘bulk’ concentrations of ionic metabolites, the gradient of which drives their electrochemical transport through the pathways.” Spitzer, Jan J. & Bert Poolman. 2005. “Electrochemical structure of the crowded cytoplasm.” TRENDS in Biochemical Sciences. 30(10):536-541. doi: 10.1016/j.tibs.2005.08.002. p. 536.

“As an approximation, we divide the physicochemical cytoplasmic phenomena into only two spatial and temporal hierarchies: the bigger (3-30 nm) and slower diffusing (millisecond-and-longer) macro-molecular complexes, which are pseudo-equilibrated with the smaller (0.1-3 nm) and faster diffusing (micro-seconds-to-milliseconds) aqueous ionic metabolites. Our ‘structure’ of the anionically stabilized cytoplasm is then transient and is unlikely to persist throughout the volume of the whole cell.” Spitzer, Jan J. & Bert Poolman. 2005. “Electrochemical structure of the crowded cytoplasm.” TRENDS in Biochemical Sciences. 30(10):536-541. doi: 10.1016/j.tibs.2005.08.002. p. 537.

“First, there is no cytoplasmic ‘bulk’ concentration of ions and metabolites (as is often assumed in biophysical models and in the design and interpretation of in vitro experiments); rather, each pool has its own bulk concentration of ions and metabolites. Therefore, the electro-chemical gradients between the pools provide the force to transport ionic metabolites throughout the cytoplasm and through the membrane….

“Second, the electrochemical pools are interconnected by electrolyte pathways (or gaps) through which ions and metabolites are either transported or prevented from being transported. In effect, the charged macromolecular surfaces are ‘wired’ by electrolyte pathways and pools. The electrolyte pathways provide a rationale for the low apparent diffusion coefficients and the heterogeneity of protein diffusion in the cytoplasm of bacteria.” Spitzer, Jan J. & Bert Poolman. 2005. “Electrochemical structure of the crowded cytoplasm.” TRENDS in Biochemical Sciences. 30(10):536-541. doi: 10.1016/j.tibs.2005.08.002. p. 539.

“Spitzer has defined Maxwellian switches and the related distributions of ions for electrolyte pathways equilibrated with charged ions. For cytoplasmic ions, the pathways are equilibrated with a mixture of electrolytes containing monovaloent and divalent anions…. … electrolyte pathways differ in their ability to pass or exclude anions. For example, a pathway could enable all ions to pass to variable degrees; alternatively, only cations and monovalent anions might be allowed to pass, or the pathways could exclude all anions. We propose that such ‘semi-conducting’ pathways assist in the execution of logical operations; in other words, the ‘output’ (the ions that are forbidden pass) is determined by the surface and middle electrostatic potentials (the ‘set points’).” Spitzer, Jan J. & Bert Poolman. 2005. “Electrochemical structure of the crowded cytoplasm.” TRENDS in Biochemical Sciences. 30(10):536-541. doi: 10.1016/j.tibs.2005.08.002. p. 539; reference: Spitzer, Jan. 2003. “Maxwellian double layer forces; from infinity to contact.” Langmuir. 19:7099-7111.

“Glass-like systems are non-Markovian, that is, are characterized by historical memory whereby the present state of the system depends on the entire previous history, and accordingly the future states are not precisely predictable. This nonergodic behavior is caused by competing short- and long-range interactions which result in frustration and can produce complex patterns. Notably, the glass-like phases share with biological systems at least two fundamental features: (i) historical memory and the resulting contingency (nonergodicity) and (ii) complexity. These parallels have been drawn previously by Laughlin and Pines and Laughlin et al., who suggested that modern physical theory of glasses might substantially inform different areas of theoretical biology.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. pp. E8678-9; references: Laughlin, R.B. & D. Pines. 2000. “The theory of everything.” PNAS USA. 97:28-31; Laughlin, R.B. D. Pines, J. Schmalian, B.P. Stojkovic & P. Wolynes. 2000. “The middle way.” PNAS USA. 97:32-37.

“SOC [self-organized criticality] is a property of dynamical systems with extended degrees of freedom and pronounced nonlinearity whereby the system goes through serial ‘avalanches’ separated in time by intervals of stability. Under the original SOC concept, self-similar (power-law) scaling of avalanche sizes is the distinctive feature of the critical dynamics…. The behavior of systems with SOC dynamics is obviously reminiscent of the punctuated equilibrium model in evolutionary biology….” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8679.

“Extinction of the least-fit organisms disrupts their local environments and causes concomitant extinction of their closest neighbors. After a short burn-in, such systems self-organize into a critical quasi-equilibrium which is interrupted by avalanches of extinction, with the avalanche size following a power-law distribution.

“So far, the exact conditions leading to SOC have not been identified despite considerable effort. However, a notable connection has been shown to exist between competing interactions and frustration in spin glasses, on the one hand and SOC, on the other hand. Specifically, it has been shown that SOC is an emergent property of spin glasses with a diverging number of neighbors.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8679.

“We further submit that frustration is characteristic of an extremely broad class of hierarchical systems, within and outside biology, and accordingly appears to be the general source of complexity.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8679.

“Geometric frustrations in crystallography can be considered the prototype of frustrations in general. Some types of chemical bonds (e.g. Van der Waals and metallic) tend to the closest possible packing of atoms or ions. The local closest packing of hard discs of equal radii in a 2D Euclidean space is provided by the equilateral triangle, and the global closest packing is the triangular lattice built from such triangles. In this case, there is a unique optimal crystal lattice, with no frustrations involved. In the 3D Euclidean space, the optimal local packing is provided by the regular tetrahedron. However, it is impossible to fill the space with the tetrahedra without voids. As a result, there are infinitely many structures corresponding to the same optimal global packing which is less dense than the optimal local packing; such degeneracy is observed also for higher space dimensionalities as well.

“Another important source of frustrations is competing interactions caused by the coexistence of several types of chemical bonds (in particular, van der Waals and hydrogen, or metallic, covalent, and ionic). Typically, there is no unique optimal structure with the lowest energy; rather, frustrations lead to quasi-degeneracy.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8679.

“A notable example [of frustration in materials] is provided by the van der Waals hetero-structures (i.e., artificial structures made from different 2D materials); graphene on hexagonal boron nitride (hBN) is the simplest and the best-studied case. Graphene and hBN have the same crystal structure but with slightly different lattice periods (1.8% larger for hBN). To minimize the energy of interlayer van der Waals interactions, expansion of graphene to equalize the lattice constants is favorable but such expansion costs some energy of interactions between carbon atoms in graphene. As a result, a distinct pattern is formed at small-enough misalignment angles. Similar physics arises and leads to pattern formation when one graphene layer is rotated with respect to another. In these cases, patterns originate from the incommensurability of interactions.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8680.

“As first clearly introduced for spin glass,… modern physics considers glass to be a distinct state of matter that is intermediate between equilibrium and nonequilibrium. A characteristic property of glasses is aging, or structural relaxation. Suppose we measure a specific property of an equilibrium phase, liquid or solid, for example the resistivity of a metal (or liquid metal). ‘Equilibrium’ means that, when the measurement is repeated after a thermal cycle (slow heating and cooling down to the initial temperature), we obtain the same value of the resistivity. In glass, the measured value would slowly change from measurement to measurement. The potential energy relief (or landscape, to use a term with biological connotations) for glass is a function with many (asymptotically, infinitely many) local minima separated by barriers with an extremely broad energy distribution. Each local minimum represents a metastable state. During its thermal evolution, the system slowly moves from one minimum to another. Importantly, the glass state is noneregodic: There are many configurations which remain localized in a restricted domain of phase space.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8680.

“The existence of long-range interactions competing with short-range ones is essential for the emergence of SOC; in systems with short-range interactions only, SOC is not observed.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8680.

“In biological evolutionary dynamics, the dimensionality of the configuration space (fitness landscape) is typically very high; for example, numerous genes in a genome and numerous sites in each gene can be considered separate dimensions. Therefore, biological evolution can be expected to follow the chain of causation; competing interactions -> frustration -> glass-like state -> nonergodicity -> SOC -> evolutionary transitions/ ‘punctuated equilibrium’.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8680.

“A clear and perhaps fundamental analogy from evolutionary biology is a typical, rugged fitness landscape with elevated areas (peaks and plateaus) of high fitness, where an evolving population can travel either upward, under the pressure of selection, or horizontally in a (quasi)neutral evolutionary regime, separated by valleys of low fitness that can be crossed only by genetic drift (thermal fluctuation). In particular, the classical NK model of evolution on rugged fitness landscapes has been developed within the spin-glass framework.” Wolf, Yuri I., Mikhail I. Katsnelson & Eugene V. Koonin. 2018. “Physical foundations of biological complexity.” PNAS. 115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. p. E8681.

“In summary, we have revisited the quantum aspects of photosynthetic light harvesting. It has become clear from basic considerations that there is no equivalence between quantumness of the processes and coherences observed in femtosecond spectroscopy experiments. Even the very fundamental question if nonstationary coherences in photosynthetic systems can be excited by sunlight still awaits full clarification. Whatever the state preparation is, the dynamics will be governed by the associated couplings of the system and its interaction with the bath. Furthermore, the claims of the persistence of these coherences in femtosecond experiments have been critically reevaluated. In particular, detailed analysis of the exemplar system in quantum biology–the FMO [protein] complex–shows unambiguously the absence of long-lived interexciton coherence on relevant time scales in this system, both at cryogenic and physiological temperatures.” Cao, Jianshu, Richard J. Cogdell, David F. Coker, Hong-Guang Duan, Juergen Hauer, Ulrich Kleinekathoefer, Thomas L.C. Jansen, Tomas Mancal, R.J. Dwayne Miller, Jennifer P. Ogilvie, Valentyn I. Prokhorenko, Thomas Renger, Howe-Siang Tan, Roel Tempelaar, Michael Thorwart, Erling Thyrhaug, Sebastian Westenhoff & Donatas Zigmantas. 2020. “Quantum biology revisited.” Science Advances. 6:eaaz4888. p. 8.

“On the other hand, we cannot make an accurate prediction for a small number of throws [e.g. of a coin]. We can only assign probabilities which do not specify the outcome exactly. Thus there exist very numerous, quite simple and reasonable questions which do not have binary answers [yes or no]. We shall now define an open system of propositions as one with this particular property. It seems clear on very general grounds that there can be various degrees of ‘openness’ of an abstract system.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 8-9.

“Two objects of quantum theory composed of equivalent nuclei, having the same number of electrons, etc. and being in the same quantum state are utterly indistinguishable. A large number of indistinguishable objects of this kind is required to verify the statistical predictions of the theory. Such a set of atoms or molecules, each having the same composition and all being in the same quantum state, will be denoted as a fully homogeneous class….

“Modern physics, or much of it, deals not so much with objects as it does with homogeneous classes, where one member of the class is completely substitutable for the next. We think that much if not most of the gulf that still yawns between the physics of biomolecules and biology proper results from the conceptual difficulties which arise when observational material as inhomogeneous as that of biology is forced into the mold of a conceptual scheme which is too narrow for it.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 14.

“It is a natural tendency of the human mind, he [Claude Bernard] says, to insist always on knowing the causes of phenomena. But there are first causes which are intrinsically inaccessible to us. Since life, he says, represents first and foremost creativity, the explanation of the basic nature of life would lead us into the study of first causes, which are beyond the scope of science. He quotes Newton as saying that he who concerns himself with first causes shows by this very fact that he is a not a scientist. Science is concerned with secondary or proximate causes, and the laws of physics and chemistry represent such proximate causes.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 19-20.

“A vastly closer and more satisfactory approach to the problem [relationship of biological theory to physical theory] than the traditional one can be effected by recognizing that modern science through kinetic theory and quantum mechanics is moving in the direction of a more open logical structure. The more numerous the questions which are intrinsically unanswerable in physical theory and which can be recognized and precisely defined as such, within the framework of the established theory, the more likely it becomes that the traditional difficulties which surround our problem can be minimized.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 21.

“We shall state as one such rule that homogeneous classes are obtained by selection of subclasses of an inhomogeneous class [measuring each item to place only exactly same items into a selected, homogeneous class] Such a process requires of course that we can observationally identify each member of the inhomogeneous class with respect to chemical composition and quantum state.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 27.

“This irrelevance of molecular arrangements for macroscopic results [when considering homogeneous classes as physics does] has given rise to the tendency to confine physics and chemistry to the study of homogeneous systems as well as homogeneous classes…. But experience shows that the objects of biology are radically inhomogeneous both as systems (structurally) and as classes (generically)…. … we consider physics as the science dealing essentially with homogeneous systems and classes, and biology as the science of inhomogeneous systems and classes.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 34-5.

“If an inhomogeneous class is of finite membership, the success of the procedure for obtaining homogeneous classes can no longer be guaranteed; we may quite simply run out of specimens during the process of selection before we have reached a point where an adequate homogenization in terms of a subclass has been achieved.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 36.

“A further terminology is sometimes convenient. A set of abstractions in which all classes are finite (and some of them are radically inhomogeneous) will be designated as a finite universe of discourse.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 37.

“So far as the homogeneity or inhomogeneity of classes is concerned, it is interesting to note that this has a remarkable counterpart in the history of Western philosophy. To see this, we need merely replace the concept of classes by the related one of the philosophers, that of universals.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 38.

“In the preceding we have repeatedly spoken of an open theory as one in which many questions have no binary (yes-or-no) answers.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 45.

“We then noted that in a system as extraordinarily complex as an organism, prediction may be far more limited than one would think at first sight. This brings us to the chief problem: Can there be a theory which is ‘more open’ than the probabilistic ones, and what is the nature of this openness? We propose that there can be theories which contain sets of regularities not all derivable from a common set of axioms. This is only possible, of course, in a statistical universe of discourse where the statistical features, in a manner of speaking, buffer these regularities so that no mutual inconsistencies can appear. To be specific, then, we assume that there exist regularities in the realm of organisms whose existence cannot be logic-mathematically derived from the laws of physics, nor can a logico-mathematical contradiction be construed between these regularities and the laws of physics. In brief, the existence of such regularities can be neither proved nor disproved on the basis of the laws of physics. Questions regarding the derivation of these regularities from the laws of physics belong to the unanswerable kind.

“Notice, however, that physics was defined as the science of homogeneous classes (classes that may be taken as of infinite membership [example the hydrogen atom for quantum theory]). Our assumption can therefore be stated in more specific terms by saying that in inhomogeneous classes of finite membership there may exist regularities which have no equivalent in the corresponding homogeneous classes.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 45-6.

“… the working hypothesis… … the chief characteristic of organisms is that they form classes which are radically inhomogeneous (where the number of members of any class is negligibly small compared to the number of internal states compatible with the characteristics of the class.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 48.

“One of the chief purposes of biological theory as conceived here is to specify the limitations of physical prediction.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 53.

“… biological theory deals with the regularities pertaining to class membership, whether the members of the class are distinct individuals or whether they represent the same individual at a succession of points in time.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 57.

“Life is the repetitive production of ordered heterogeneity.” Quotation of R. D. Hotchkiss. 1958. In: “Concepts of Biology.” Behavioral Science. 3(2). April. Reproduced as Publication 560 of the National Academy of Science-National Research Council. p. 129. Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 61.

“Molecular ecology means that individual reactions are interrelated in such a way that what one does is an existential requirement for its neighbors, and vice versa.” Quotation of P. Weiss. 1958. In: “Concepts of Biology.” Behavioral Science. 3(2). April. Reproduced as Publication 560 of the National Academy of Science-National Research Council. p. 140. Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 63.

“We can, however, think in an abstract way of the picture of a biological system at a given instant of time. We shall designate such an instantaneous picture as a system event. The life process is then schematized as a series of transformations between system events.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 66.

“Certain characteristics of living tissue are determined at the expense of destroying it….As a rule the investigator needs to grind up enough material so that he can make chemical determinations in vitro. Such quantities, descriptive of the organism under study, will be designated as its homogeneous components….

“At the other end of the scale there is the notion of a microscopic state fully determined in all its details to within the limitations set by quantum mechanics. Ideally, this corresponds to a description of the state of the entire system in terms of a single wave function of quantum theory. Such a state of maximum knowledge is in biology an idealization, although according to the notions of quantum mechanics an entirely legitimate one. It will be designated as a microstate….

“Now the most conspicuous fact about the microstates is their extraordinarily large number.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 67-8.

“… the concept of autonomous or, rather, semi-autonomous biology makes sense to us only if it says precisely this: There are observable regularities in biological classes which are intrinsically impossible to deduce in their entirety logico-mathematically from the laws of physics.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 74.

“Having discussed the first of the two conditions set down above–the condition which says that an actual microstate, although unknown, is statistically speaking an immensely rare event among possible microstates–we take up the second condition. This condition says, roughly speaking, that the variability of microstates must be coupled, through a suitable cascade of feedback cycles, into the dynamics of the macrovariables, which thereby lose part of their physical predictability. The assumption that a coupling of this type exists is at present no more than an hypothesis. It is the one hypothesis of a physical nature that we require….

“That organisms show structure as well as inhomogeneities of this structure at any level has been known for a long time….Electron microscopy has shown that in organic tissue there exist structures of various kinds at all levels down to the atomic one, and also inhomogeneities corresponding to these structures. One cannot doubt that there are also physico-chemical processes whose magnitude corresponds to these levels, and these processes almost certainly involve all kinds of feedback couplings. Therefore, the idea that there are dynamical couplings all the way up and down between the macrovariables and the microstates is in a qualitative way in excellent agreement with the empirical evidence.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 78-9.

“… we cannot help thinking that in the course of the original appearance of life on earth there was a gradual evolution from a very primitive type of organization with correspondingly simple couplings to types containing more and more complex couplings.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 81.

“He [Kant] starts out by positing dogmatically that rigid Newtonian causality must reign throughout the physical world. He then declares that the idea of such a clock-work universe is incompatible with his moral sensibilities. He tries to resolve the conflict by effecting what may well be called a forced marriage between physical and psychological epistemology. He claims that the external world, being meaningless without an observing subject, is filtered through the mind of the subject, and in this filtering process the contradictions can be made to disappear….

“The development of quantum mechanics differed from that of other physical theories in that there was no pre-existing conceptual scheme which could later be formulated in mathematical terms. Instead, the situation was somewhat the reverse; the original discoveries were largely mathematical, and a suitable scheme of interpretation had thereupon to be formed. It was exactly at this point that the founders of quantum theory made use of the Kantian philosophy, which happened to be conveniently at hand and widely known…. Thus if we read in a text on the interpretation of quantum theory that the physical interaction between a measuring device and a measured object corresponds to the relationship between the observing subject and the observed object we are not dealing with any straightforward consequence of the formal theory; what we are seeing is in fact a version of Kantian philosophy.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 86-7.

“One might ask whether there is any specific scale along which indeterminacy increases more and more…. Experience shows that the only possible basis for a scale of this kind is not geometrical dimensions but energy. The smaller the energy, the more it is to be expected that statistical elements will enter into the determination of the microscopic state relative to the macrovariables.

“To illustrate this, consider the average energy per atom in a complex system such as organic tissue. It is of course well known that by far the largest energies occur in the chemical bonds of saturated molecules. As a result, these molecules and the geometrical conformations associated with their bonds are extremely stable…. But it would be infinitely more difficult to determine the precise location or orientation of these molecules on a sufficiently refined microscopic scale. The latter task would involve following their diffusive motions and would lead us immediately into a realm of small energies….

“It is within the domain of these small energies that we have to look for the immense variability of admissible microstates…. In this connection one cannot fail to mention a configurational change which is so common in organic tissue, that is, the resonant interchange of single and double bonds that constantly takes place in the innumerable organic molecules which have conjugated bonds….

“… we should remember that the enzymatically induced reactions in living tissue do not as a general rule involve an irreversible dissipation of large amounts of energy….

“Hence there exists in living tissue an immense number of configurational arrangements which differ from each other by only small energies, these energy differences being as a rule either of thermal order or else of a magnitude a few times thermal energy. From our viewpoint, this immense reservoir of microstates has a double meaning…. …it indicates the presence of an immense microscopic indeterminacy which can only be treated statistically within the context of inductive inferences. On the other hand, this variability coexists with the stability of the saturated molecules, including of course the macromolecules, which constitute what we have called the homogeneous components. Their lifetime in the absence of enzymatically mediated reactions would be almost unlimited on the scale of cellular processes.

“Our problem here is not that of the mere distinction between these two types of energy levels…. The essential problem concerns the degree of coupling between them.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 93-6.

“… there is universal agreement about one basic fact: the only way the deterioration of information by noise can be prevented, or at least reduced, is by means of redundancy, that is, the presence of the same information several times over.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 98.

“… most likely, a basic aspect of biological relationships is intrinsic and irreducible logical complexity. By this we mean that due to the absence of pervasive rigid categories (binary answers to questions) it may not be possible to resolve complicated relationships of order into a set of comparatively simple ones each of which can be separately studied, after which they can be composed so as to account successfully for the behavior of the system as a whole.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 103.

“It appears that intrinsic logical complexity becomes scientifically significant as a property of finite, inhomogeneous classes.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 104.

“Our contention is that the understanding of the mechanistic processes is a prerequisite for a broader analysis of the functioning of the organism that arises, not through the operation of some separate agency but as a result of the radical inhomogeneity of the microscopic state of the system combined with its intrinsic indeterminacy.

“A pervasive asymmetry is thus seen to be characteristic of the relationship of mechanistic to autonomous components in the organism’s dynamics. This asymmetry corresponds precisely to that prevailing between the macrovariables and the immense reservoir of microstates. Very often the macrovariables can be considered by themselves, and, according to the laws of classical physics and chemistry, their mutual relationships can be analyzed in determinate form for some finite length of time (until, that is, the coupling into the inhomogeneous microstates begins to make precise analysis and corresponding prediction impossible). The fact that the relationship of the mechanistic to the autonomous process components is dependent upon, and therefore largely patterned after, the physical relationship of macrovariables and microstates has been the origin of many of the difficulties and misconceptions which have arisen in biological theorizing. The tendency of so many investigators who are concerned with specific macroscopic mechanisms to make short shrift of any organismic concepts, and to generalize mechanistic views too readily beyond their original limits, can no doubt be traced to this source.

“Now from the preceding arguments we can draw a conclusion of great importance. If the autonomous components of organismic behavior cannot exist by themselves but can act only by way of the coupling of the radically inhomogeneous but at the same time indeterminate microstructure into the macrovariables, then one may also expect that there exist no abstract and general principles which could be applied to the autonomy of organisms, considered as a phenomenon of its own. In other words, there should be no general laws of ‘pure’ biology; whatever laws there are can be formulated only in relation to specific physico-chemical mechanisms which are realized in more or less extensive classes of organisms. We need hardly say that this is an explicit application of the idea of intrinsic logical complexity outlined above….

“Since the autonomy of the modes of behavior is therefore always relative, and incomprehensible apart from the mechanisms into which the indeterminate, radically inhomogeneous substratum is coupled, we should properly always speak of semi-autonomy.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 105-6, 107.

“In the history of physical science at least, efforts at theory construction have almost invariably tended to take one of two alternative courses. Either the fundamental laws were assumed as given and novel types of precise deductions from them were sought, as in the case of the kinetic theory of matter, where atoms or molecules were assumed to obey mechanical laws of motion, and new and on the surface quite distinct properties, in this case the laws of heat and thermodynamics, were derived from them….

“The second case which has repeatedly occurred in the history of physical science is that certain laws of physics that were meant to apply to a limited domain had, outside this domain, to be modified, both mathematically and conceptually, to obtain a novel theory. This is clearly so with quantum physics, where Newtonian mechanics remains valid for macroscopic phenomena, but as we descend into the microscopic domain, the realm of atoms and molecules, these classical concepts fail and a new theory, quantitatively different from the old one, takes over.

“The time-honored dualism of mechanistic and vitalistic concepts in biology expresses the motion that the observed biological regularities are either logico-mathematically derivable from the laws of atomic and molecular physics or else require specific modification of these laws. Our present theory does not agree with either of these ideas.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 107-8.

“We propose that what appears as such integration [in the understanding of the properties and dynamics of an organism] (and therefore is so often attributed to some ‘vital forces’) can be wholly expressed in terms of the relationship of the individual to the class.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 109.

“What we find in nature is the extraordinary stability of classes; we see these classes maintain their characteristics in great detail over untold generations. In figurative language we can express this by saying that out of an immense number of possible processes leading from one system event to subsequent ones, the organism ‘selects’ those processes that ensure the stability of the class. ‘Selection’ is of course purely a convenience of speech; it does not here pre-suppose a selecting agency but only expresses in alternate language the stability of classes to that degree in which it is an autonomous phenomenon: out of an immense number of possible transformations from one system event to a later one only an immensely small fraction is actually realized, and these represent the stable properties of the class. The fact that we are thus always dealing with immensely rare events precludes our being able to derive the corresponding prediction wholly from physical laws; it precludes also that we could ever arrive at a contradiction with these laws.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 110.

“But in our theory such a scheme would have no operational meaning, since such deviations from the second law could not be verified: The ‘selection’ of certain immensely rare processes which ensure the stability of classes is withdrawn from direct observation.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 111.

“A ‘theory of organisms,’ no matter how closely it fits the facts of direct observation, will not be fully satisfactory at a more fundamental level unless it embodies the valid expression of an idea so often emphasized throughout the history of biology, namely, that organisms represent a separate form of matter: this implies almost certainly that biological theory must be outside the dichotomy, mechanism-vitalism.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. pp. 123-4.

“The theory of preformation proclaimed that there is a complete replica, a miniature model of the adult, contained in every germ. The theory of epigenesis on the other hand, held that the germ is merely a piece of organic substance endowed with the ‘potential’ of growing up into an adult, without precise correspondence in information content. It seems clear that these two viewpoints are intimately related to the mechanistic and vitalistic philosophies, respectively, and one could indeed identify them with these….” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 126.

“… there is the universal fact of biochemical kinetics–that all biochemical reactions proceed with a minimal dissipation of free energy–a fact that can only be interpreted by saying that the organism makes no provisions for separating ‘information’ from ‘noise.’ The power of this argument for the epigenetic character of cellular processes has been rather overlooked in the biological literature.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 127.

“What we wish to emphasize is that the assumption of a finite universe of discourse containing radically inhomogeneous classes seems to provide a suitable abstract understructure within which the existence of hierarchies in biology can be conceived, whereas the traditional, relatively more rigorous and inflexible logic and formalism of physical science appears rather powerless in the face of these phenomena.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 135.

“We may define individuality in a purely formal manner by saying that it represents the actual existence of a configuration (or of a process) which is an immensely rare occurrence if viewed abstractly against an immense number of possible configurations (or processes).” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 135.

“It is not much of a generalization to say that individuality clearly increases as one rises on the evolutionary scale [because they contain relatively large numbers of possible microstates and so are more surely singular occurrences]. One might even use individuality broadly as a measure of evolutionary advance. Man is then the ‘highest’ of organisms quite simply because men, due to the complexity of their brains, can exhibit a vastly higher degree of individuality than any other kind of organism.” Elsasser, Walter. 1966. Atom and Organism. Princeton UP. p. 137.

“The ‘major transitions in evolution’ are mainly about the rise of hierarchy, new individuals arising at ever higher levels of nestedness, in particular the eukaryotic cell arising from prokaryotes, multicellular individuals from solitary protists and individuated societies from multicellular individuals. Some lists include human societies as a major transition, but based on a comparison with the non-human transitions, there are reasons for scepticism. (i) The foundation of the major transitions is hierarchy, but the cross-cutting interactions in human societies undermine hierarchical structure. (ii) Natural selection operates in three modes-stability, growth and reproductive success–and only the third produces the complex adaptations seen in fully individuated higher levels. But human societies probably evolve mainly in the stability and growth modes. (iii) Highly individuated entities are marked by division of labour and commitment to morphological differentiation, but in humans differentiation is mostly behavioural and mostly reversible. (iv) As higher-level individuals arise, selection drains complexity, drains parts, from lower-level individuals. But there is little evidence of a drain in humans. In sum, a comparison with the other transitions gives reasons to doubt that human social individuation has proceeded very far, or if it has, to doubt that it is a transition of the same sort.” McShea. Daniel W. 2023. “Four reasons for scepticism about a human major transition in social individuality.” Philosophical Transactions of the Royal Society: B. 378:20210403. doi: 10.1098/rstb.2021.0403. p. 1.

“… Ellen Clarke lists a number of features that have been taken in the literature to be defining of individuality: reproduction, life cycles, genetics, sex, developmental bottlenecks, germ-soma separation, policing mechanisms, spatial boundaries or contiguity, immune response, fitness maximization, cooperation and/or conflict, co-dispersal, adaptations, metabolic autonomy, and functional integration. I do not adopt any one of these here, but will simply note that all represent some functional capacity and all are therefore likely the product of natural selection. And thus my own understanding of individuality is consistent with this approach: higher-level wholes, consisting of multiple lower-level entities, are individuals to the extent they have been acted upon directly by natural selection. Absent selection at the level of the whole, the higher-level whole remains a mere aggregation, an entity with a minimum of individuality. And the greater the duration or intensity with which selection has acted, the greater the degree of individuality. So in this view, the features above do not define individuality, but insofar as they are the product of natural selection, they are indicators of it.” McShea. Daniel W. 2023. “Four reasons for scepticism about a human major transition in social individuality.” Philosophical Transactions of the Royal Society: B. 378:20210403. doi: 10.1098/rstb.2021.0403. p. 2; reference: Clarke, Ellen. 2010. “The problem of biological individuality.” Biological Theory. 5:312-325. doi: 10.1162/BIOT_a_00068.

“Selection operates in three modes: persistence, growth and reproductive. In reproductive mode, individuals with a greater propensity to survive and reproduce leave more surviving offspring, and their descendants replace those with a lower propensity. This is the conventional understanding of selection.

“Selection in growth mode is different…. For selection in this mode (and indeed generally), fitness is success in the competition for resources, more specifically for energy, and the entity with a propensity to commandeer more of it succeeds, on average. For selection in growth mode, there is a critical assumption, namely that neither competitor is reproducing, or if they are, they have an equal propensity to leave surviving offspring.

“Finally consider persistence mode. A protist might be fitter than its competitors if it is able to encyst for long periods of time and thereby survive longer. Its competitors go extinct, perhaps by chance, as all species inevitably do, while the fitter individual persists.” McShea. Daniel W. 2023. “Four reasons for scepticism about a human major transition in social individuality.” Philosophical Transactions of the Royal Society: B. 378:20210403. doi: 10.1098/rstb.2021.0403. p. 4.

“Based on these comparisons, I want to draw attention to two alternative, and mutually exclusive, conclusions: (1) humans have not proceeded very far toward individuality at the social level and are unlikely to proceed very far in the future, given the expected weakness of selection at that level; or (2) if humans have advanced significantly toward individuality at the social level, they have done so by a very different route than the earlier major transitions at the colony level, sufficiently different that the markers that characterize these other major transitions are not present.” McShea. Daniel W. 2023. “Four reasons for scepticism about a human major transition in social individuality.” Philosophical Transactions of the Royal Society: B. 378:20210403. doi: 10.1098/rstb.2021.0403. p. 6.

“The famous philosopher Sir Karl Popper became fascinated by the idea that the Baldwin effect, while still based on Darwin’s theory of variation and selection, can easily be interpreted as a process that indirectly conveys traits of the individual into its genome.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 5.

“… as Popper explains, knowledge can only be achieved through the exploration of theories and expectations. Knowledge is gained by establishing a theory or expectation, and then checking it for veracity. When an assumption remains unrefuted, it contributes to the growth of knowledge. This method of trial and error elimination, based on logical reasoning, is the only possible method to gain new knowledge about the world or the environment, for both brains and living systems like cells, plants, or animals….” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 8.

“… one cannot deduce the truth of any theory from observed facts. There is only one way to profit from the making of theories: to use them as conjectures and to keep looking for counterexamples.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 9.

“According to Popper, the most distinguishing features of human life – such as activity or curiosity, pursuing aims, solving problems, and trying to get true knowledge about reality – pertain not just to human life, but fundamentally to the whole micro-cosmos of the cell.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 9.

“This ‘world 3′ theory is about the biological importance of knowledge existing independently of individuals in language and books. One facet of this theory states that, from a biological point of view, ‘objective knowledge’ is a biological instrument enabling us to transfer individual experience to the next generation without the help of the genetic apparatus. The entire world of knowledge, which Popper calls ‘world 3′, contains not only knowledge of present and former generations but it also contains knowledge no human has put into it. For example prime numbers and laws of geometry were not invented, but discovered by man. They were discovered by ‘interaction with world 3′, meaning that we give something into the world of knowledge and we get back new knowledge that, independently of man, was, as it were, waiting in ‘world 3′ to be discovered.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 16.

“Thus, beside the two other worlds – the ‘world 1′ of physical things and the ‘world 2′ of subjective feelings – ‘world 3′ adds a realm of wealth in the areas of logic, mathematics, knowledge, and even of wisdom about our lives. From a biological point of view ‘world 3′ has enormously changed our biological habitat.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 17.

“Popper’s ideas should be classified as spirituality because it is neither blind chance nor a mechanic selection process, but preferences, feelings and will of the organisms that determine the direction of evolution.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 52.

“‘… I [Popper] realized for the first time that biochemistry is fundamentally not reducible to chemistry.’

“And he continues: even if a complete reduction were ever possible, the fact would remain that an applied science can never be reduced to a theoretical science. That is a fact, because applied sciences are about aims; and this fact brings in teleology.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 53; subquote: Popper, Karl. Karl-Popper Sammlung, Klagenfurt. 493-6. p. 13.

“So, all processes in a wind turbine can, without any exception, be reduced to physical processes. But hardly any part of the construction can be explained in a purely physical way: literally all we can see – from the form of the rotor blades, the chosen building material, the height of the mast to the position of the plant – is only explicable if we talk about the purpose of the wind turbine.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 53.

“All new knowledge comes by trial and error elimination, or more exactly, by the constructing of theories or expectations in the brain (or in the cell) and the testing of their consequences in the world. This logic of acquiring new knowledge is the reason why – also in practical life – no living thing can attain new knowledge about its environment without having learned it by trial and error elimination, or, in other words, by construction and criticism. There is no other way to get new knowledge about the world….

“Popper states that the growth of knowledge cannot start from nothing. From the very beginning organisms have to produce tentative expectations.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. pp. 54-5.

“All his life Popper cherished and developed this theory: the theory that animals, plants, and bacteria have knowledge in the sense of inbuilt expectations about the world around them.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 55.

“… the aim of science is to give satisfying explanations. Thus the discussion is not about ‘Are all events or processes in our world based on physics and chemistry?’ (which is undoubtedly the case). Rather it is about ‘Are all events or processes in the living world explicable by physics and chemistry?’. This is undoubtedly not the case, not even in the unanimated world.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 66.

“Things which are ‘based on’ certain processes but not ‘explained by’ the theories of the underlying processes may be called ‘emergent’ or produced by ‘emergence’. These words sound a bit metaphysical. They are metaphysical, but they are neither incomprehensible nor unclear. They are metaphysical only according to Popper’s particular definition of a metaphysical statement as a theory which cannot be empirically falsified. Since in science we are always in search of simpler explanations we always have to look out for reduction. However, we must not believe in reducibility or irreducibility. Both are possible, and we have to find out which is applicable in each individual instance. Often reductions are possible. By talking of emergence or emergent processes we assume that nobody will ever find a reduction. However, it is something we can never know or prove. Therefore no scientist should be prevented from trying to reduce the laws of an emergent process to the well-known laws of the processes on which they are based. As a result it is always questionable to call a theory ‘scientific’ when it can only be falsified in a very distant future.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 68.

“A concrete definition of ‘emergence’ was given in his Kenan Lecture in 1969 by his tetrad schema of problem-solving:
P1 –> TS –> EE –> P2
P1: initial problem; TS: tentative problem solution; EE: error elimination; P2: the solution that is burdened with new but hopefully less urgent problems.

“This schema explains emergence in the world of organisms which are all problem-solvers: problem P2 is emergent, because the solution of problem P1 is not known in advance. So P2 is often something really novel in the world.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 70.

“In his book The Open Universe, Popper demonstrated that indeterminism is a necessary but not sufficient condition for emergence and openness of the future. If all things were determined, freedom and emergence would be impossible. The great cosmological emergences are atoms, molecules, life, subjective mind (such as feelings, thoughts, and wishes), and objective mind (such as language, writing, and books).” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 70.

“These two theories, the ‘active Darwinism’ and the ‘interaction with world 3′, a theory which has only been briefly touched on here, were Popper’s most original biological contributions.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 72.

“The acquisition of new knowledge and the occurrence of real activity are, in my opinion, the most striking features of all living things…. Activity is no mystery when we think of volcanos, oceans and tornados. However, it becomes a profound mystery when we think of it as purposeful actions which are undertaken by the likes of roses, bees, or leopards. The nature of these learned activities is completely different to the physical activities of the earth’s geographic features. How did this easily recognizable ‘real activity’ which is apparently able to pursue goals and to overcome difficulties on its way to these goals, come into the world?” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 73.

“The most important feature of objective knowledge is its existence outside the brain, for example in books and libraries. In comparison to this, subjective knowledge is the awareness of knowing something, e.g. I know that I know the birth date of Winston Churchill, and this awareness cannot exist outside a brain. I can say ‘I know something’, the book cannot.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 74.

“The point is thus: Popper’s epistemological logic says that all knowledge entering the world for the first time comes, without any exception, by the method of trial and error. There is logically no other method possible. Popper’s reasoning must have consequences for molecular biology as well as for our understanding of the origin of all life. That is the case because the origin of life, as we have heard in Popper’s Medawar Lecture, depends heavily on suitable adaptation, and adaptation always depends on knowledge of the environment. Therefore, on logical grounds from the very beginning of existence, life was bound to the method of trial and error.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 75.

“The entire Darwinian evolution is a process of continuously increasing knowledge about how to deal with the environment…. This knowledge must have been acquired through variation and selection, on purely logical grounds. Variation and selection, of course, is the biological equivalence of Popper’s trial and error elimination.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 75.

“Apparently there is a contradiction between the generally accepted central dogma [Weismann barrier] and the likewise commonly accepted fact that DNA contains a lot of knowledge about the world. In order to eliminate this contradiction and to learn something from it, I am going to defend these two theses:
“(1) The central dogma as a guiding research idea cannot be understood without distinguishing between ‘information transfer’ and ‘acquiring new knowledge’.
“(2) The central dogma is valid for acquiring new knowledge; it is invalid for information transfer, meaning:
“(2a) the transfer of information from protein to RNA or DNA is not forbidden and depends only on evolutionary utility and biochemical feasibility.
“(b) It is new knowledge about the world that cannot be transferred to DNA or RNA, but can only be gained by the method of trial and error.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 79.

“The more demanding problem is: In what way does knowledge enter the body, the cells, and the DNA code? Popper always vehemently denied that it was via the direct way. His analysis of the problem showed that theories maintaining the direct way boil down, after some consideration, to the untenable assertion that knowledge can simply fall into a kind of bucket, say the brain, the cell, or the DNA….

“If [new] knowledge has already been acquired, one can forget the method of trial and error and instead copy or transfer it as ‘information’ or ‘data’ from one ‘bucket’ into another.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. pp. 80, 81.

“Crick did not offer any justification of his central dogma… However, to exclude a priori a uni-directional information flow is absurd…. … information can normally be transferred in all directions, except if there is a physical reason preventing this transfer. What is not true for the dissemination of existing information is true for new knowledge: facts or laws of nature cannot automatically be translated from nature into a set of symbols. Only the process of trial and error – or variation and selection – can fill any suitable ‘bucket’. It is not direct information flow that is impossible, but the direct procurement of new knowledge. This is what I call ‘Popper’s exclusion principle’. It is based on logic.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 87.

“If we consider not just DNA but the entire genome, then the many information transfers which were discovered by the new branches of molecular biology, called ‘epigenics’, ‘gene regulation’, and ‘evo-devo’, prove that the genome is learning not just by trial and error but also by information transfer.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 88.

“For example, in a situation of an increased need for protein, new knowledge can be learned by the body or the brain in the normal way, by the method of trial and error. It can then be changed into information, say signals of a regulatory system, and then transferred signals or information can enter the genome. No principle exists to stop this kind of learning.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 88.

“As we have seen, there are two biological processes of learning: (i) learning new knowledge by trial and error and (ii) ‘information’ transfer of recently or formerly learnt knowledge, which has already been transformed into inbuilt or coded information…. These two processes are very different from one another in terms of the kind of activity which defines them.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 89.

“Surely, a complete physical separation between the two processes of information transfer and acquiring new knowledge is not possible. The latter consistently draws upon already inbuilt or coded information.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 90.

“Goals or purposes are only pursued by living things. As they generally cannot reach their goals without overcoming some difficulties, the overall behaviour of all life is problem solving. Thus, ‘problem solving’ is another word for pursuing goals by overcoming difficulties; and to repeat what Popper’s book title says: all life is problem solving.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 90.

“Real activity is necessary to get new knowledge about the environment. This knowledge is necessary for adaptation. Therefore acquiring new knowledge is always a purposeful activity which supports other goal-orientated activities such as survival, providing food, or propagation. Furthermore, these vital goals cannot be approached without trying to get new knowledge about the world. In all these cases the method of trial and error is inevitable. This method makes use of several kinds of real activity: (i) by varying the trials, (ii) by varying the criterion of error elimination or selection, (iii) by exploring the reality as a criterion of error elimination, and (iv) by saving new knowledge as inbuilt or coded information, in order to recall it for the purpose of solving later problems.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. pp. 90-1.

“Both knowledge and activity are the basis of Popper’s new interpretation of Darwinism as active Darwinism. Evolution is not driven by the mechanical process of variation and elimination, but by the activity of organisms concerned with problem-solving and gaining new knowledge….” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 91.

“The role of natural selection is merely to separate already existing organisms that are well adapted from those that are not.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 93.

“However, Popper remained loyal to Darwin and explained that Darwinism is not wrong, but incomplete….

“Thus, Popper did not refute the Darwinian principle of variation and natural selection, but diagnosed it as being incomplete. It is not complete because it neglects the activity of the individual, which plays an important role in evolution….

“Popper’s view of the role of natural selection can be illustrated by considering a judge who gives low marks for the less original dance performances in an ice-skating competition: even the candidate with the worst score is much more creative and active than the judge.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. pp. 94, 95.

“Looking 1000 years back our gene-line ramifies with each generation leading back to millions of equally matched foremothers and forefathers. In sharp contrast, our cell-line leads back to exactly one woman.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 100.

“The simplest form of real activity might be found in chemical reactions. Some chemical compounds ‘want’ to combine with other chemical compounds. It is, of course, a ‘want’ in quotation marks, but nonetheless there exists a real chemical attraction, a ‘chemical affinity’, or ‘chemical potential’. And this kind of chemical attraction is directed towards a goal. Iron reacts with the moisture and the oxygen of the air and is converted into rust. The complete conversion of iron into rust is, as it were, the goal of iron, water, and oxygen: it what they are aiming at.

“Thus, chemical affinity can be understood as a very simple form of will.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 103.

“Chemical reactions depend on probabilities or what Popper calls ‘propensities’.

“Propensities are probabilities which effect physical or chemical processes like forces. A garden ladder with some wobbly rungs may have a propensity of 30% of letting the gardener fall. This value is not easily calculated; however, we know that its value must be between zero and 100%. Additionally we know the propensity increases as the rungs get wobblier. Propensities make things happen if their value is greater than zero. Because of this property of making things happen, propensities are similar to forces or potentials. Things happen in a deterministic way if their value equals exactly 100%.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 104.

“Chemical reactions depend on several propensities at the same time. An outcome of 100% of the expected products is very rare, because even chemistry is not deterministic. That means, chemical machines are partly free and partly unfree, as it is with human beings.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 104.

“He [Popper] even sketched some fleeting ideas about the origin of life being produced by propensities: ‘The case of chemistry – growth of the possibility space versus destruction or elimination of possibilities and propensities. Hypothesis: propensities > 0 realise themselves in time.’” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 105.

“Another intended point [by Popper] was on ‘What precedes life were propensities for synthesis; and later propensities for solving problems of propagating. The possibility space expands; and so emerges activity and freedom. (And propensity for further expansion of the propensity space.)’” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 105.

“Additionally, Popper recognized that quantum mechanics did not function as a source of pure chance but as the origin of propensities, meaning goal-orientated probabilities.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 106.

“Propensities are not probabilities like those we know from playing dice. They are not the number of observed events divided by the number of possible events, but real physical quantities concerning single events like the probability of falling off a ladder with a wobbly rung.

“The difference between propensities and probabilities lies in the fact that propensities are based on real physical states, while the existence of probabilities is only in our mind: we do not know the future of a system (whether the dice will show the ‘6′) but we know the result of a statistical calculation. This result of a prediction is called ‘probability’, while the actual physical cause is called ‘propensity’.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. pp. 108-9.

“The first scientist who presented a formula for propensities was Albert Einstein. That was as early as 1916. Einstein did not use the word ‘propensities’ but called them ‘transition probabilities’. They were the cause for light absorption and light emission of molecules. For the first time special probabilities came into physics. These, similar to forces, are the real causes – and the only causes – of certain physical processes.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 109.

“He [Popper] was the first who discovered that propensities are not a measure of our subjective ignorance (for instance knowing something with 30% certainty) but the objective property of a physical situation.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 109.

“All these variables [travel, friends, books, memory, etc.] come with a certain propensity into play. What finally is our ‘will’ is not the result of neuronal currents but of complex calculations of propensities. As such, will can be defined as a network of propensities

“The contents of our will, the things we want, are not calculable in advance, because we cannot predict the outcome of probability processes.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 110.

“Darwinism is the attempt to reduce biology to physics and chemistry and this means explaining life away. Popper’s new Darwinism and his philosophy of biology brings life back into the world and into science: ‘Spirit from matter!’ Mind and matter are not opposites.

“Darwinism is based on blind chance and a non-creative selection. Popper’s active Darwinism stresses two elements of activity which superimpose Darwin’s mechanism of natural selection: (a) objective propensities and (b) individual preferences.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. pp. 110-1.

“The new story of creation might be told in this way: In the beginning there were chemical propensities, and these propensities became real activity. Real activity enabled knowledge about the world to enter the world in the form of inbuilt knowledge and even as coded knowledge. Real activity became will, desire, and preference. It enabled organisms to look for a better world and to solve problems. For each newly-discovered environment or newly-developed behaviour, the selection pressure supported the more creative cells or individuals and their suitable genes. In the end, humans learnt to speak and write. Life was able to build up huge quantities of exosomatic knowledge. Exosomatic knowledge is now continuously exchanged between all humans.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 111.

“Popper’s new interpretation of Darwinism offers a biologically founded world view in which the creative forces of evolution are not due to deadly competition and blind chance but are based on the activity of all organisms, on their use of knowledge, on their untiring search for a better environment controlled by their own preferences, and on their problem-solving.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 113.

“In later years I used to say (alluding to Orwell’s ‘all animals are equal, but some are more equal than others’) ‘All things are processes, but some are more processes than others’ – namely, living things, organisms. And I stressed that, though even atoms and molecules and rocks are processes, rivers and flames and, especially, trees and birds are more processes than molecules and rocks: they are processes on a higher level – a higher level or degree of process-like character.” Popper, Karl. 1989. “Letter to a Friend.” Niemann, Hans-Joachim. 2014. Karl Popper and the Two New Secrets of Life. Tuebingen: Mohr Siebeck. p. 135; Appendix D of Niemann book.

START HERE (for reviewing to my spreadsheet summary)
“We show that performing a reaction of the same starting materials [3 different amino acids] but under different environmental conditions will consistently yield different chemical ensembles. These can lead to the emergence of distinct order, structure, and function, ‘programmed’ by the environment, and challenge the view that a complexity-first approach, instead of targeting specific product molecules, will only yield intractable tar.” Surman, Andrew J., Marc Rodriguez-Garcia, Yousef M. Abul-Haija, Geoffrey J.T. Cooper, Piotr S. Gromski, Rebecca Turk-MacLeod, Margaret Mullin, Cole Mathis, Sara I. Walker, & Leroy Cronin. 2019. “Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions.” PNAS. 116(12):5387-5392. doi: 10.1073/pnas.1813987116. p. 5387.

“We chose three types of environmental condition to vary: (i) the presence of soluble salts, (ii) the presence of minerals, and (iii) the mixing history (the order of precursor addition over multiple reaction cycles)…..

“Remarkably, we found that all three variations to the environmental conditions led to differentiation of consistently distinct chemical ensembles in terms of peak distribution and intensities….” Surman, Andrew J. et al [see above]. 2019. “Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions.” PNAS. 116(12):5387-5392. doi: 10.1073/pnas.1813987116. p. 5389.

“Having established that variation to the environment can guide condensation reactions to yield chemical ensembles which are distinct in composition and oligomer sequence, we must then ask if this can also drive functional differences. To assess this, we first observed the effect of the different G/A/H-derived chemical ensembles on the progression of a simple and well-known reaction system, the decomposition of para-nitrophenyl acetate (pNPA, colorless) to release para-nitrophenyl (pNP, yellow). While absolute rates of the reaction in the presence of our ensembles were much lower than would be expected for catalysis by pure evolved/designed peptide catalysts we found clear and reproducible differences between the effects of many of the environmentally differentiated ensembles.” Surman, Andrew J. et al [see above]. 2019. “Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions.” PNAS. 116(12):5387-5392. doi: 10.1073/pnas.1813987116. p. 5390.

“To explore whether condensation reactions of such a complex mixture could be directed by the environment, we performed a series of experiments in which we subjected a standardized SD Mix [Spark Discharge Mix of chemicals similar to the Miller-Urey type discharges with many carboxylic acids, alcohols, aromatic species, and amino acids] to similar condensation conditions in the presence of the same series of minerals with which we previously treated AA reactions. LC-MS fingerprinting of the resulting chemical ensembles revealed that reaction in different mineral environments yielded chemical ensembles with a range of compositions which are almost all reproducibly distinct.” Surman, Andrew J. et al [see above]. 2019. “Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions.” PNAS. 116(12):5387-5392. doi: 10.1073/pnas.1813987116. p. 5391.

“Indeed, our demonstration of salts and minerals guiding the differentiation of distinct functional ensembles from simple building blocks are an experimental demonstration of Cairns-Smith’s ideas that inorganic materials can program complex organic chemistry to yield differently fit populations, beyond simply selecting for particular molecular targets.” Surman, Andrew J. et al [see above]. 2019. “Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions.” PNAS. 116(12):5387-5392. doi: 10.1073/pnas.1813987116. p. 5392.

“Although we chose to focus on animal-bacterial interactions, we expect the application of new technology to reveal similar trends among and between Archaea, fungi, plants, and animals.” McFall-Ngai, Margaret, Michael G. Hadfield, Thomas C.G. Bosch, Hannah V. Carey, Tomislav Domazet-Loso, Angela E. Douglas, Nicole Dubilier, Gerard Eberl, Tadashi Fukami, Scott F. Gilbert, Ute Hentschel, Nicole King, Staffan Kjelleberg, Andrew H. Knoll, Natacha Kremer, Sarkis K. Mazmanian, Jessica L. Metcalf, Kenneth Nealson, Naomi E. Pierce, John F. Rawls, Ann Reid, Edward G. Ruby, Mary Rumpho, Jon G. Sanders, Diethard Tautz & Jennifer J. Wernegreen. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3229.

“Thus, the discovery that at least one choanoflagellate, Salpingoeca rosetta, responds to signals from specific bacteria to initiate colony formation through cell division hints at an ancient involvement of bacteria in the initiation of multicellularity.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3230.

“Bacterial influence on gut evolution certainly intensified with the subsequent origin of the coelom, a body cavity in which the organs are suspended.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3230.

“Evolution with animals, whether in symbiosis or via shared habitats, has also influenced the distribution and diversification of bacteria. For example, 90% of the bacterial species in termite guts are not found elsewhere. Such specialization, while increasing efficiency, comes with a cost: for every animal species that goes extinct, an unknown number of unique bacterial lineages that have evolved to depend on this animal niche disappear as well.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3230.

“Microbial communities in the vertebrate gut respond to the host diet over both daily and evolutionary time scales, endowing animals with the flexibility to digest a wide variety of biomolecules and cope with and even flourish under conditions of diet change. For example, the gut microbiome of most people in the United States is adapted to digest a high-fat, high-protein diet, whereas populations in rural Malawi and the Amazonas of Venezuela have distinct microbial consortia and functional gene repertoires optimized for breaking down complex carbohydrates.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3231.

“… the gut bacterium Bacteroides plebeius, found in some Japanese people, bears a gene transferred horizontally from the marine bacterium Zobellia galactanivorans, giving the gut symbiont the capacity to degrade seaweed polysaccharides. More generally, human-associated bacteria have a 25-fold higher rate of gene transfer than do bacteria in other environments, highlighting the important role of gene transfer in host-associated bacterial communities.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3231.

“”Although not all genome-size reduction occurs in symbiosis, a long history of intimate association with insects has resulted in highly reduced genomes in their intracellular symbionts; for example, the endosymbiont Candidatus Hodgkinia cicadicola of the Arizona cicada has a genome size <144 kb, smaller than that of some organelles.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3231.

“Bacteria feeding on dead animals in the sea, and likely on land, repel animal scavengers by producing noxious metabolites; these products allow the bacteria to effectively outcompete organisms 10,000 times their size.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3234.

“For much of her professional career, Lynn Margulis, a controversial visionary in biology, predicted that we would come to recognize the impact of the microbial world on the form and function of the entire biosphere, from its molecular structure to its ecosystems. The weight of evidence supporting this view has finally reached a tipping point. The examples come from animal-bacterial interactions, as described here, and also from relationships between and among viruses, Archaea, protists, plants, and fungi. These new data are demanding a reexamination of the very concepts of what constitutes a genome, a population, an environment, and an organism.” McFall-Ngai, Margaret et al [see above]. 2013. “Animals in a bacterial world, a new imperative for the life sciences.” PNAS. 110(9):3229-3236. p. 3234.

“To sustain any coherent vision requires one to make an attempt to span fields of knowledge, and as human knowledge expands exponentially, the task becomes ipso facto more difficult. Should we therefore abandon the attempt? Certainly we must conclude that attempting such a synthesis is something that scientists with respectably constrained vision can from now on never attempt. However, with luck, some will be foolhardy enough to try, since the constrained vision is not – absolutely not – a feature of science, but of the nature of the contemporary science establishment.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. xviii.

“If a neuropsychologist had to choose three things to characterise most clearly the functional contribution of the right hemisphere, they would most probably be the capacity to read the human face, the capacity to sustain vigilant attention, and the capacity to empathise.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. xxii.

“Neurological research reveals a consistent picture of how the two hemispheres contribute to the richness of experience. Essentially this is that the right hemisphere tends to ground experience; the left hemisphere then works on it to clarify, ‘unpack’ and generally render the implicit explicit; and the right hemisphere finally reintergrates what the left hemisphere has produced with its own understanding, the explicit once more receding, to produce a new, now enriched, whole….

“This is to deny the importance of the left hemisphere’s contribution, just to make clear that it works its necessary effects at an intermediate stage. Problems arise when this is treated as the end stage. In terms of the metaphor of the Master and his emissary, the Master realises the need for an emissary to do certain work on his behalf (which he, the Master, must not involve himself with) and report back to him. That is why he appoints the emissary in the first place. The emissary, however, knowing less than the Master, thinks he knows everything and considers himself the real Master, thus failing to carry out his duty to report back. The right hemisphere’s view is inclusive, ‘both/and’, synthetic, integrative; it realises the need for both. The left hemisphere’s view is exclusive, ‘either/or’, analytic and fragmentary – but, crucially, unaware of what it is missing. It therefore thinks it can go it alone.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. xxiv.

“You might think that as brains evolve to become larger, the interhemispheric connections would increase in tandem. But not at all: they actually decrease relative to brain size. The bigger the brain, the less interconnected it is. Rather than taking the opportunity to increase connectedness, evolution appears to be moving in the opposite direction. And there is a close relationship between the separation of the hemispheres on the one hand and the development of something that keeps cropping up in this unfolding story: the asymmetry of the hemispheres. Because it turns out that the greater the brain asymmetry, too, the smaller the corpus callosum [connector between the hemispheres], suggesting that the evolution both of brain size and of hemisphere asymmetry went hand in hand with a reduction in interhemispheric connectivity. And, in the ultimate case of the modern human brain, its twin hemispheres have been characterised as two autonomous systems.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. pp. 18-9.

“Animals and birds may not have the problems posed by our frontal lobes to deal with, but they do already experience competing needs…. There is a need to focus attention narrowly and with precision, as a bird, for example, needs to focus on a grain of corn that it must eat, in order to pick it out from, say, the pieces of grit on which it lies. At the same time there is a need for open attention, as wide as possible, to guard against a possible predator.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 25.

“In general terms, then, the left hemisphere yields narrow, focussed attention, mainly for the purpose of getting and feeding. The right hemisphere yields a broad, vigilant attention, the purpose of which appears to be awareness of signals from the surroundings, especially of other creatures, who are potential predators or potential mates, foes of friends; and it is involved in bonding in social animals.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 27.

“The frontal lobes are particularly highly developed in humans. Their function is to yield distance – necessary for our most characteristically human qualities, whether that be foresight or empathy.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 30.

“The distinction I am trying to make is between, on the one hand, the way in which we experience the world pre-reflectively, before we have had a chance to ‘view’ it at all, or divide it up into bits – a world in which what later has come to be thought of as subjective and objective are held in a suspension which embraces each potential ‘pole,’ and their togetherness, together; and, on the other hand, the world we are more used to thinking of, in which subjective and objective appear as separate poles. At its simplest, a world where there is ‘betweenness’, and one where there is not. These are not different ways of thinking about the world: they are different ways of being in the world. And their difference is not symmetrical, but fundamentally asymmetrical.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 31.

“Ultimately if the left hemisphere is the hemisphere of ‘what’, the right hemisphere, with its preocccupation with context, the relational aspects of experience, emotion and the nuances of expression, could be said to be the hemisphere of ‘how’.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 93.

“I believe the essential difference between the right hemisphere and the left hemisphere is that the right hemisphere pays attention to the Other, whatever it is that exists apart from ourselves, with which it sees itself in profound relation. It is deeply attracted to, and given life by, the relationship, the betweenness, that exists with this Other. By contrast, the left hemisphere pays attention to the virtual world that it has created, which is self-consistent, but self-contained, ultimately disconnected from the Other, making it powerful, but ultimately only able to operate on, and to know, itself.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 93.

“… new experience of any kind – whether it be of music, or words, or real-life objects, or imaginary constructs – engages the right hemisphere. As soon as it starts to become familiar or routine, the right hemisphere is less engaged and eventually the ‘information’ becomes the concern of the left hemisphere only.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 94.

“There are those who believe that music is a useless spin-off, or epiphenomenon, of the development of language; there are those, on the contrary, who believe that language itself developed out of musical communication (a kind of singing); and finally there are those who hold that music and language developed independently but alongside one another, out of a common ancestor, which has been dubbed ‘musilanguage’.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 102.

“So language is a hybrid. It evolved from music and in this part of its history represented the urge to communicate; and to the extent that it retains right-hemisphere empathic elements, it still does. Its foundations lie in the body and the world of experience. But referential language, with its huge vocabulary and sophisticated syntax, did not originate in a drive to communicate, and from this point of view, represents something of a hijack. It has done everything it can to repudiate both its bodily origins and its dependency on experience–to become a world unto itself.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 125.

“I suggest that there are two opposing ways of dealing with the world that are both vital but are fundamentally incompatible, and that therefore, even before humans came on the scene, required separate treatment, even neurological sequestration from one another. One tendency, important for being able to get things from the world for one’s own purposes, involves isolation of one thing from the next, and isolation of the living being, perceived as subjective, from the world, perceived as objective. The drive here is towards manipulation, and its ruling value is utility. It began in my view by colonising the left hemisphere, and with the increasing capacity for distance from the world mediated by the expansion of the frontal lobes as one ascends the evolutionary tree, resulted in a physical expansion of the area designed to facilitate manipulation of the environment, symbolically and physically, in the higher monkeys and apes. Eventually that expansion became the natural seat of referential language in humans.

“The other tendency was centripetal, rather than centrifugal: towards the sense of the connectedness of things, before reflection isolates them, and therefore towards engagement with the world, towards a relationship of ‘betweenness’ with whatever lies outside the self. With the growth of the frontal lobes, this tendency was enhanced by the possibility of empathy, the seat of which is the right frontal expansion in social primates, including humans.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. pp. 127-8.

“… [Earlier] I suggested that the hemispheres were not just randomly assorted ‘databanks’, but had coherent and possibly irreconcilable sets of values, imaged in the left hemisphere’s control of manipulation through the right hand, and the evolution of language out of music, with language coming to reside largely in the left hemisphere, and music largely in the right.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 133.

“Attention is a moral act: it creates, brings aspects of things into being, but in doing so makes others recede.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 133.

“If one had to characterise the left hemisphere by reference to one governing principle it would be that of division. Manipulation and use require clarity and fixity, and clarity and fixity require separation and division. What is moving and seamless, a process, becomes static and separate – things. It is the hemisphere of ‘either/or’: clarity yields sharp boundaries. And so it makes divisions that may not exist according to the right hemisphere.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 137.

“But belief in terms of the right hemisphere is different, because its disposition towards the world is different. The right hemisphere does not ‘know’ anything in the sense of certain knowledge. For it, belief is a matter of care: it describes a relationship, where there is a calling and an answering, the root concept of ‘responsibility.’ Thus if I say that “I believe in you’, it does not mean that I think that such-and-such things are the case about you, but can’t be certain that I am right. It means that I stand in a certain sort of relation of care towards you, that entails me in certain kinds of ways of behaving (acting and being) towards you, and entails on you the responsibility of certain ways of acting and being as well. It is an acting ‘as if’ certain things were true about you that in the nature of things cannot be certain. It has the characteristic right-hemisphere qualities of being a betweenness: a reverberative, ‘re-sonant’, ‘respons-ible’ relationship, in which each party is altered by the other and by the relationship between the two, whereas the relationship of the believer to the believed in the left-hemisphere sense is inert, unidirectional, and centres on control rather than care…

“This helps illuminate belief in God. This is not reducible to a question of a factual answer to the question ‘does God exist?’, assuming for the moment that the expression ‘a factual answer’ has a meaning. It is having an attitude, holding a disposition towards the world, whereby that world, as it comes into being for me, is one in which God belongs. The belief alters the world, but also alters me.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 170.

“The left hemisphere is always engaged in a purpose: it always has an end in view, and downgrades whatever has no instrumental purpose in sight. The right hemisphere, by contrast, has no designs on anything. It is vigilant for whatever is, without preconceptions, without a predefined purpose. The right hemisphere has a relationship of concern or care with whatever happens to be.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 174.

“… the right hemisphere deals with the world before separation, division, analysis has transformed it into something else, before the left hemisphere has re-presented it. It is not that the right hemisphere connects – because what it reveals was never separated; it does not synthesize – what was never broken down into parts; it does not integrate – what was never less than whole.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 179.

“If the implicit grounds the explicit, it would imply that one’s feelings are not a reaction to, or a superposition on, one’s cognitive assessment, but the reverse: the affect comes first, the thinking later. Some fascinating research confirms that affective judgment is not dependent on the outcome of a cognitive process. We do not make choices about whether we like something on the basis of explicit assessment, a balance sheet, weighting up its parts. We make an intuitive assessment of the whole before any cognitive processes come into play, though they will, no doubt, later be used to ‘explain’, and justify, our choice. This has been called ‘the primacy of affect’. We make an assessment of the whole at once, and pieces of information about specific aspects are judged in the light of the whole, rather than the other round.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 184.

“Despite the left hemisphere’s conviction of its own self-sufficiency, everything about the relationshp of the hemispheres to one another and to reality suggests the primacy of the right hemisphere, both in grounding experience (at the bottom level) and reconstituting left-hemisphere-processes experience once again as living (at the top level).” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 209.

“According to Heidegger, what were anciently seen as the Apollonian, more rationalistic, and Dionysian, more intuitive, aspects of our being have become grossly unbalanced. Nietzsche claimed that the constant opposition between these two very different tendencies led to a fruitful incitement to further and ever higher levels of life and creativity… But the war between these tendencies has become, according to Heidegger, no longer creative but merely destructive. We have become ‘pre-eminently endowed with the ability to grasp and delimit’: the Apollonian has triumphed at the expense of the Dionysian.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 232.

“… many imaging studies have now confirmed that there appears to be a predominance of left-sided activation during hypnosis…. … in the hypnotic state, there is abnormally increased activation in the left hemisphere. In hypnosis the right hemisphere is not activated, even during a typically ‘right-hemisphere’ task, using overall EEG power as the criterion.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 236.

“Today all the available sources of intuitive life – cultural tradition, the natural world, the body, religion and art – have been so conceptualised, devitalised and ‘deconstructed’ (ironised) by the world of words, mechanistic systems and theories constituted by the left hemisphere that their power to help us see beyond the hermetic world that it has set up has been largely drained from them.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 244.

“Each cultural shift can be seen as a response to the eventual inauthenticity of the world according to one or other of the hemispheres, but for the right hemisphere the route back has to be through engagement with an attractive power beyond itself.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 255.

“However, I believe he [Julian Jaynes in The Origin of Consciousness in the Breakdown of the Bicameral Mind] got one important aspect of the story back to front. His contention that the phenomena he describes came about because of a breakdown of the ‘bicameral’ mind – so that the two hemispheres, previously separate, now merged – is the precise inverse of what happened. The phenomena came about because of a relative separation of the two chambers, the two hemispheres. Phenomena that were previously uncomplicatedly experienced as part of a relatively unified consciousness now became alien….

“Putting it at its simplest, where Jaynes interprets the voices of the gods as being due to the disconcerting effects of the opening of a door between the hemispheres, so that the voices could for the first time be heard, I see them as being due to the closing of the door, so that the voices of intuition now appear distant, ‘other’; familiar but alien, wise but uncanny – in a word, divine.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 262.

“My thesis is that the separation of the hemispheres brought with it both advantages and disadvantages. It made possible a standing outside of the ‘natural’ frame of reference, the common-sense everyday way in which we see the world. In doing so it enabled us to build on that ‘necessary distance’ from the world and from ourselves, achieved originally by the frontal lobes, and gave us insight into things that otherwise we could not have seen, even making it possible for us to form deeper empathic connections with one another and with the world at large. The best example of this is the fascinating rise of drama in the Greek world, in which the thoughts and feelings of our selves and of others are apparently objectified, and yet returned to us as our own. A special sort of seeing arises, in which both distance and empathy are crucial.

“But the separation also sowed the seeds of left-hemisphere isolationism, allowing the left hemisphere to work unchecked. At this stage in cultural history, the two hemispheres were still working largely together, and so the benefits outweighed by a long way the disadvantages, but the disadvantages became more apparent over time.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 262.

“What is clear is that there was originally no single word to convey the simple function of sight tout court. There were originally only words for relations with things, the quality of the experiences, how the ‘seer’ stood towards the ‘seen’ In other words sight had not been abstracted yet from its context within the lived world, where it is reverberative, itself alive, an expreessive of betweenness — not yet thought of as unidirectional, detached, dead: not yet observation.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 266.

“The most familiar point of commonality in pre-Socratic philosophy is an attempt to reconcile a sense of the apparent unity of the phenomenal world with its obvious diversity. This suggested that there should be some common originary principle, or arche, from which all things came: the multiplicity of appearances, phenomena, being a reflection of the mutability of the primary substance, which underlies everything and could metamorphose between different states….

“However, Anaximander, Thales’ pupil, took things much further. He posited that all things arise from and ultimately return to, an originary principle that he called the ‘unbounded’ or the ‘indefinite” (apeiron). This carries with it the suggestion of something that cannot be qualified, and therefore must be approached apophatically (apeiron litearlly means undefined, or unlimited), and that has neither beginning nor end, and therefore is an endless source, from which things eternally arise and to which they eternally return, forever in process, rather than an arche that simply occupies a static point in time, or acts as origin of a chain of causation.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 267.

“We are not so used to hearing speech as a succession of separate building blocks, rather than as an utterance as a whole, that it is hard to imagine that even the separations between words were not regularised in writing, so that all was written continuously, until the Byzantine period.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 277.

“… money is homogeneous, and hence homogenises its objects and its users, eroding uniqueness: it is impersonal, unlike talismanic objects, and weakens the need for bonds, or for trust based on a knowledge of those with whom one is exchanging. It becomes a universal aim, corrupting even death ritual, and threatening other values as it transcends and substitutes for them; and it becomes a universal means, including to divine good will or to political power.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 279.

“One of the defining features of the Renaissance must be its opening of the eyes to experience, initially almost exclusively personal experience, in preference to what is ‘known’ to be the case, the teachings of scholastic theory and received opinion….

“… it seems to me that the Renaissance started out with a huge expansion of the right hemisphere’s way of being in the world, into which, initially, the work of the left hemisphere is integrated. And it is this that accounts for the astonishing fertility and richness, as well as the remarkable breadth of concern, to this day memorialised in the concept of the Renaissance man, of this period.

“As the Renaissance progresses, there becomes evident, however, a gradual shift of emphasis from the right hemisphere way of being towards the vision of the left hemisphere, in which a more atomistic individuality characterised by ambition and competition becomes more salient; and originality comes to mean not creative possibility but the right to ‘free thinking’, the way to throw off the shackles of the past and its traditions, which are no longer seen as an inexhaustible source of wisdom, but as tyrannical, superstitious and irrational – and therefore wrong. This becomes the basis of the hubristic movement which came to be known as the enlightenment.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. pp. 328, 329.

“The value of rationality, as well as whatever premises it may start from, has to be intuited: neither can be derived from rationality itself. All rationality can do is to provide internal consistency once the system is up and running.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 330.

“… the rise of modern Western man is associated with an accentuation of the difference between the hemispheres, in other words the evolution of a more, rather than less, ‘bicameral’ mind. The further accentuation of this difference in the Enlightenment, through the striving for an objective, scientific detachment – independent as far as possible of the ‘confounding’ effects of whatever is personal or intuitive, or whatever cannot be made explicit and rationally defended – led to an entrenchment of this separation. Much as the voices of the gods, from being a naturally integrated part of the world as experienced, came to appear alien to the Ancient Greeks, so at the Enlightenment the promptings of the right hemisphere, excluded from the world of rationalising discourse in the left hemisphere, came to be seen as alien. I believe this is the origin of the rise of the experience of the ‘uncanny’, the darker side of the age of the Enlightenment.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 350.

“… I will develop the view that Romanticism is a manifestation of right-hemisphere dominance in our way of looking at the world. Here I am reminded of the fact that the right hemisphere is more inclusive, and can equally use what the left hemisphere uses as well as its own preferred approach, whereas the left hemisphere does not have this degree of flexibility or reciprocity.

“Whereas for the Enlightenment, and for the workings of the logical left hemisphere, opposites result in a battle which must be won by ‘the Truth’, for the Romantics, and for the right hemisphere, it is the coming together of opposites into a fruitful union that forms the basis not only of everything that we find beautiful, but of truth itself.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 354.

“But it is the Industrial Revolution which enabled the left hemisphere to make its most audacious assault yet on the world of the right hemisphere – or perhaps one should say that the left hemisphere’s most daring assault was the Industrial Revolution.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 386.

“But what if the left hemisphere were able to externalise and make concrete its own workings – so that the realm of actually existing things apart from the mind consisted to a large extent of its own projections? Then the ontological primacy of right-hemisphere experience would be outflanked, since it would be delivering – not ‘the Other’, but what was already the world as processed by the left hemisphere….

“In essence this was the achievement of the Industrial Revolution. It is not just that this movement was obviously, colossally, man’s most brazen bid for power over the natural world, the grasping left hemisphere’s long-term agenda. It was also the creating of a world in the left hemisphere’s own likeness.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 386.

“Heisenberg, in the 1950s, wrote that technology no longer appears
‘as the product of a conscious human effort to enlarge material power, but rather like a biological development of mankind in which the innate structures of the human organism are transplanted in an ever-increasing measure into the environment of man.’” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 387; subquote: Heisenberg, W. 1958. The Physicist’s Conception of Nature. NY: Harcourt Brace. p.153.

“The importance of Sass’s work is that it demonstrates how the nature of attention alters what it finds; and specifically that when we cease to act, to be involved, spontaneous and intuitive, and instead become passive, disengaged, self-conscious, and stare in an ‘objective’ fashion at the world around us, it becomes bizarre, alien, frightening – and curiously similar to the mental world of the schizophrnenic. Sass explores the idea that ‘madness … is the end-point of the trajectory [that] consciousness follows when it separates from the body and the passions, and from the social and practical world, and turns in upon itself. For Sass, as for Wittgenstein, there is a close relation between philosophy and madness. The philosopher’s ‘predilection for abstraction and alienation – for detachment from body, world and community’, can produce a type of seeing and experiencing which is, in a literal sense, pathological.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 393; reference/subquote: Sass, L.A. 1994. The Paradoxes of Delusion: Wittgenstein, Schreber, and the Schizophrenic Mind. Cornell UP. p. 12.

“So Anton van Zijderveld, in his excellent study of cliche, notes that ‘it can be observed that speech becomes gross and hyperbolic, music loud and nervous, ideas giddy and fantastic, emotions limitless and shameless, actions bizarre and foolish, whenever boredom reigns…. Scheler speaks of our ‘”culture” of entertainment’ as a collection of ‘extremely merry things, viewed by extremely sad people who do not know what to do with them.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 400; reference: van Zijderveld, Anton. 1979. On Cliches: the Supersedure of Meaning by Function in Modernity. Routledge & Kegan Paul. p. 84; Scheler, M. 1998. Resentiment. Marquette UP. p.126.

“The difference [between modernism and post-modernism] depends on the level of consciousness. In the Enlightenment, although the process of alienation of the observing subject was well under way, there was yet little doubt that there existed a world for it to observe….

“A couple of hundred years and another level of self-consciousness later, the observing subject is not just aware, but aware of its own awareness….

“Post-modern indeterminacy affirms not that there is a reality, towards which we must carefully, tentatively, patiently struggle; it does not posit a truth which is nonetheless real because it defies the determinacy imposed on it by the self-conscious left-hemisphere interpreter (and the only structures available to it). On the contrary, it affirms that there is no reality, no truth to interpret or determine. The contrast here is like the difference between the ‘unknowing’ of a believer and the ‘unknowing’ of an athiest. Both believer and atheist may quite coherently hold the position that any assertion about God will be untrue; but their reasons are diametrically opposed…. One says ‘I do not know’, the other ‘I know – that there is nothing to know.’ One believes that one cannot know: the other ‘knows’ that one cannot believe.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. pp. 426, 427.

“… it appears essential for the creation of full human consciousness and imagination that the right hemisphere places itself in a position of vulnerability to the left. The right hemisphere, the one that believes, but does not know, has to depend on the other, the left hemisphere, that knows, but doesn’t believe. It is as though a power that has an infinite, and therefore intrinsically uncertain, potential Being needs nonetheless to submit to be delimited – needs stasis, certainty, fixity – in order to Be. The greater purpose demands the submission. The Master needs to trust, to believe in, his emissary, knowing all the while that that trust may be abused. The emissary knows, but knows wrongly, that he is invulnerable. If the relationship holds, they are invincible; but if it is abused, it is not just the Master that suffers, but both of them, since the emissary owes his existence to the Master.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 428.

“[In considering what the left hemisphere’s world would look like] The left hemisphere prefers the impersonal to the personal, and that tendency would in any case be instantiated in the fabric of a technologically driven and bureaucratically administered society. The impersonal would come to replace the personal. There would be a focus on material things at the expense of the living. Social cohesion, and the bonds between person and person, and just as importantly between person and place, the context in which each person belongs, would be neglected, perhaps actively disrupted, as both inconvenient and incomprehensible to the left hemisphere acting on its own. There would be a depersonalisation of the relationships between members of society, and in society’s relationship with its members. Exploitation rather than co-operation would be, explicitly or not, the default relationship between human individuals, and between humanity and the rest of the world. Resentment would lead to an emphasis on uniformity and equality, not as just one desirable to be balanced with others, but as the ultimate desirable, transcending all others. As a result individualities would be ironed out and identification would be by categories: socioeconomic groups, races, sexes, and so on, which would also feel themselves to be implicitly or explicitly in competition with, resentful of, one another.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 431.

“We stand or sit there [viewing modern art] solemnly contemplating the genius of the artwork, like the passive, well-behaved bourgeois that we are, when we should be calling someone’s bluff. My bet is that our age will be viewed in retrospect with amusement, as an age remarkable not only for its cynicism, but for its gullibility.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 442.

“What ultimately unites the three realms of escape from the left hemisphere’s world which it has attacked in our time – the body, the spirit and art – is that they are all vehicles of love.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 445.

“Think of something as basic as classical conditioning, whereby a stimulus (ringing a bell, previously associated with the provision of food) produces a ‘conditioned response’ in Pavlov’s dog (salivation). This is thought of as a linear process, the arrow hitting its target. Thus the dog is reduced to a machine. But a slightly different way of thinking of this would be that there is a context to everything, context being a circular, concentric concept, rather than a linear one. If one imagines Pavlov’s dog, in a different experiment, having repeated experience of the bell being rung after it has started eating, rather than just before it gets food, one would have to say that, when the dog hears the bell in the absence of food, it experiences an association (a mini-context) in which these two events tend to co-occur. It would have as much reason to start to salivate when it heard the bell, but in doing so it would appear less mechanical, less as though its behaviour were caused by the bell. The dog is reduced to a mechanism by the temporal sequencing, an essential part of the concept of causation, and by the stripping away of the context to focus on a sequence…. The dog, too, is appreciating associations or contexts (a right-hemisphere function), not just acting like a left-hemisphere machine: we know, for example, that the sound of its master’s voice evokes to a dog an image of its master’s face, not because the voice ‘causes’ the face but because they are part of a whole experience.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 446.

“… philosophy does not answer our questions but shakes our belief that there are answers to be had; and in doing so it forces us to look beyond its own system to another way of understanding. One of the reasons reading Heidegger is at the same time so riveting and such a painful experience is that he never ceases to struggle to transcend the Cartesian divisions which analytic language entails, in order to demonstrate that there is a path, a way through the forest, the travelling of which is in itself the goal of human thinking…. Perhaps inevitably Heidegger’s last writings are in the form of poems.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. pp. 450-1.

“The Japanese have nothing that corresponds to the Platonic Idea, and in fact no abstractions in general: they have never developed the dichotomy between the phenomenological world and the world of ideas. Nakamura writes:
‘The Japanese are willing to accept the phenomenal world as Absolute because of their disposition to lay a greater emphasis upon intuitive sensible concrete events, rather than upon universals. This way of thinking with emphasis upon the fluid, arresting character of observed events regards the phenomenal world itself as Absolute and rejects the recognition of anything existing over (and above) the phenomenal world.’” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 452; subquote: Nakamura, H. 1993. Ways of Thinking of Eastern Peoples: India-China-Tibet-Japan. U of Hawaii Press. pp. 553, 350.

“In general the Japanese place far more emphasis on individual existing things than on generalities, are more intuitive, and less cognitive, when compared with Westerners, and are not so easily swayed by logic or system-building.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 453.

“Shizen, the Japanese word for nature, also links it clearly to the right-hemisphere way of being. Its derivation means ‘of itself’, ‘spontaneously’ (it is in fact an adverb, not a noun), as opposed to whatever is brought about through calculation or by will. It is all that is ‘just as it is’. Everything about the Japanese attitude to nature, expressed both in mythology and in everyday life, suggests an attitude of mutual trust, dependence and interrelationship between man and nature. While shizen does, of course, refer to the natural world of grass, trees and forest, it also means the land and the landscape, as well as the ‘natural self’ considered as a physical, spiritual and moral being….” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 453.

“What Oriental cultures also emphasise is the value of what is fleeting, something that has been appreciated in the West only rarely, that is to say during the Renaissance and in the Romantic period. The impermanence of nature is seen as the Buddhahood, or essence of the divine. In the west, with our recording apparatus of every kind, we value what we can grasp and hold. But life and everything living refuses this approach. It changes as we hold it.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 453.

“In a further twist, both Japanese and American participants primed with Japanese scenes attended more to contextual information than did those primed with American scenes. This last finding, in particular, is fascinating, and tends to confirm my view that the brain creates its own projections in the outer world, which in turn help to influence the workings of the brain in a mutually reinforcing, and self-perpetuating, way.” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 456.

“As Karl Popper put it, ‘bold ideas, unjustified anticipations and speculative thought, are our only means for interpreting nature: our only organon, our only instrument for grasping her.’” McGilchrist, Iain. 2019. The Master and His Emissary: The Divided Brain and the Making of the Western World, New Expanded Edition. Yale UP. p. 460; Popper, Karl. 1980. The Logic of Scientific Discovery. London: Routledge & Kegan. p. 280.

“The task is to make kin in lines of inventive connection as a practice of learning to live and die well with each other in a thick present. Our task is to make trouble, to stir up potent response to devastating events, as well as to settle troubled waters and rebuild quiet places. In urgent times, many of us are tempted to address trouble in terms of making an imagined future safe, or stopping something from happening that looms in the future, of clearing away the present and the past in order to make futures for coming generations. Staying with the trouble does not require such a relationship to times called the future. In fact, staying with the trouble requires learning to be truly present, not as a vanishing pivot between awful or edenic pasts and apocalyptic or salvific futures, but as mortal critters entwined in myriad unfinished configurations of places, times, matters, meanings.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 1.

“An ubiquitous figure in this book is SF: science fiction, speculative fabulation, string figures, speculative feminism, science fact, so far.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 2.

“This book argues and tries to perform that, eschewing futurism, staying with the trouble is both more serious and more lively. Staying with the trouble requires making oddkin; that is, we require each other in unexpected collaborations and combinations, in hot compost piles. We become-with each other or not at all.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 4.

“… Marilyn Strathern…. taught me that ‘it matters what ideas we use to think other ideas (with)’…. She embodies for me the arts of feminist speculative fabulation in the scholarly mode. It matters what matters we use to think other matters with; it matters what stories we tell to tell other stories with; it matters what knots knot knots, what thoughts think thoughts, what descriptions describe descriptions, what ties tie ties. It matters what stories make worlds, what worlds make stories.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 12; subquote: Strathern, Marilyn. 1992. Reproducing the Future. Manchester, UK: Manchester UP. p. 10.

“… I–we–have to relearn how to conjugate worlds with partial connections and not universals and particulars.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 13.

“Humans as humus has potential, if we could chop and shred human as Homo, the detumescing project of a self-making and planet-destroying CEO. Imagine a conference not on the future of the Humanities in the Capitalist Restructuring University, but instead on the Power of the Humusities for a Habitable Multispecies Muddle!” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 32.

“The earth of the ongoing Chthulucene is sympoietic, not autopoietic….

“… the term sympoiesis [is] for ‘collectively-producing systems that do not have self-defined spatial or temporal boundaries. Information and control are distributed among components. The systems are evolutionary and have the potential for surprising change.’” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 33; subquote: Dempster, M. Beth. 1998. “A Self-Organizing Systems Perspective on Planning for Sustainability.” MA thesis, Environmental Studies, U of Waterloo.

“Tool, weapon, word: that is the word made flesh in the image of the sky god; that is the Anthropos.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 39.

“In this terrible time called the Anthropocene, Latour argues that the fundamentals of geopolitics have been blasted open. None of the parties in crisis can call on Providence, History, Science, Progress, or any other god trick outside the common fray to resolve the troubles.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 40; reference: Latour, Bruno.

“Those who tell Gaia stories or geostories are the ‘Earthbound,’ those who eschew the dubious pleasures of transcendent plots of modernity and the purifying division of society and nature.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 41.

“Both the Anthropocene and the Capitalocene lend themselves too readily to cynicism, defeatism, and self-certain and self-fulfilling predictions, like the ‘game over, too late’ discourse I hear all around me these days, in both expert and popular discourses, in which both technotheocratic geoengineering fixes and wallowing in despair seem to coinfect any possible common imagination.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 56.

“Sympoiesis is a simple word; it means ‘making-with.’ Nothing makes itself; nothing is really autopoietic or self-organizing…. Sympoiesis enfolds autopoiesis and generatively unfurls and extends it.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 58.

“The critics are a crucial part of the holobiome of making science, and I am not a disinterested observer.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 67.

“We relate, know, think, world, and tell stories through and with other stories, worlds, knowledges, thinkings, yearnings. So do all the other critters of Terra, in all our bumptious diversity and category-breaking speciations and knottings. Other words for this might be materialism, evolution, ecology, sympoiesis, history, situated knowledges, cosmological performance, science art worldings, or animism, complete with all the contaminations and infections conjured by each of these terms.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 97.

“We are compost, not posthuman; we inhabit the humusities, not the humanities. Philosophically and materially, I am a compostist, not a posthumanist.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 97.

“Anna Tsing… suggests that the inflection point between the Holocene and the Anthropocene might be the wiping out of most of the refugia from which diverse species assemblages (with or without people) can be reconstituted after major events….

“Right now, the earth if full of refugees, human and not, without refuge.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 100; reference: Tsing, Anna. 2015. “Feral Biologies.” Paper for ‘Anthropological Visions of Sustainable Futures” conference. University College London. February 12-14.

“I am calling all this the Chthulucene–past, present, and to come. These real and possible time-spaces are [named] … after the diverse earthwide tentacular powers and forces and collected things with names like Naga, Gaia, Tangaroa, Terra, Haniyasu-hime, Spider Woman, Pachamama, Oya, Gorgo, Raven, A’akuluujjusi, and many many more. ‘My’ Chthulucene, even burdened with its problematic Greek-ish rootlets, entangles myriad temporalities and spatialities and myriad intra-active entities-in-assemblages–including the more-than-human, other-than-human, inhuman, and human-as-humus.” Haraway, Donna. 2016. Staying with the Trouble: Making Kin in the Chthulucene. Duke UP. p. 101.

“A summary of the surprising facts will include at least the following: Piraha is the only language known without number, numerals, or a concept of counting. It also lacks terms for quantification such as ‘all,’ ‘each,’ ‘every,’ ‘most,’ and ‘some.’ It is the only language known without color terms. It is the only language known without embedding (putting one phrase inside another of the same type or lower level, e.g., noun phrases in noun phrases, sentences in sentences, etc.). It has the simplest pronoun inventory known, and evidence suggests that its entire pronominal inventory may have been borrowed. It has no perfect tense. It has perhaps the simplest kinship system ever documented. It has no creation myths–its texts [transcribed by outsiders] are almost always descriptions of immediate experience or interpretations of experience; it has some stories about the past, but only of one or two generations back. Piraha in general express no individual or collective memory of more than two generations past. They do not draw, except for extremely crude stick figures representing the spirit world that they (claim to) have directly experienced.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 621.

“The phonemic inventory of Piraha women is the smallest in the world, with only seven consonants and three vowels, while the men’s inventory is tied with Rotokas and Hawaiian for the next-smallest inventory, with only eight consonants and three vowels.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 621.

“The Piraha people communicate almost as much by singing, whistling, and humming as they do using consonants and vowels. Piraha prosody is very rich, with a well-documented five-way weight distinction between syllable types.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 621.

“In 1980, at the Piraha’s urging, my wife and I began a series of evening classes in counting and literacy. My entire family participated, with my three children sitting with Piraha men and women and working with them. Each evening for eight months my wife would try to teach Piraha men and women to count fo ten in Portuguese. They told us that they wanted to learn this because they knew that they did not understand nonbarter economic relations and wanted to be able to tell whether they were being cheated. After eight months of daily efforts, without ever needing to call them to come for class (all meetings were started by them with much enthusiasm), the people concluded that they could not learn this material, and classes were abandoned. Not one learned to count to ten, and not one learned to add 3 + 1 or even 1 + 1–only occasionally would some get the right answer.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 625.

“When the Piraha hear a boat coming, they will line up on the riverbank and wait for it to come into sight. They will say, ‘The boat ‘ibipio (‘arrived’).’ They will watch a boat disappear around the corner and say, ‘the Boat ‘ibipio (‘left’).’ When a match is lit, they say that the match ‘ibipiai (where -ai is the verb form and ‘o the incorporated form). They will repeat the same expression when the match goes out. They especially use this for a flickering match and love to watch one, saying ‘keep on ‘ibipiai.’ After discussions and checking of many examples of this, it became clearer that the Piraha are talking about liminality–situations in which an item goes in and out of the boundaries of their experience. This concept is found throughout Piraha culture. Piraha’s excitement at seeing a canoe go around a river bend is hard to describe; they see this almost as travelling into another dimension. It is interesting, in light of the postulated cultural constraint on grammar, that there is an important Piraha term and cultural value for crossing the border between experience and nonexperience.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 629.

“The Piraha do not create fiction, and they have no creation stories or myths….

“When pressed about creation, for example, Piraha say simply, ‘Everything is the same,’ meaning that nothing changes, nothing was created.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 630.

“Now let us consider a final unusual feature of Piraha–that the Piraha continue to be monoloingual in Piraha after more than 200 years of regular contact with Brazilians and other non-Piraha…. Simply, Portuguese is incommensurate with Piraha in many areas and culturally incompatible, like all Western languages, in that it violates the immediacy-of-experience constraint on grammar and living in so many aspects of its structure and use. The Piraha say that their heads are different. In fact, the Piraha language is called ‘apaitiiso ‘a strainght head’, while all other languages are called ‘apagaiso ‘a crooked head’.” Everett, Daniel L. 2005. “Cultural Constraints on Grammar and Cognition in Piraha.” Current Anthropology. 46(4):621-46. [Page numbering might be off] p. 630.

“We use the following quote to describe our initial and basic definition of phylosymbiosis, namely ‘microbial community relationships that recapitulate the phylogeny of their host.’ Phylosymbiosis is first and foremost a significant association between host phylogenetic relationships and host-associated microbial community relationships wherein ‘phylo’ refers to the host clade and ‘symbiosis’ refers to the microbial community in or on the host.” Lim, Shen Jean & Seth R. Bordenstein. 2020. “An introduction to phylosymbiosis.” Proceedings of the Royal Society: B. 287:20192900. doi: 10.1098/rspb.2019.2900. p. 2; subquote: Brucker R.M. & S.R. Bordenstein. 2013. “The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science. 341:667-669. doi: 10.1126/science.1240659.

“… importantly it [phylosymbiosis] may also be driven by relatively short-term changes in microbiome composition. Indeed, a recent Drosophila melanogaster study revealed the effects of gut microbiome changes on host genomic divergence in as little as five generations. This suggests that rather than being passive agents of phylosymbiosis, microbial communities have the potential to induce host genomic changes that could, in turn, impact the establishment, maintenance or breakdown of phylosymbiosis.” Lim, Shen Jean & Seth R. Bordenstein. 2020. “An introduction to phylosymbiosis.” Proceedings of the Royal Society: B. 287:20192900. doi: 10.1098/rspb.2019.2900. p. 2.

“Besides gut or faecal microbiomes, animal surface microbiomes have also been analysed for phylosymbiotic associations, which for example occur on mammalian skin and passerine feathers, but not on amphibian skin.” Lim, Shen Jean & Seth R. Bordenstein. 2020. “An introduction to phylosymbiosis.” Proceedings of the Royal Society: B. 287:20192900. doi: 10.1098/rspb.2019.2900. p. 6.

“Phylosymbiosis has been assessed in plants, mainly to distinguish the effects on host phylogeny and soil determinants on microbial beta diversity. A comparative analysis of lycopods, ferns, gymnosperms and angiosperms across a coastal tropical soil chronosequence indicated host phylogeny is a secondary but statistically significant factor shaping root-associated bacterial community structure, after soil age.” Lim, Shen Jean & Seth R. Bordenstein. 2020. “An introduction to phylosymbiosis.” Proceedings of the Royal Society: B. 287:20192900. doi: 10.1098/rspb.2019.2900. p. 7.

“… we will make the effort to show that the individuals of this community (the first, full-fledged, minimal living organisms) indeed realize their identity both: (i) as material systems/organizations that distinguish themselves from other systems/organizations, staying the same individual that each of them was, previously in time (i.e., they constitute token) identities); and (ii) as material systems/organizations that are, for all relevant purposes, equivalent to other systems/organizations in the group, sharing the same potentialities held by any other member of that group (i.e., they constitute type identities).” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 3.

“This [passage from token identities to type identities in prebiotic evolution] will lead us to propose the main thesis of this work: biogenesis can – and should – be conceived as a process of evolutionary development of increasingly complex protocells until they accomplish biological ‘inter-identity’, eliminating the previous, more precarious and diverse populations of interacting individuals.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 3.

“Accordingly, the actual sizes, shapes, and composition of these compartmentalized systems would be quite diverse, and in continuous change, because different chemical reactions (involving other simple, prebiotically plausible molecular species, like additional amphiphiles/surfactants, aminoacids, small peptides …) would be intrinsically linked to their dynamics, affecting both the inner aqueous core and the properties of the actual boundary (e.g., membrane permeability, fluidity, etc.)….

“Among the numerous transformations that these early protocellular systems could undergo (e.g., constrained diffusion and transfer of their components, membrane transient breakage and re-sealing processes, deformations, shrinkage, swelling, aggregation into clusters…), we will highlight two of special significance: fission and fusion.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 4.

“Under those conditions [of a population of dividing and colliding protocells without a significant statistical change in makeup], the stability of most individuals in the population (tokens) would be quite precarious: the lack of regulatory mechanisms on the growth/shrinkage dynamics of the protocells would lead, most of the times, to breakage or decay (due to osmotic imbalances or insufficient material resources in the aqueous environment) and subsequent reassembling phenomena. In turn, groups of relatively similar protocells could be distinguished in the population, but just in terms of global, self-organization properties that would correspond to statistical patterns deriving from those ever-changing compartmentalized entities and their ongoing out-of-equilibrium dynamics, fostered by the underlying chemistry.

“However, the situation would radically change if fission events started to establish more consistent ‘kind correlations’ between different members of the population. In other words, if some protocellular systems developed molecular mechanisms (and a somewhat more complex organization) that enabled them to channel growth and reproduce themselves: i.e., if they managed to generate highly similar protocellular systems – ‘kind’ begetting ‘kind.’” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. pp. 4-5.

“Furthermore, for the process [reproductive-like] to be recurrent, protocells must be self-productive in the first place, so that they can minimally control their growth dynamics and divide in such a way that the ‘offspring’ resembles the original state of the ‘mother’ protocell…. Besides, these prebiotic self-productive systems should harbor a minimal degree of organizational diversity, in such a way that the same reproduction mechanisms could be realized by means of potentially different individuals.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 5.

“Trivial forms of reproduction, like the multiplication of supramolecular structures, per se, would not lead us very far. Yet, if the protocellular system gets too complex, its reproduction will become accordingly difficult, causing a deep bottleneck. At this juncture, a compromise solution must be reached, in which the material organization involved is complicated enough – but not more – to be able to generate controlled cycles of growth and division (including the coordinated duplication of all of its components and transformations, their adequate spatial distribution and temporal synchronization, … so that the cycle ends up in the physical multiplication and subsequent propagation of the original organization). In other words, the appearance of protocells capable of self-reproduction, in a minimal but biologically significant sense, required protocells that had already achieved not only a certain degree of functional diversity in their organization, but also the integration of all the aforementioned processes, with mechanisms to orchestrate and modulate the necessary changes in the compartment, together with changes in the internal reaction network, in response to environmental fluctuations or stimuli.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 5.

“At the level of the population, the transition from dynamic but globally stationary protocell organizations to reproducing ones will also have, of course, important and observable consequences: remarkably, much more obvious asymmetries (in terms of the underlying groups and population sub-structure) will start flourishing in the protocell suspension, since some of them will now be endowed with the intrinsic, capacity to generate similar entities/organizations and thus, potentially, to take over the whole population (or a good part of it)….

“… the most relevant point here is that tokens start having an intrinsic potential to generate types in the population. And this radically changes the scene: proto-families of individuals with relatively higher similarities among them will emerge….” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 5.

“Indeed, phylogenetic studies projecting as far backwards as possible, together with analyses from micropaleontology and comparative ‘minimal-cell’ microbiology, point toward a population of unicellular prokaryotes, sharing the same basic biochemistry and a set of fundamental biomolecular mechanisms, as the end of the process of biogenesis and the beginning of biological evolution, sometime between 3,500 and 4,000 million years ago.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 8.

“There is also quite widespread consensus on the fact that horizontal gene transfer was ubiquitous at that stage [of prokaryotes just after LUCA], so this original population of organisms is typically conceived as a strongly communal society of microbes, which shared many of the molecular innovations that were encoded in their collective genetic repertoire. In contrast, the debate turns fierce when theoretical proposals attempt to go further back and postulate stages before LUCA….” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 8.

“The first aspect to underline… is that the chemistry in development – toward a biochemistry – implies an increase in complexity but, at the same time, a reduction of possibilities. So to speak, in order to play a more and more complex game of molecules, in continuous transformation, a progressively higher number of rules must be fixed by the emerging prebiotic systems [protocellular populations]. These specific functional rules involve a set of high-order structures and control mechanisms of diverse nature (spatial, kinetic, energetic,… control mechanisms), which operate as enabling constraints that, thanks to their concurrent action (harnessing and coupling chemical reactions and other basic processes taking place in the system and its close surroundings), open somehow the space of possibilities for new protocell dynamic behaviors. Therefore, the most interesting and relevant restrictions in prebiotic chemistry are those that allow for – and potentially enhance – functional performance and diversification, which, among other things, are critical to establish a process of evolution by natural selection.

“Second, but not less important in order to eventually reach a ‘LUCA-like’ population, protocellular systems need to implement strategies for reproduction that are increasingly reliable, ensuring fission events in which traits are inherited with higher and higher fidelity from one generation to the other.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 8.

“… all the evidence to date suggests that, at least when it happened on the Earth, the final ‘phase transition’ from prebiotic to biological evolution must have been remarkably narrow and uniform. Only such a singularity can explain, at the same time: first, the universality of biophysical/biochemical mechanisms supporting all forms of life on the planet; second, the huge gap between chemistry and biology, with the wiping out of other possible systems inhabiting the ‘middle-lands’ of complexity; and third, the amazing adaptive and diversification capacities of living organisms, once biological evolution got started.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 9.

“… biological identity is singular, among other things, because the processes of construction of tokens and types get intrinsically interconnected during biogenesis…. … we will argue that those processes necessarily imply system-system and system-environment interactions of diverse kind, so the use of the idea of ‘inter-identity’ is perfectly justified and, in fact, within the biological domain, it represents a more adequate theoretical choice than bare ‘identity.’” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 10.

“… the road toward biological ‘hyper-complexity’ only seems accessible for heterogeneous protocellular systems (compartmentalized chemical mixtures) that manage to tame spontaneous fission and fusion processes in order to increase their robustness and, at the same time, gain control on their own variability. It is precisely during this transition toward reproductive protocellularity that a new ‘token-type’ relationship emerges in nature. Until that stage, tokens did not have generative power, as far as types were concerned (i.e., the process of coming to existence of each token belonging to a type was, in principle, independent from that of any other particular token within the same type).” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 10.

“A first observation is that the production of these genealogical types is based on the organizational dynamics of individuated tokens, which must recursively grow, reshape their boundary, duplicate their key components and distribute them in such a way that, when fission occurs, two (or more) similar tokens are actually produced. This implies a steady organizational continuity, the system, strictly speaking, cannot remain the same: it must establish ‘cycles,’ i.e., well-ordered sequences of states in which the progressive creation of an ‘embryo,’ a duplicate of that organization, is naturally integrated within the dynamics of the reproductive token (that is, within the same compartmentalized individual).” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. p. 10.

“Biological organisms, together with all their preceding, simpler forms of individuality, beginning from the first relevant self-organizing and self-assembling phenomena, are necessarily open systems that require the management of matter and energy resources, taken up from the environment, in order to achieve their own, autonomous construction. Just by itself, this dynamic and asymmetric ‘system-environment’ relationship would be enough to argue that the identity of any living being is, in reality, an identity constructed in interaction, or an inter-identity….

“A second line of argument to state that any biological identity is intrinsically interactive has to do with the fact that populations of living organisms, right from their very beginning, must be ecologically organized….

“After all, no living cell can develop its ontogenetic existence in an abiotic environment, but in a confederacy or consortium of metabolic reciprocities – i.e., in the context of an ecological organization.” Ruiz-Mirazo, Kapa, Ben Shirt-Ediss, Miguel Escribano-Cabeza & Alvaro Moreno. 2020. “The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution.” Frontiers in Physiology. 11(530):1-15. doi: 10.3389/fphys.2020.00530. pp. 11, 12.

“Systems biology combines quantitative experimental data from complex molecular networks (e.g. biochemistry, cell biology in the living cell) with computational modeling. Here, computational modeling does not refer to statistical models or models of data mining but rather to a mathematical or ‘virtual’ representation of the living system of interest in the computer, where there is also a correspondence between parts of the biological system and parts of the model. This representation allows a computational analysis using systems theoretical approaches.” Huebner, Katrin, Sven Sahle & Ursula Kummer. 2011. “Applications and trends in systems biology in biochemistry.” The FEBS Journal. 278:2767-2777. pp. 2767-8.

“When everything was in place [for author and the dog Strongheart – famous dog from the movies of the Twenties – on a sandhill above a Southern California beach] and I was sitting cross-legged in the middle of the blanket, I gave him the formal nod for which he had been impatiently waiting and off he raced as fast as his legs could carry him. At that moment school began for me.

“With distance in his eyes, his energy full-on, hard sand under his feet, an ocean to dash into whenever he felt the urge and no one to boss him, Strongheart was a magnificent object to watch, much more so at such times, indeed, than in his films, great as those films were. In making motion pictures he always had to operate within certain restricted and carefully regulated patterns in order to blend his actions with those of the human actors and thus harmonize the flow of the story. But on a deserted beach, with no one to interfere with his mental and physical action, he provided superthrilling entertainment every second. Part of the time he performed on the beach, part of the time in the ocean, and the rest of the time he relaxed and planned what to do next.

“I never tired of being student-audience for him during these beach sessions. His zest for living … his vitality … his powerful and almost catlike agility … his enthusiasm … his sense of wonder and appreciation … his complete interest in the immediate thing he was doing … all these were delightfully educational and entertaining. He had a tremendous ability to extract fun, happiness and satisfaction out of each moment, and he never permitted life to become uninteresting, either for himself or for those around him.

“Watching him that day as his student-observer, with the Pacific Ocean giving him just the kind of a background he needed, I could not recall when I had seen more majestic composition, or more perfect co-ordination in action. It was as if a poem had assumed the form of a dog in order to express in meaning and rhythm what could not possibly be said in written or spoken words. All that Strongheart was exhibiting in physical form and in action out there on the beach was simply the expression of his splendid character, the radiation in endless living combinations of his truly great inner qualities, the very qualities I had been finding in him day by day with the help of my book of synonyms and dictionary.

“Then I knew that what I was actually being privileged to watch was not a dog expressing great qualities, but rather, great qualities expressing a dog. He was radiating them from deep within himself, flinging them out as freely and as lavishly as the sun does its rays. He was not trying in the least to achieve this effect; he was just letting it happen.” Boone, J. Allen. 1954. Kinship With All Life. HarperSanFrancisco. pp. 57-9.

“One morning in the early days of our friendship [with a fly called “Freddie”], while Freddie was standing in the palm of my hand getting his wings stroked, I decided that it was high time to get a bridge for practical two-way thought traffic set up between us so that each of us could share his state of mind, as well as the beat of his heart, with the other. Such communicating bridges had worked successfully with Strongheart, with other animals, and even with an army of ants, so why not with this intelligent and lively little fly?

“As I began the effort of trying to couple our minds and hearts in this manner, I carefully reminded myself of the two basic facts that I had always found to be of the greatest importance in efforts of this kind: (1) That inherently Freddie the Fly and I as living beings were inseparable parts of an interrelated, interfunctioning and all-including Totality. (2) That neither he nor I were originating causes for anything, but instead were individual living expressions of a universal divine Cause or Mind that was ever speaking and living Itself through each of us and through everything else.

“With these thoughts in the forefront of my thinking, I began silently talking across to Freddie as a fellow being, just as I had learned to do with Strongheart, I would ask the little fellow in my hand a question, and then give careful heed to all freshly arriving mental impressions, the kind of impressions or sudden intuitive knowings I had been learning to receive from animals, birds, snakes, insects and various other kinds of wisdom-sharing kinsfolk.” Boone, J. Allen. 1954. Kinship With All Life. HarperSanFrancisco. pp. 135-6.

“With the advent of Systems Chemistry, the remit of chemistry has expanded to also include the design and synthesis of systems of molecules, that harbor systems-level properties that go well beyond the sum of their parts (i.e., emergent properties). Among the most intriguing and challenging of such properties is life.” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. p. 146.

“Self-replicating molecules have been made based on many different molecular designs; reaction networks have been identified that enable chemical complexity to be built up; any different forms of compartmentalization have been investigated, including bilayer vesicles, microdroplets, coacervates, and even absorption on surfaces. Finally, out-of-equilibrium chemical systems are attracting renewed attention particularly in the area of self-assembly. Only the implementation of Darwinian evolution in chemical systems outside the realm of biology/ biomolecules has not yet received much attention.” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. p. 146.

“The current frontier in the de novo synthesis of life encompasses the binary integration of different subsystems; the first reports combining replication (mostly enzyme-mediated) with compartmentalization or replication with metabolism have appeared. Furthermore, methodology has been developed to maintain compartments and replicators out-of-equilibrium.” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. p. 146.

“Stacking of the central aromatic rings, together with β-sheet formation between the peptide side groups, allows a specific macrocycle to assemble (in the example … this is the hexamer)…. The 1-D assemblies grow from their ends, and, when subjected to mechanical energy through agitating the sample, the stacks break, exposing additional stack ends. This growth-breakage mechanism enables exponential growth of the fibers and the self-replicating macrocycles from which they are constituted….

“The exponential replication mediated by the growth-breakage mechanism solves a problem that has thwarted the replicator field for decades: the inhibition of replication resulting from the tendency of replicators to remain associated with each other. Most other systems of self-replicators involve the ligations of two precursor molecules on a template to produce a dimer of the template, which needs to dissociate before further replication can take place. Dissociation is normally difficult, resulting in parabolic growth, as opposed to exponential growth. Szathmary showed that parabolic replicators tend to co-exist indefinitely, while exponential replication leads to survival of the fittest and extinction of the weakest replicators. Thus, parabolic replicators cannot normally undergo Darwinian evolution, while exponential replicators can.” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. pp. 147, 148; reference: Szathmary, Eors & I. Gladkih. 1989. “Sub-exponential growth and coexistence of non-enzymatically replicating templates.” J. Theor. Biol. 138:55-58.

“The synthesis of life requires the integration of the different functional subsystems. We recently succeeded in integrating self-replication with a proto-metabolism by making use of the proven potential of peptide assemblies to catalyze chemical reactions. Following a number of not very fruitful attempts at engineering catalytic sites into our self-replicators, we discovered that the already existing systems already exhibited impressive catalytic activity for several different chemical reactions, without needing any structural alterations. Specifically, hexamer replicators made from building block [cyclic disulfide] were able to catalyze a retro-aldol and an FMOC cleavage reaction….

“The fact that structures that were selected solely on their ability to self-replicate also exhibit additional and promiscuous catalytic activity is significant. Such chance emergence of function resembles a mechanism of evolutionary invention called co-option, where a feature that emerged as it provided a certain function was also capable of fulfilling a completely unrelated one (a famous example in evolutionary biology are feathers, which are believed to have originated as they improved temperature control, but were then co-opted to facilitate flight).” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. p. 150.

“One of the simplest ways of maintaining self-replicating systems out of equilibrium is by placing them in a flow reactor, in which precursors are continuously supplied and part of the reaction mixture is removed. In such setup outflow means death. For homogeneous systems, death through outflow is nonselective (i.e., each replicator has the same probability of being removed in a given time span) and any selection is therefore solely based on the efficiency of replication. We recently implemented a replication-destruction regime in which death is mediated chemically and is therefore potentially selective (i.e., different replicators may exhibit different levels of resilience against chemical decomposition). In such systems, replicator persistence depends on a combination of replication efficiency and resilience to destruction.” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. p. 150.

“Finally, it is not unreasonable to expect that the ability to synthesize life may have an impact that is at least similar to the impact made by the ability to synthesize organic molecules. It is tempting to draw a parallel between these two developments. It was long thought that organic molecules could only be produced by living organisms. The idea that a ‘life force’ was needed was eventually refuted by demonstrating that such molecules could also be obtained synthetically (a famous example is the synthesis of urea by Woehler in 1828). These demonstrations gave rise to the field of organic chemistry which has made a tremendous impact in areas ranging from medicine to materials. We are now getting closer to being able to synthesize life (and demonstrating that it is not only a product of existing forms of life). Just like urea was not exactly the most impressive or useful example of an organic molecule, the first form of synthetic life is equally unlikely to impress, when compared to even the simplest currently living organism. Yet, just like the many human-made organic molecules that followed the synthesis of urea, the subsequent forms of human-made life (living technology) are likely [to] be at least similarly impactful, but in ways that may currently be difficult to predict.” Otto, Sijbren. 2022. “An Approach to the De Novo Synthesis of Life.” Accounts of Chemical Research. 55:145-155. doi: 10.1021/acs.accounts.1c00534. p. 152.

“”Cell physiology shows us that endogenous synthesis is a necessary condition to consider a molecular component functional in the most basic biological sense: that is, functional with regard to the (proto-metabolic) organisation that it belongs to. According to this orgnisational conception,… a component is functional in so far as it contributes in a specific, distinctive way to the overall maintenance of the far-from-equilibrium system that brought it about.” Shirt-Ediss, Ben, Sara Murillo-Sanchez & Kepa Ruiz-Mirazo. 2017. “Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research.” Beilstein Journal of Organic Chemistry. 13:1388-95. doi: 10.3762/bjoc.13.135. p. 1391.

“One needs to try different combinations of precursors, taking part in various reactive and self-assembling processes, and study their mutual compatibility and overall integration dynamics. We will refer to this as the problem of minimal functional integration in a prebiotic context: namely, the quest to determine the experimental conditions under which the simplest – but at the same time sufficiently robust – systems with autonomous functional components could develop.” Shirt-Ediss, Ben, Sara Murillo-Sanchez & Kepa Ruiz-Mirazo. 2017. “Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research.” Beilstein Journal of Organic Chemistry. 13:1388-95. doi: 10.3762/bjoc.13.135. p. 1391.

“Far-from-equilibrium behaviour is not only ubiquitous in cell biology but is also at the heart of Darwinian evolution. By having biomolecules (and also entire organisms) that are constantly formed and broken down, the functions carried out by the molecular assemblies (or the organisms) can undergo a process of selection and adaptation. The stability of the resulting far-from-equilibrium supramolecular structures does not derive directly from thermodynamics, but from the degree of adaptation of their function to the environment.” Mattia, Elio & Sijbren Otto. 2015. “Supramolecular systems chemistry.” Nature Nanotechnology. 10:111-119. doi: 10.1038/nnano.2014.337. p. 111.

“The predominance of far-from-equilibrium thermodynamics in biology contrasts starkly with the mode of operation in most man-made supramolecular systems, for which three different thermodynamic regimes may be identified:

“1. Equilibrium assemblies. Systems that are likely to persist for a long time due to their thermodynamic stability.

“2. Kinetically trapped assemblies. Systems that are transiently durable, trapped in a local minimum of the energy landscape. It would take time, or activation energy, for them to be converted to more stable structures.

“3. Far-from-equilibrium assemblies. Systems that require a continuous supply of energy to persist. If the energy supply stops, the system would fall apart and end up in a thermodynamic minimum state (or in a kinetic trap en route). The continuous energy-driven transformation that these structures undergo makes it possible for them to have interesting, and sometimes unpredictable, emergent functions.

“The field of supramolecular chemistry started with the study of systems under thermodynamic control, but is currently seeing a shift towards kinetically controlled and far-from-equilibrium systems, where the richest functions can be harnessed.” Mattia, Elio & Sijbren Otto. 2015. “Supramolecular systems chemistry.” Nature Nanotechnology. 10:111-119. doi: 10.1038/nnano.2014.337. p. 111.

“Most bilayer vesicles formed from phosopholipids are examples of supramolecular systems under kinetic control: they form rapidly under certain conditions, but are usually transient products that can convert to the more stable hydrated crystals. Depending on the conditions of formation, the shape and size of the vesicles can be controlled, reflecting different kinetically trapped states. Transitions between states are possible, for example, by allowing vesicles to fuse. However, such transitions are only feasible if the new state has a lower thermodynamic stability than the old state.” Mattia, Elio & Sijbren Otto. 2015. “Supramolecular systems chemistry.” Nature Nanotechnology. 10:111-119. doi: 10.1038/nnano.2014.337. p. 112.

“Thermodynamically stable structures, on the other hand, are often sturdy and can be used for structural purposes or for their recognition properties, but are the most limited when it comes to functional potential. Both equilibrium and kinetically trapped systems are limited to the functions that correspond to the properties of the single relatively stable state in which they exist.

“In contrast, far-from-equilibrium systems owe their function to a continuous transitioning between different structures, rather than to the properties of one particular assembly and, most importantly, to the fact that they use an energy source…. Thus, when it comes to systems chemistry, the field of chemistry dealing with complex chemical systems exhibiting unpredictable emergent properties, supramolecular systems that operate far from equilibrium have by far the richest functional potential.” Mattia, Elio & Sijbren Otto. 2015. “Supramolecular systems chemistry.” Nature Nanotechnology. 10:111-119. doi: 10.1038/nnano.2014.337. p. 118.

“First, we identify three key properties of agency: individuality, asymmetry and normativity and argue why these are good candidates for necessary and sufficient conditions for agency….

“First of all, in order for a system to be an agent, there must be a distinction between the system and its environment. This we shall call the individuality condition….

“In a sense yet to be properly disclosed, an agent as a whole drives itself, breaking the symmetry of its coupling with the environment so as to modulate it from within. We call this condition interactional asymmetry….

“When considering agency we presuppose that the interaction is not random or arbitrary but makes some ‘sense’ for the agent itself. Agents have goals or norms according to which they are acting, providing a sort of reference condition, so that the interactive modulation is carried out in relation to this condition….

“Planets cannot ‘fail’ to follow the laws of nature. Agents, however, actively regulate their interactions and this regulation can produce failure or success according to some norm. This is what we call the normativity condition.” Barandiaran, Xabier, Ezequiel Di Paolo & Marieke Rohde. 2009. “Defining Agency: individuality, normativity, asymmetry and spatio-temporality in action.” Adaptive Behavior Journal. 17(5):367-386. doi: 10.1177/1059712309343819. [page numbering might be off a little] pp. 370, 371, 374.

“Minimal life-forms already come to satisfy the necessary and sufficient conditions for agency. This does not imply, however, that living organization is necessary for agency, nor that all forms of agency need to trace their normative or individuality conditions back to living organization. What minimal life provides is a clear and precise illustration of how individuality, normativity and interactional asymmetry conditions emerge from a naturalized framework that can be fully operationalized and even synthesized.” Barandiaran, Xabier, Ezequiel Di Paolo & Marieke Rohde. 2009. “Defining Agency: individuality, normativity, asymmetry and spatio-temporality in action.” Adaptive Behavior Journal. 17(5):367-386. doi: 10.1177/1059712309343819. [page numbering might be off a little] p. 377.

“The field of supramolecular chemistry and molecular self-assembly has entered a new phase in which the use of chemical reactions to create out-of-equilibrium molecular assemblies is becoming more common. These dynamic assemblies have vastly different properties than their in-equilibrium counterparts, which include the ability to be controlled over space and time or the ability to self-replicate.” Riess, Benedikt, Raphael Kurt Groetsch & Job Boekhoven. 2020. “The Design of Dissipative Molecular Assemblies Driven by Chemical Reaction Cycles.” Chem. 6:552-578. Doi: 10.1016/j.chempr.2019.11.008. p. 552.

“With the unique features that dissipative self-assembly offers us and the scalability of synthetic chemistry, we can envision exciting materials for the future. For example, a supramolecular polymer that heals itself after externally applied damage, as our skin does.” Riess, Benedikt, Raphael Kurt Groetsch & Job Boekhoven. 2020. “The Design of Dissipative Molecular Assemblies Driven by Chemical Reaction Cycles.” Chem. 6:552-578. Doi: 10.1016/j.chempr.2019.11.008. p. 553.

“Out of equilibrium, we can find complex behavior such as pattern formation, self-replication, molecular evolution, motion, the exertion of forces, and oscillations. These synthetic assemblies with complex behavior can be ideal model systems for biological assemblies and teach us the fundamentals of molecular self-assembly in living systems.” Riess, Benedikt, Raphael Kurt Groetsch & Job Boekhoven. 2020. “The Design of Dissipative Molecular Assemblies Driven by Chemical Reaction Cycles.” Chem. 6:552-578. Doi: 10.1016/j.chempr.2019.11.008. pp. 574-5.

“Let us thumb through the catalogue of viral genomes: here we find the familiar double-stranded DNA, including both linear and circular genomes, but also some with not-so-familiar twists–poxviruses, for example, covalently closing both ends of their linear double-stranded DNA genomes. We also find an abundance of themes not found anywhere among the domains of cellular life: thus, there are viruses with single-stranded DNA genomes and viruses with single-stranded RNA genomes, the latter including some that are negative-sense, some positive-sense, and some part positive and part negative (ambisense). Additionally, there are viruses with double-stranded RNA genomes, and if that isn’t bizarre enough, there are viruses with segmented RNA genomes (to which the influenza belongs), whose virions incorporate a precise complement of eight different RNA segments.

“Equally impressive are the reoviruses, with genomes composed of a dozen different segments of double-stranded RNA. Replicate that! And there are retroviruses, whose genomes are sometimes RNA (in the virion), and at other times double-stranded DNA (upon entering a host cell). Hepadnaviruses, possible cousins to the retroviruses, have gapped double-stranded DNA genomes with a bit of RNA thrown in, which they, too, convert to DNA by means of reverse transcriptase.

“This diversity of genome styles each comes with its own uniquely-tailored replication system dictated in part by the need (shared by all viruses) to generate mRNA (because all viruses rely on host cells for translation). Importantly, there is very little if any phylogenetic evidence for a common ancestry connecting all the different viral types, or for grouping viruses together. Attempts to prove the existence of a last universal common ancestor of all viruses may be folly, as it is entirely possible that no such ancestor ever existed (that it, what we lump together as ‘viruses’ actually represent uniquely evolved biological entities that happen, just by chance, to have taken on obligate intracellular parasitism as a mode of existence). At best, and by stretching the limits of phylogenetic comparisons, some of the RNA viruses can be combined into hypothetical ‘supergroups.’” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 8: Virus in the Room. By Welkin Johnson. pp. 25-6.

“Our place in the world comes with an obligation to interact with microbes at numerous levels, within and without our bodies. We depend on microbial by-products to survive, and we are nodes in larger webs of microbial interaction that define the planet. From this perspective, we are indeed ‘microbial’–inside, outside, and all around. Microbiome research has nudged our knowledge of ourselves to that we understand we occupy some peripheral node in this larger scheme, far from the center of biological interactions on the planet. Our node will eventually disappear, but the extinction of Homo sapiens will not lead to the collapse of the global ecosystem (whereas our persistence will continue to produce major problems for macroorganisms).” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 12: The Microbial Nature of Humans. By Maureen O’Malley. pp. 44-5.

“So, how big can cells get? The champion seems to be another marine alga, Caulerpa, which can reach 3 meters in length. It is multinucleated, which seems almost like cheating…. Among the largest uninucleated single cells are the foraminifera called “Nummulites, which can reach 5 cm in diameter…. Of course, birds’ eggs are even larger and they are unicellular and uninucleated….” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 33: Let’s Not Forget acetabularia. By Elio Schaechter. pp. 134-5.

“According to a paper from Albert Einstein Medical School, fungi can also use radiation as a source of energy–not exactly one’s view of radiation as something malevolent and baneful. Had we paid attention to the news from Chernobyl, we would not have been surprised because the walls of the still-hot reactor have become covered with mold. Not only that, but it has been known for some time that fungal species search out radioactive particles, i.e., manifest radiotropism.” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 35: Fungal Alchemy: Using Radiation as a Source of Energy. By Elio Schaechter. p. 141.

“Unicellular Haptoglossa [a fungus] motile spores (zoospores) differentiate in a few hours into a fancy structure called a ‘gun cell,’ which is capable of injecting a projectile–a spore–in toto into a grazing rotifer or a nematode. Once inside, the spore develops into a vegetative fungal body that consumes the host and grows to fully occupy its body cavity in a few days.” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 36: Arms and the Fungus. By Elio Schaechter. p. 143.

“An underwater microbial mat has been found in fairly shallow waters off the coast of Chile and, according to headlines, it’s the size of Greece, or about 132,000 km2 (or for us norteamericanos, about the size of Alabama).” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 39: Commuting to Work. By Elio Schaechter. p. 153.

“In short, the mitochondria-centric hypothesis for eukaryotic genesis ignores the important uniqueness of the eukaryotic cytoskeleton. So, let’s take the cytoskeleton into consideration….

“To summarize her [Julie Theriot’s article] major points: While we now know that the cytoskeleton is present and broadly conserved across all domains of life (with diverse proteins in the actin, tubulin, and intermediate filament families), bacteria notably lack a special class of cytoskeleton-related proteins: the nucleated filament assembly factors and the motor proteins. Eykaryotes make ample use of these tools. By providing a mechanism for polarized assembly that permits motor protein directionality and inherently oriented filament growth, the eukaryotic cytoskeleton is the architectural machinery that achieves functions such as chromosome movement, vesicle and organelle transport, and endocytosis. These, in turn, help the cell attain sizes and complexities that otherwise would be unattainable.” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 55: By Chance and Necessity: The Role of the Cytoskeleton in the Genesis of Eukaryotes. By Daniel P. Haeusser. pp. 216-7.

“Blobel’s article became a classic, and spawned a small industry concerned with the molecular mechanisms that target proteins to the recipient membrane and then either translocate or insert them. In a nutshell, the information that specifies a nascent protein’s disposition is contained in its sequence. One segment of that sequence recognizes a receptor protein embedded in the target membrane, commonly part of the translocon; other segments specify whether the amino acid chain is to be taken clear across the membrane or inserted, and with what orientation. Membrane proteins may be processed concurrently with their translation, or after their production is complete. In prokaryotic cells the proteins are produced and handled directly; in eukaryotic cells they are first inserted into the membrane of the endoplasmic reticulum, and then transferred to their target membrane by cargo vesicles…. What concerns us here is the inference that membrane heredity is a fundamental principle of biology. A functional membrane, studded with a particular set of enzymes, transport carriers, and receptors, can never be generated de novo; it must arise from a pre-existing membrane, either by modification (for example, the membranes that surround bacterial spores) or else by growth and division or vesiculation. Moreover, since proteins will only be inserted after interaction with a complementary receptor (and that includes the receptor protein itself), a growing ‘genetic’ membrane propagates its own kind.” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 57: On the Continuity of Biological Membranes. By Franklin M. Harold. pp. 226, 227; reference: Blobel, Guenter. “Intracellular Protein Topogenesis.”

“Organelles make an impressive example of the persistence of membranes, but one could wish for more of them. A likely one comes from the Archaea, whose membranes all display a distinctive complement of lipids and ion-translocating ATPases, even though their environments range from volcanic hot springs to the open ocean and the stomach of cows; it cannot be natural selection alone that maintained the archaeal signature!” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 57: On the Continuity of Biological Membranes. By Franklin M. Harold. p. 229.

“Anaerobic eukaryotes lacking conventional respiration are widespread, represented by over a thousand species. In these, ATP is produced by substrate-level phosphorylation, chiefly by the decarboxylation of pyruvate, which is commonly associated with mitochondria or their evolutionary relatives.” Schaechter, Elio. 2016. In the Company of Microbes: Ten Years of Small Things Considered [A blog on microbiology]. Washington, DC: American Society for Microbiology Press. Chapter 60: Begetting the Eukarya: An Unexpected Light. By Franklin M. Harold. p. 245.

“The first approaches to define the holobiont consisted of characterizing the set of microbial taxa common to all individuals of a certain species, the core microbiota. Later definitions, enabled by massively increased sequencing efforts, included the core set of functional genes that ensured homeostasis of the holobiont. However, holobiont functioning is not only determined by the processes carried out by the individual members, but also by the interactions among them. Consequently, holobionts can be regarded as complex ecosystems to which the concepts and methodologies from ecology can he applied to understand the drivers of holobiont stability….

“Moreover, the holobiont performs functions that cannot be accomplished by the partners separately. The microbiome provides essential functions to the host and together they mediate the interactions of the holobiont with the surrounding organismal community.” Pita, L., L. Rix, B.M. Slaby, A. Franke & U. Hentschel. 2018. “The sponge holobiont in a changing ocean: from microbes to ecosystems.” Microbiome. 6(46):1-18. doi: 10.1186/s401168-018-0428-1. pp. 1-2.

“Bacteria-bacteria network analysis of the core microbiota in different sponge species has revealed a low connective network with very few strong and many weak unidirectional interactions (i.e., amensalism (-/0) and commensalism (+/0) prevailed over cooperation (+/+) and competition (-/-). These findings are consistent with mathematical models that predict that weak and non-cooperative interactions help to stabilize highly diverse microbial communities, whereas cooperation yields instability in the long term by fueling positive feedbacks.” Pita, L., L. Rix, B.M. Slaby, A. Franke & U. Hentschel. 2018. “The sponge holobiont in a changing ocean: from microbes to ecosystems.” Microbiome. 6(46):1-18. doi: 10.1186/s401168-018-0428-1. p. 4.

“Comparisons between metagenomes of sponge-associated and seawater microbial consortia have identified gene features enriched in sponge symbionts that might be relevant to the symbiosis. These features have been found in the microbiomes of multiple sponge species from various geographic regions, but they are mediated by different microbial taxa and carried out by different, although analogous, pathways. This functional convergence hints to features that are necessary for microbial persistence in the host as well as holobiont success, and therefore can be considered core functions of the sponge microbiome.” Pita, L., L. Rix, B.M. Slaby, A. Franke & U. Hentschel. 2018. “The sponge holobiont in a changing ocean: from microbes to ecosystems.” Microbiome. 6(46):1-18. doi: 10.1186/s401168-018-0428-1. p. 5.

“In order to persist within sponges, microbes must avoid phagocytosis by the host cells. Eukaryotic-like protein domains (ELPs), such as ankyrin repeat proteins, tetratricopeptide repeat proteins, and leucine-rich repeat proteins, were found to be highly enriched in and also expressed by sponge symbionts. ELPs mediate protein-protein interactions and are hypothesized to play a role in the evasion of phagocytosis.” Pita, L., L. Rix, B.M. Slaby, A. Franke & U. Hentschel. 2018. “The sponge holobiont in a changing ocean: from microbes to ecosystems.” Microbiome. 6(46):1-18. doi: 10.1186/s401168-018-0428-1. p. 5.

“Sponge hosts may be viewed as ecosystem engineers, since they provide a certain habitat that selects for the presence and persistence of certain microbes, but not others. They also control their microbial residents by specifically recognizing and differentiating between foreign and symbiotic microbes, likely via the innate immune system. The innate immune system, traditionally investigated in the context of pathogenesis, allows colonization and long-term maintenance of the symbiosis. Pattern recognition receptors (PRRs) sense microbial ligands, but the activated response is context-dependent: symbiont-derived signals promote homeostasis, whereas pathogens induce an inflammatory response.” Pita, L., L. Rix, B.M. Slaby, A. Franke & U. Hentschel. 2018. “The sponge holobiont in a changing ocean: from microbes to ecosystems.” Microbiome. 6(46):1-18. doi: 10.1186/s401168-018-0428-1. pp. 6-7.

“Highly diverse holobionts can be considered as complex ecosystems in which the actions and interactions of the various members shape the overall functioning of the holobiont. These individual ecosystems in turn interact with and influence neighboring holobionts, such that they are further integrated into larger communities and ecosystems that interact at successively larger scales…. Key examples of this concept of ‘nested ecosystems’ are the chemoautotrophic symbionts associated with hydrothermal vent animals or the phototrophic symbionts associated with reef-building corals that supply nutrition for their hosts who in turn support the larger communities in these unique ecosystems.” Pita, L., L. Rix, B.M. Slaby, A. Franke & U. Hentschel. 2018. “The sponge holobiont in a changing ocean: from microbes to ecosystems.” Microbiome. 6(46):1-18. doi: 10.1186/s401168-018-0428-1. p. 7.

“While we have previously described a giant vesicle (GV)-based model protocell in which amplification of DNA was linked to self-reproduction, the ability of a protocell to recursively self-proliferate for multiple generations has not been demonstrated. Here we show that newborn daughter GVs can be restored to the status of their parental GVs by pH-induced vesicular fusion of daughter GVs with conveyer GVs filled with depleted substrates.” Kurihara, Kensuke, Yusaku Okura, Muneyuki Matsuo, Taro Toyota & Kentaro Suzuki. 2015. “A recursive vesicle-based model protocell with a primitive model cell cycle.” Nature Communications. 6:8352. doi: 10.1038/ncomms9352. p. 1.

“Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed, life provides the best demonstrations of complex and functional out-of-equilibrium systems….” Merindol, Remi & Andreas Walther. 2017. “Materials Learning from Life: Concepts for Active, Adaptive and Autonomous Molecular Systems.” Chem. Soc. Rev. 46:5588-5619. doi: 10.1039/C6C500738D.

“But it is one thing to share the pluralists’ distrust of mass discourse and quite another to trust the rule of experts. The problem of knowledge, I will argue, has little to do with the virtues and vices traditionally imputed to the public. It centers on the limits of expertise–and on the need to debunk the pluralists’ epistemic hubris. This arrogance goes back to Plato, who impugned rhetoric as a ‘knack akin to cookery,’ yet feared it so much he restricted its use to philosopher kings, who were o determine the Truth and then use rhetoric to dupe the public into behaving well. This may be the oldest extant defense of false consciousness as an instrument of social control. Adams and Jefferson–still a century before Marx–joined their classical educations to their appreciation of Realpolitik to read Plato as condoning republican social control. Like Adam smith (1776), they feared that workers might be alienated by dull, repetitive labor. They read Rousseau as wanting a hidden hand to create illusions of self-government to socialize individuals into the collective will. And so, ‘If the people think they govern,’ William Penn intoned, ‘they will be governed.’ By the 1930s, Walter Lippmann was calling for an ‘engineering of consent.’ And today, as we shall see, pluralists unblushingly duplicate Plato’s arguments for the vile necessity of rhetoric. Thus, kin the Platonic vision, rhetoric is either terrible or trifling–truth’s enemy or its simpleton servant. Persuasion researchers are at worst the servants of power, or at best the dung beetles of the social sciences.” Willard, Charles Arthur. Liberalism and the Problem of Knowledge: A New Rhetoric for Modern Democracy. University of Chicago Press. 1996. pp. 8-9.

“What Descartes is concerned with in his natural philosophy are internal or intrinsic causes, and these are missing in the case of foetal development. What is at issue, then, is intrinsic goal-directedness. Such intrinsic or internally generated goal-directedness is a feature of Aristotelian natural philosophy, where it was thought to be characteristic of any natural process. There, organic processes, such as a seed developing into a tree, and inorganic processes, such as the fall of a body to the earth, are put down to intrinsic goal-directedness. Mechanism dismantles the conceptual apparatus whereby processes are construed as being intrinsically goal-directed, because it removes the doctrine of forms, which is crucial to the notion of something striving to realize its natural state.” Gaukroger, Stephen. 2006. The Emergence of a Scientific Culture: Science and the Shaping of Modernity 1210-1685. Oxford UP. p. 338.

“… in a system of self-assembly driven self-replication, the assembly process generates the combination of a substrate-binding pocket and a catalytically active lysine residue. This configuration does not only enable the catalysis of a retro-aldol reaction with activities comparable to the best designer enzymes, but also the cleavage of FMOC groups with high efficiencies. Notably, the latter transformation liberates an alkene, which promotes the formation of molecules that replicators use for replication, thereby exerting a positive feedback on replication. Such chance invention of new function at the molecular level is essential for open-ended evolution and marks a pivotal step in the process by which replicators can acquire metabolic activity. The catalytic promiscuity exhibited by this system further augments the evolutionary significance of these findings.” Ottele, Jim, Andreas S. Hussain, Clemens Mayer & Sijbren Otto. 2020. “Chance Emergence of Catalytic Activity and Promiscuity in a Self-Replicator.” Nature Catalysis. 3:547-553. 10.1038/s41929-020-0463-8. p. 547.

“Indeed, RNA molecules have been developed that catalyse reactions and RNA molecules have been made that can self-replicate, but no synthetic RNA molecules exist yet that can do both. The central problem appears to be that catalysis requires folding, while replication requires an unfolded strand.” Ottele, Jim, Andreas S. Hussain, Clemens Mayer & Sijbren Otto. 2020. “Chance Emergence of Catalytic Activity and Promiscuity in a Self-Replicator.” Nature Catalysis. 3:547-553. 10.1038/s41929-020-0463-8. p. 547.

“In conclusion, a self-assembling self-replicator was found to be able to catalyse not only its own formation, but also two other chemical transformation, that are each very different in nature from the replication reaction, i.e. the systems shows [sic] catalytic promiscuity.” Ottele, Jim, Andreas S. Hussain, Clemens Mayer & Sijbren Otto. 2020. “Chance Emergence of Catalytic Activity and Promiscuity in a Self-Replicator.” Nature Catalysis. 3:547-553. 10.1038/s41929-020-0463-8. p. 550.

“Thus, these results reveal how replication and metabolism, two key characteristics of life, can autonomously become integrated and mark an important advance towards the de-novo creation of a minimal form of life, which now ‘merely’ requires the functional integration of a compartmentalisation system. The present system of self-assembly driven self-replicators has the important advantage over other replicators in that sites for catalytic activity (the sides of the fibres) are distinct from the sites of self-replication (occurring at the fibre ends). The catalytic promiscuity exhibited by the system is a highly desirable feature in early evolution, as it allows catalysing different reactions while only having to replicate a single entity. Catalytic promiscuity is also an important pathway for evolutionary inventions, as it enables a system that evolved for one purpose to be co-opted for another purpose.” Ottele, Jim, Andreas S. Hussain, Clemens Mayer & Sijbren Otto. 2020. “Chance Emergence of Catalytic Activity and Promiscuity in a Self-Replicator.” Nature Catalysis. 3:547-553. 10.1038/s41929-020-0463-8. p. 550.

“For many scientists, metabolism consists in the set of chemical transformations that sustain, at the most basic level, a living organism, by providing it with molecular building blocks and energy to synthesize/repair all of its components…. An alternative approach would be to consider metabolism in its own terms: namely, as a chemistry thtat is strongly linked to biological phenomena, but not fully subordinate to them. From that standpoint, one could think about metabolic processes that are not necessarily part of a full-fledged biological organism.” Lauber, Nino, Christoph Flamm & Kepa Ruiz-Mirazo. 2021. “‘Minimal metabolism’: A key concept to investigate the origins and nature of biological systems.” BioEssays. 43:2100103. doi: 10.1002/bies.202100103. pp. 1-2.

“A number of synthetic small-molecule machines have been developed previously, including molecular muscles, synthesizers, pumps, walkers, transporters and light and electrically driven rotary motors. However, although biological molecular motors are powered by chemical gradients or the hydrolysis of adenosine triphosphate (ATP), to date there are no synthetic small-molecule motors that can operate autonomously using chemical energy (i.e. the components move directionally as long as a chemical fuel is present). Here we describe a system in which a small macrocycle is continuously transported directionally around a cyclic track when powered by irreversible reactions of a chemical fuel, fluorenylmethoxycarbonyl chloride (Fmoc-Cl). Key to the design is that the rate of reaction of Fmoc-Cl with reactive sites on the cyclic track is faster when the macrocycle is far from the reactive site than when it is close.” Wilson, Miriam R., Jordi Sola, Armando Carlone, Stephen M. Goldup, Nathalie Lebrasseur & David A. Leigh. 2016. “An Autonomous Chemically Fuelled Small-Molecule Motor.” Nature. 534:235-240. doi: 10.1038/nature18013. p. 235.

“Systems chemistry has been defined as the science of studying networks of interacting molecules, to create new functions from a set (or library) of molecules with different hierarchical levels and emergent properties. Examples that make use of holistic, systems-level design approaches, include self-selection of complex and self-folding structures, self-replication of supramolecular structures, emergence of positive-feedback catalytic functions with through recruitment of cofactors, reaction-diffusion catalytic systems, chemical oscillators, and designed clock-reactions. It has been recognized that peptides are particularly useful as components of designed complex chemical systems….

“The field of supramolecular peptide systems integrates systems chemistry with peptide nanotechnology.” Sheehan, Fahmeed, Deborah Sementa, Ankit Jain, Mohit Kumar, Mona Tayarani-Najjaran, Daniela Kroiss & Rein V. Ulijn. 2021. “Peptide-Based Supramolecular Systems Chemistry.” Chemical Reviews. 121:13869-13914. doi: 10.1021/acs/chemrev.1c00089. p. 13870.

“Life itself is not an additive collection of multiple functional units, but an integrated whole of complex interdependent processes. Therefore, a holistic design, where multiple factors like supramolecular structures, encoded chemical functions, spatiotemporal control, catalysis, and molecular recognition come together and are collectively considered, is required for the development of active and adaptive matter with life-like properties. Although we are still far from creating chemical structures that resemble the active and adaptive properties of living systems, recent examples discussed in this review show that short peptides [2 to 6 amino acid sequences] possess many properties relevant to life and that, increasingly, the design of these properties can be integrated to create functional materials with properties that rely on the chemical nature of the components and, crucially, on interactions and reactions between these components.” Sheehan, Fahmeed, Deborah Sementa, Ankit Jain, Mohit Kumar, Mona Tayarani-Najjaran, Daniela Kroiss & Rein V. Ulijn. 2021. “Peptide-Based Supramolecular Systems Chemistry.” Chemical Reviews. 121:13869-13914. doi: 10.1021/acs/chemrev.1c00089. p. 13903.

“The move from a concept where peptide sequence and structure dictates properties and functions, to one where molecular interactions and reactions between multiple peptide modalities, and in some cases under the influence of externally applied energy, collectively dictate properties represents a new way in which chemistry can be understood, studied, and applied, thus being a true paradigm shift. The collection of papers reviewed here clearly demonstrates that short peptides are exceptionally well suited to systems chemistry investigations because they are chemically rich and modular, and they can be designed to perform a wide range of functions, including catalysis, self-assembly, compartmentalization, and supramolecular recognition.” Sheehan, Fahmeed, Deborah Sementa, Ankit Jain, Mohit Kumar, Mona Tayarani-Najjaran, Daniela Kroiss & Rein V. Ulijn. 2021. “Peptide-Based Supramolecular Systems Chemistry.” Chemical Reviews. 121:13869-13914. doi: 10.1021/acs/chemrev.1c00089. p. 13903.

“… peptide-based systems chemistry will ultimately give rise to new solutions and insights that have not been explored by biology, and we expect the designs will be robust and rational.” Sheehan, Fahmeed, Deborah Sementa, Ankit Jain, Mohit Kumar, Mona Tayarani-Najjaran, Daniela Kroiss & Rein V. Ulijn. 2021. “Peptide-Based Supramolecular Systems Chemistry.” Chemical Reviews. 121:13869-13914. doi: 10.1021/acs/chemrev.1c00089. p. 13903.

“However, despite its [plate count method to determine viability of microbial samples’] widespread use, it cannot be considered a universal approach, as 95% of all cultivated and published species belong to just 5 of 53 recognized bacterial phyla. Furthermore, it has long been recognized that microbial cells may exist in ‘cryptobiotic’, ‘dormant’, ‘moribund’, or ‘latent’ states, in which they will not form colonies on nutrient media but may have other measurable activity (and therefore can still have an important role to play in disease or economic loss). In the case of environmentally acquired samples, it has been estimated that 1% (or fewer) of the microscopically observable organisms are scored as viable by the plate count method.” Davey, Hazel M. 2011. “Life, Death, and In-Between: Meanings and Methods in Microbiology.” Applied and Environmental Microbiology. 77(16):5571-5576. doi: 10.1128/AEM.00744-11. p. 5571.

“More recently, several distinct physiological states have been demonstrated in Pseudomonas fluorescens…. These included intact cells with normal energy metabolism, deenergized cells, depolarized cells, and permeabilized cells.” Davey, Hazel M. 2011. “Life, Death, and In-Between: Meanings and Methods in Microbiology.” Applied and Environmental Microbiology. 77(16):5571-5576. doi: 10.1128/AEM.00744-11. p. 5574.

“The microbiome is a complex and diverse ecosystem and defined as the collection of all host-associated microorganisms and their genes. It is acquired through vertical transmission and environmental exposure and includes microbes of all kingdoms: bacteria, archaea, prokaryotic and eukaryotic viruses, fungi, protozoa, and the meiofauna. These microorganisms co-evolved with their respective hosts over millions of years, thereby establishing a mutually beneficial, symbiotic relationship on all epithelial barriers. Thus, the microbiome plays a pivotal role in virtually every aspect of mammalian physiology, particularly in the development, homeostasis, and function of the immune system.” Runge, Solveig & Stephan Patrick Rosshart. 2021. “The Mammalian Metaorganisms: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.” Frontiers in Immunology. 12:702378. doi: 10.3389/fimmu.2021.702376. p. 1.

“The gastrointestinal bacterial microbiome does not only shape immunity at its corresponding barrier site but also exerts powerful effects on systemic immune responses. Among the most affected organs are the lung, the brain, and the liver whose physiology is influenced via the so-called gut-lung, gut-brain or gut-liver axis.” Runge, Solveig & Stephan Patrick Rosshart. 2021. “The Mammalian Metaorganisms: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.” Frontiers in Immunology. 12:702378. doi: 10.3389/fimmu.2021.702376. p. 6.

“The microbiota-mediated influence on brain homeostasis also affects the progression of several brain pathologies including psychiatric disorders like autism spectrum disorder, as well as neurological diseases such as Alzheimer’s disease, Parkinson’s diseases, multiple sclerosis, and stroke.” Runge, Solveig & Stephan Patrick Rosshart. 2021. “The Mammalian Metaorganisms: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.” Frontiers in Immunology. 12:702378. doi: 10.3389/fimmu.2021.702376. p. 6.

“Similar to intestine, another part of the digestive tract, the oral cavity, has a niche-specific bacterial microbiome.” Runge, Solveig & Stephan Patrick Rosshart. 2021. “The Mammalian Metaorganisms: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.” Frontiers in Immunology. 12:702378. doi: 10.3389/fimmu.2021.702376. p. 6.

“The respiratory bacterial microbiome differs markedly between the upper and lower respiratory tract….” Runge, Solveig & Stephan Patrick Rosshart. 2021. “The Mammalian Metaorganisms: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.” Frontiers in Immunology. 12:702378. doi: 10.3389/fimmu.2021.702376. p. 9.

“Archaea have been detected in plant tissues and on plant surfaces. However, most of the studies on plant-archaea interactions are limited to metagenome analysis and only suggest the possibility that archaea have on plants, but to not suggest how archaea directly affect plants….

“Archaea themselves are expected to have many beneficial properties for plants that have not yet been identified due to experimental and technical challenges.” Jung, Jihye, Jun-Seob Kim, Julian Taffner, Gabriele Berg & Choong-Min Ryu. 2020. “Archaea, tiny helpers of land plants.” Computational and Structural Biotechnology Journal. 18:2494-2500. doi: 10.1016/j.csbj.2020.09.005. p. 2498.

“Evidence shows that our resident microbes orchestrate the adaptive immune system, influence the brain, and contribute more gene functions than our own genome.” Rees, Tobias, Thomas Bosch & Angela E. Douglas. 2018. “How the microbiome challenges our concept of self.” PLOS Biology. 16(2):1-7. doi: 10.1371/journal.pbio.2005358. p. 1.

“By current estimates, approximately half of the cells in our body are microbial.” Rees, Tobias, Thomas Bosch & Angela E. Douglas. 2018. “How the microbiome challenges our concept of self.” PLOS Biology. 16(2):1-7. doi: 10.1371/journal.pbio.2005358. p. 2.

“… the key services that animals, from sponges to humans, gain from their microbiome are nutritional and defense against natural enemies. This commonality is unsurprising because interactions with the microbiome are near universal in extant animals and more ancient than the evolutionary origin of animals: our ancestors were multi-organismal before they were multicelllular.” Rees, Tobias, Thomas Bosch & Angela E. Douglas. 2018. “How the microbiome challenges our concept of self.” PLOS Biology. 16(2):1-7. doi: 10.1371/journal.pbio.2005358. p. 2.

“Microbiome science has the exciting–the important–potential to catalyze the breakdown of the anachronistic barriers between the natural and the human sciences and enable a truly integrated understanding of what it means to be human, after the illusion of the bounded, individual self. The human is more than the human.” Rees, Tobias, Thomas Bosch & Angela E. Douglas. 2018. “How the microbiome challenges our concept of self.” PLOS Biology. 16(2):1-7. doi: 10.1371/journal.pbio.2005358. p. 6.

“… a fundamental issue in using chemical input is microscopic reversibility, which makes their use in producing useful work challenging. This issue can be circumvented by external pumping, i.e., externally modulating the chemical environment, and hence reaction coordinate, leading to an energy ratchet mechanism, which is the default pathway when light is used as the input…. One can also make the argument that there must be a value for using chemical input as nature settled on chemical activation for most biological machines…. What stands is that chemically activated machines are functionally more biocompatible, and so it will/ might be easier to integrate them into and with biological systems.” Aprahamian, Ivan. 2020. “The Future of Molecular Machines.” ACS Central Science. 6:347-358. doi: 10.1021/acscentsci.0c00064. p. 354.

“When one is asked what is the future of the field of artificial molecular machines, the looming question seems to be–when will there be real-life applications?… Considering the frenzy activity in the field, I am optimistic that with time, there will be such applications, but for these to come to fruition, more cooperation with industry is needed.” Aprahamian, Ivan. 2020. “The Future of Molecular Machines.” ACS Central Science. 6:347-358. doi: 10.1021/acscentsci.0c00064. p. 355.

“Finally, it seems that the field [systems chemistry especially synthetic] is at a crossroads. In certain aspects, it has reached maturity as we have a much better understanding of how to design and control molecular motion, and in general we know, at least theoretically, what needs to be done to translate this motion into useful work. On the other hand, the field is in its infancy as we still do not know the nitty-gritty details of how to integrate molecular systems together nor to the outside world to achieve the complexity found in nature. Considering the influx of new ideas, development of new switchable systems and motors, and the growing interest in the field from different disciplines, one thing is for sure, exciting times lie ahead of us.” Aprahamian, Ivan. 2020. “The Future of Molecular Machines.” ACS Central Science. 6:347-358. doi: 10.1021/acscentsci.0c00064. p. 356.

“Remarkably, all the protein in all organisms is made by the catalytic activity of the RNA component of the ribosome, the cellular machine that reads genetic information and makes protein molecules. This observation suggests that RNA dominate an early stage in the evolution of life.” Szostak, Jack. 2018. “How Did Life Begin.” Nature. 557:S-13-S15. pp. S13-14.

“Non-equilibrium structures and organization are sustained by non-equilibrium inputs of matter and energy. Second, NEQ [non-equilibria] differs by push versus pull, i.e. by supply versus demand. Near-equilibrium processes are pulled toward equilibria, a tendency towards a state of minimum free energy. They are governed by the second law of thermodynamics. By contrast, FFE [far from equilibrium] is pushed by input energy and matter that are out of equilibrium. Imagine a flood that carves a new river bed; it does not aim to go any particular place, it just pushes water, which flows through a path of least resistance. Evolution does not steadily march towards predetermined goals, like second law equilibrium restoring processes do. The NEQ realm is broad and innovative….” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 4.

“… Orgel and others argued that there is severe difficulty in achieving biochemistry-like reactions with only prebiotically available catalysts. On the other hand, important recent experiments have achieved significant reactions using prebiotically available catalysts. Even so, chemistry in the prebiotic era was hostile to chemical innovation. The catalysts for those reactions were mineral surfaces or metal ions, many of which were spatially immobile (not accessible to substrates), capable only of catalysing limited reactions, each only under limited and different conditions, and only where substrates were sufficiently concentrated.

“Biology is more innovative than prebiotic chemistry. Biology’s catalysts–mostly proteins–are mobile and can go where the substrates are; can be altered to work in different environments, including just in water, or in membranes; can operate at whatever ambient temperature is needed for the organism; and are readily tunable to any degree that is needed to fit within whole reaction pathways and cycles. Protein catalysts could be called programmable, in the sense that their extraordinarily wide range of capabilities can be controlled by just a simple single kind of process, namely mutating amino acid sequences.” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 4.

“The early discovery, by physical chemical processes, of catalysts that are explorable and optimizable through random changes of sequences of monomers in a polymer chain is arguably one of the most important steps made during the origins of life because of its capacity for rapid trial-and-error invention of complex chemical processes and diverse functionalities, all brought together under single conditions.” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 5.

“There are many plausible prebiotic processes that can polymerize individual amino acids into peptides, or nucleic acids into short DNA or RNA molecules. But these polymerizations all suffer from the so-called Flory problem, namely that the resultant chains are mostly very short (~2–8-mers); longer chains are exponentially less probable.

“Known prebiotic polymerizations also do not address (i) how the randomness in polymerized sequences leads to ordered and informational sequences, and (ii) how such processes became autocatalytic, leading to stable steady states of production of long-chain informational-sequence polymers.

“The foldamer catalyst hypothesis offers an explanation. In this hypothesis, chains are polymerized using two types of monomers: hydrophobic (H) and polar (P), as modern-day proteins are. When H and P monomers are linked into long chains, like today’s proteins, different HP sequences spontaneously fold in water to different ‘native’ structures. The structures are driven by the oil-water principle that hydrophobic monomers seek to minimize contact with water.

‘According to this hypothesis, some short-chain HP sequences will compactify in aqueous solutions into structures that have some exposure of their hydrophobic residues on their surface. Call those hydrophobic surfaces landing pads, and those chains catalysts. If a second short peptide chain lands its own H monomers on the sticky hydrophobic surface of the first one, a catalyst, then the second chain will undergo an enhanced rate of covalent elongation because of the sticky localization of the chain and an H monomer to be added. [Longer defense of how this process gives the three properties sought up above follows but requires accompanying graphics]” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 5.

“Short proteins function as hormones, signalling molecules, growth factors, venoms, antibiotics and more. Enzymatic activities are known in chains even as short as dipeptides, and including ATP binding activity. 7-mer amyloid peptides can catalyse reactions and auto-catalyse their own formation. So, amyloid structures might have been prebiotic catalysts. Moreover, proteins are highly promiscuous binders. For example, half the yeast proteome has protein-protein binding affinities stronger than 1 kcal mol-1.” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 6.

“The catpath mechanism is a non-equilibrium reaction-diffusion mechanism that brings reactions together in space based on their related functionalities. In this process, a catalyst A, fixed at a given location, draws a catalyst B in its spatial neighbourhood; the effective attraction between the catalysts (cats) is mediated by a common substrate or product, on which they both act….

“In the catpath mechanism, a mobile catalyst molecule B, which converts 2s to 3s, diffuses toward the position of a catalyst molecule A, which converts 1s to 2s…. This attraction is a reaction-diffusion process. Because the A cats are continuously supplied with 1s, so they continuously produce 2s. These product 2s will diffuse away from the parent A at some rate, but will concentrate around A for certain relative speeds. The B cats have a binding affinity for their substrates, 2s in this case. So Bs will diffuse toward the 2s, thus toward the A cats. In this way, A and B cats are attracted to each other, mediated by a small molecule substrate/product in common.

“The catpath process contrasts with two standard situations: (1) two independent particles will simply diffuse away from each other, or (2) two particles with mutual affinity will come together and bind each other. The catpath attraction is not based on a binding affinity, A-B; rather, it is an example of function driving structure: processes that have a common mediator come together. Unlike simple A-B binding affinity, catpath is a non-equilibrium force; there is no attraction unless 1s are continuously supplied. It is driven only by the commonality of the small-molecule agent that is the product of one cat and the substrate of the other.” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 7.

“…nucleic acids at high concentrations assemble into non-covalent base stacks even without a backbone…. Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 9.

“We have postulated two stages in Pchem2Bio [physical chemistry transition to biology]: forming a nearbiotic soup requiring only peptide foldamers and metabolites, followed by cellular encapsulation and informational molecules.” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 9.

“There is a plausible explanation for biology’s current division of labour in which proteins are functional and DNA is informational. For functionality, you need sequence-structure relations: changing the sequence, changes the structure, changes the function. The physics that enables this is folding. Proteins fold better–and for essentially all sequences–than RNA does. For information, and for memory-like actions, you specifically want the opposite. You want a type of molecule that can store all information the same, with no preferences, with the absolute minimum possible sequence structure relationships. DNA is an almost perfect informational molecule: it is very stiff, has no fold and its double-strandedness protects either strand from binding to external agents (apart of course, from transcription and such.)” Dill, K.A. & L. Agozzino. 2021. “Driving forces in the origins of life.” Open Biology. 11:200324. doi: 10.1098/rsob.200324. p. 9.

“GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism-first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems–hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced.” Lancet, Doron, Raphael Zidovetzki & Omer Markovitch. 2018. “Systems protobiology: origin of life in lipid catalytic networks.” Journal of the Royal Society Interface. 15:20180159. doi: 10.1098/rsif.2018.0159. p. 1.

“We address the doubts regarding whether mutually catalytic networks may evolve. We show that the lability of single compositional mutations does not stand in the way, because compositional information stability is assured by the attractor dynamics of entire composomes. We show how environmental chemical changes induce transitions from one composomal state to another, including preliminary evidence for open-ended compositional evolution.” Lancet, Doron, Raphael Zidovetzki & Omer Markovitch. 2018. “Systems protobiology: origin of life in lipid catalytic networks.” Journal of the Royal Society Interface. 15:20180159. doi: 10.1098/rsif.2018.0159. p. 30.

“The adequacy of GARD to serve as a model for pre-RNA life is also demonstrated by the observed thermodynamic and kinetic traits that befit a precursor to present-day living cells. This includes attractor-like transitions from random assemblies to self-organized composomes, which involve a negative entropy change. These facets, along with permanently being away from equilibrium, exchanging matter and energy with its environment and being able to amplify small fluctuations, establish GARD composomes as dissipative systems, hallmarks of life.” Lancet, Doron, Raphael Zidovetzki & Omer Markovitch. 2018. “Systems protobiology: origin of life in lipid catalytic networks.” Journal of the Royal Society Interface. 15:20180159. doi: 10.1098/rsif.2018.0159. p. 30.

“In vitro transcription translation (IVTT) kits have revolutionized the field of synthetic biology by providing a reliable, customizable tool for the expression of proteins in entirely synthetic contexts.” Yewdall, N. Amy, Alexander F. Mason & Jan C.M. van Hest. 2018. “The hallmarks of living systems: towards creating artificial cells.” Interface Focus. 8:20180023. doi: 10.1098/rsfs.2018.0023.

“Synthetic biology has traditionally been divided into two distinct approaches. The first is ‘top-down’, where cells are modified using molecular biology and metabolic/genetic engineering techniques. The alternative approach is concerned with constructing cell-like structures known as artificial cells (also known as protocells or synthetic cells) from scratch out of non-living building blocks. This endeavour is sometimes referred to as ‘bottom-up’ synthetic biology.” Elani, Yuval. 2021. “Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology.” Angewandte Chemie. 133:5662-5671. doi: 10.1002/anie.202006941. p. 5663.

“As a field, top-down synthetic biology is well developed and has already produced several breakthroughs including the biosynthesis of drug precursors, the development of organisms for biofuel production, engineered cell therapies, and the creation of new responsive and multifunctional materials. By contrast, the discipline of artificial cells is less mature in terms of demonstrated applications…. There are now several dedicated large-scale international centres and initiatives devoted to building artificial cells from the bottom up.

“The most dominant form of artificial cells involve cell-sized capsules, such as liposomes, polymersomes, coacervates, proteinosomes and hydrogel particles, which act as the chassis. These compartments can be functionalised with biomolecular components, including transmembrane channels, enzymes, cytoskeletal elements, gene circuits, and transcription;/translation machinery. In doing so, cellular characteristics can be mimicked. These include cellular processes and behaviours (e.g. signalling cascades, communication, motility, energy generation, replication, and computation) as well as architectural motifs (e.g. membranes, organelles, and tissues).” Elani, Yuval. 2021. “Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology.” Angewandte Chemie. 133:5662-5671. doi: 10.1002/anie.202006941. p. 5663.

“Top-down and bottom-up synthetic biology have largely evolved in parallel to each other, and they still exist as distinct sub-fields with little by way of meaningful overlap. However, we are reaching a point where links between the two approaches can be made through the construction of hybrid cells composed of both living and synthetic components.” Elani, Yuval. 2021. “Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology.” Angewandte Chemie. 133:5662-5671. doi: 10.1002/anie.202006941. p. 5664.

“… the fact that synthetic cells are not living means that one can engineer them to produce otherwise toxic compounds. Moreover, as biocompatibility issues are no longer critical with non-living cells, one can incorporate wholly non-biological building blocks, allowing biological capabilities to be surpassed. These non-biological additions could include electronic components, functional nanoparticles, and novel molecular machines (e.g. DNA origami or nano-electrical elements). Third, the use of synthetic cells reduces biosafety, regulatory, and public perception hurdles. They do not replicate, are not alive, are not autonomous, and are not functional for long periods without active human intervention–at least for the foreseeable future. In this respect, they have more in common with traditional nanotechnologies and microrobots than with living organisms. For these reasons, they are not considered GMOs by either regulators or the public psyche. Finally, and perhaps most importantly, synthetic cells have a vastly reduced molecular complexity compared to their biological counterparts, which makes them more programmable and predictable. They are often composed of tens of distinct molecular species, compared to tens of thousands of species present in living cells.” Elani, Yuval. 2021. “Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology.” Angewandte Chemie. 133:5662-5671. doi: 10.1002/anie.202006941. p. 5664.

“Overall, three different hybridisation routes are possible….

“(i) Population hybridisation, where discrete biological and artificial cells communicate with one another across space, exchanging information and materials.

“(ii) Embedded hybridisation, where living cells are embedded inside synthetic ones or vice versa, with the encapsulated cells performing organelle-like functions within their host.

“(iii) Networked hybridisation, where artificial and biological cells exist as distinct entitites that are physically linked to one another in a network or in a tissue-like arrangement.” Elani, Yuval. 2021. “Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology.” Angewandte Chemie. 133:5662-5671. doi: 10.1002/anie.202006941. p. 5665.

“He [Francis Bacon] agreed with the nominalists that ‘in nature nothing really exists besides individual bodies, performing purely individual acts.’ As a result, the universe is a labyrinth that is impenetrable to unaided human reason.” Gillespie, Michael Allen. 2008. The Theological Origins of Modernity. U of Chicago Press. p. 37.

“God for Descartes is no longer the wild and unpredictable God of nominalism. In fact, it is precisely this God that Descartes suppresses in favor of a more rational God, or at least a God that can be comprehended by human reason. At the same time he brings God downward towards man. Descartes elevates man towards God with his claim that man has the same infinite will as God. Hobbes, by contrast, accepts a more orthodox Calvinist position that asserts the absolute power of God and the insignificance of man.” Gillespie, Michael Allen. 2008. The Theological Origins of Modernity. U of Chicago Press. p. 273.

“… ‘[Descartes from the 1647 Principles:] the whole of philosophy is like a tree, whose roots are metaphysics, the trunk physics, and the branches growing from the trunk are all other sciences, which reduce to three principal sciences, namely medicine, mechanics, and ethics.’

“On an ordinary reading of this familiar passage, and of the equally familiar context in which it appears, mechanics is not an integral part of physics, even a small part, but is one of its three major disciplinary offshoots to which all other sciences can be reduced….

“So in fact the philosophical tree in the letter-preface to the French Principles does present the state of affairs as Descartes wishes it to be understood. Theoretical mechanics depends on physics as its nomological foundation, which in turn depends on metaphysics….” Gabbey, Alan. 1993. “Descartes’s Physics and Descartes’s Mechanics: Chicken and Egg?” pp. 311-323. From: Essays on the Philosophy and Science of Rene Descartes. Voss, Stephen (ed). Oxford UP. pp. 315, 318; subquote: Adam, Charles & Paul Tannery (eds). Oeuvres de Descartes. 1964-1976. CNRS and Vrin. V. IX-2, p. 14.

“The absence in the Principles of Philosophy of the work principle or the GSP [general statical principle – Descartes’s principles of mechanics from physics and statics] is what we should have expected, given the unfinished state of the physics as Descartes saw it. When his great corpus of natural philosophy is complete, then the GSP and the properly grounded Cartesian mecanique will form an [sic] major branch on the tree, its bases firmly located somewhere among the leges physicae as applied to the complexities of Descartes’s mechanical theory of gravity [i.e., mechanics is still beholden to a physics that, like Aristotle’s, is grounded in metaphysics].” Gabbey, Alan. 1993. “Descartes’s Physics and Descartes’s Mechanics: Chicken and Egg?” pp. 311-323. From: Essays on the Philosophy and Science of Rene Descartes. Voss, Stephen (ed). Oxford UP. p. 320.

“The exclusion of formal agency as a type of natural cause is unfortunate. There are sound reasons to consider autocatalysis, and in particular autopoiesis, as agents akin to Aristotle’s formal causation that are capable of influencing the life process.” Ulanowicz, Robert E. 1989. “A Phenomenology of Evolving Networks.” Systems Research. 6(3):209-217. p. 210.

“The facts that autocatalytic configurations have characteristic lifetimes longer than their constituent parts and that overall structures actively influence the nature of allowable replacements both imply that autocatalytic behaviour cannot be regarded in reductionistic fashion as the superposition of component events at lower levels.” Ulanowicz, Robert E. 1989. “A Phenomenology of Evolving Networks.” Systems Research. 6(3):209-217. p. 211.

“The only way to make sense of the world of experience is to open up the possibility of a new way of being that could belong to form, active and causal enough to be responsible for the way things are, yet stable and independent of those things. This way of being is what Aristotle calls being-at-work. It is evident in the things around us as life, and in the cosmos as whole as the patterns of heavenly motions, but it belongs properly and directly only to forms. As it belongs to forms themselves, such being-at-work is beyond any ordinary and familiar notion of being: as the source and foundation of all other being, it is being as being, in its own right; and as the source of all wholeness and order, it is the good.” Aristotle. 1999. Metaphysics. Translated by Joe Sachs. Santa Fe: Green Lion Press. “Introduction.” by Joe Sachs. p. xxiv.

“All thinking about the way things are is a quest for what is permanent, or at least enduring, among, within, or behind them. For Parmenides and the other Eleatic thinkers, this meant a rejection of all motion as illusory, and a trust in intellect alone as the way to truth. For Thales and the other Ionian thinkers, it meant the positing of some underlying material as the only stable being amid the variety of appearances. Thus the beginning of our philosophic tradition was a search for the inert, and this impulse has never gone away. For Aristotle, such an account of things is never explanatory, since the inert cannot be responsible for its own changes and transformations.” Aristotle. 1999. Metaphysics. Translated by Joe Sachs. Santa Fe: Green Lion Press. “Introduction.” by Joe Sachs. p. xxv.

“And since Socrates exerted himself about ethical matters and not at all about the whole of nature, but in the former sought the universal and was the first to be skilled at thinking about definitions, Plato, when he adopted this, took it up as applying to other things and not to sensible ones, because of this: it was impossible that there be an common definition of any of the perceptible things since they were always changing. So he called this other sort of beings forms, and said the perceptible things were apart from these and all spoken of derivatively from these, for the many things with the same names as the forms were results of participation. He changed only the name participation, for the Pythagoreans said that beings are by way of imitation of the numbers, but Plato by way of participation, having changed the name. What this participation or imitation of the forms might be, however, they were in unison in leaving behind to be sought.” Aristotle. 1999. Metaphysics. Book A: 987b. Translated by Joe Sachs. Santa Fe: Green Lion Press. pp. 14-5.

“In the Phaedo it is put this way: that the forms are responsible for both being and becoming. Yet even if there are forms, still the things that partake of them do not come into being if there is not something that causes motion, and many other things do come into being, such as a house or a ring, of which we say there are no forms.” [Followed by note:] “Both in Plato’s dialogues and in Aristotle’s writings a first way in toward the idea of form is the pattern a craftsman has in mind when he makes something. But that example is like a temporary scaffolding that is kicked away once a sounder structure is built. In the Physics, the notion that a bed has a form is undermined the instant the idea of being-at-work is introduced. Trees have forms, so in a derivative way human artisans can rework the wood.” Aristotle. 1999. Metaphysics. Book A: 991b. Translated by Joe Sachs. Santa Fe: Green Lion Press. p. 24.

“… if the forms consist of forms (for the things of which they consist are more uncompounded than they are), those things of which the form consists, such as animal and two footed, will still have to apply to many things. If they did not, how would they be known? For there would be a form which was incapable of being attributed to more than one thing, but that doesn’t seem possible, but rather that every form is capable of being shared in.” Aristotle. 1999. Metaphysics. Book Z: 1040a. Translated by Joe Sachs. Santa Fe: Green Lion Press. p. 149.

“What’s more, material is in potency because it goes toward a form; but whenever it is at work, then it is in that form.” Aristotle. 1999. Metaphysics. Book Theta: 1050a. Translated by Joe Sachs. Santa Fe: Green Lion Press. p. 178.

“So of those things from which there is something else apart from the putting-to-use that comes into being, the being-at-work is in the thing that is made (as the activity of building is in the thing built and the activity of weaving in the thing woven, and similarly with the rest, and in general motion is in the thing moved); but of those things which have no other work besides their being-at-work, the being-at-work of them is present in themselves (as seeing is in the one seeing and contemplation in the one contemplating, and life is in the soul, and hence happiness too, since it is a certain sort of life). And so it is clear that thinghood and form are being-at-work.” Aristotle. 1999. Metaphysics. Book Theta: 1050b. Translated by Joe Sachs. Santa Fe: Green Lion Press. p. 179.

“In the first sense [Descartes’s mechanics], mechanistic biology enumerates a series of movements, each of which evokes its sequel, all necessitated a tergo, and all conceived as movements of matter. 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. pp. 35-6.

“In Aristotle’s thought… form is emphatically prior to matter…. However, 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. Indeed, it probably did not exist at all.” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 39.

“In Aristotle–and, one would suppose, in any Aristottelian view of nature–we find hylomorphism, the intimate connection of form and matter, virtually everywhere…. In the new Cartesian nature, on the contrary, we have pure matter – no form except in the residual sense of shape….” Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 42.

“‘The ordinary philosophy which is taught in the schools and universities is by contrast merely a collection of opinions that are for the most part doubtful, as is shown by the continual debates in which they are thrown back and forth. They are quite useless, moreover, as long experience has shown to us; for no one have ever succeeded in deriving any practical benefit from ‘prime matter,’ ‘substantial forms,’ ‘occult qualities’ and the like.’” Descartes, Rene. Oeuvres. 1964-82. Edited by C. Adam & P. Tannery. Paris: Vrin. Vol. VIII b, p. 26. Translation by J. Cottingham, R. Stoothoff, D. Murdoch & A. Kenny. The Philosophical Writings of Descartes. Camb UP. Vol. 3, pp. 220-1. From: Grene, Marjorie & D. Depew. 2004. The Philosophy of Biology: An Episodic History. Cambridge UP. p. 43.

“During the thirteenth century theology became both a distinct discipline and a protected profession; neither was the case earlier. Prior to the twelfth and thirteenth centuries, the term ‘theology’ was ambiguous; it stood both for the word of God (the Scriptures) and for words about God, that is, any kind of discourse on matters divine. Soon after the beginnings of its systematization, theology was established as a protected profession in the nascent universities.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 4.

“The first protective belt around theology eroded slowly, almost imperceptibly, in the sixteenth century, when ever more disciplines in the universities ceased to be taught by clergymen. Nor did the university remain the only center of research and scientific communication: courts, academies, and printers became places of meeting and sources of sustenance.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. pp. 4-5.

“Again under the impact of Protestantism, theology became secularized in yet a deeper sense. To various degrees, it encouraged the sacralization of the world, even of ‘everyday life.’ Human labor in hoc seculo was not perceived anymore as a mere preparation for the future life: it acquired its own religious value in that, if well done, it increases God’s honor. So also does the study of this world, by exposing the ingenuity of its creator.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 5.

“Within the Aristotelian and Scholastic tradition, it was forbidden to transplant methods and models from one area of knowledge to another, because it would lead to a category-mistake. This injunction suited the social reality of medieval universities well, separating theology from philosophy to the benefit of both, but it eroded considerably from the fourteenth century, when mathematical consideration started to be heavily introduced into physics, and even into ethics and theology. What was a methodological sin to Aristotle became a recommended virtue in the seventeenth century.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 6.

“Ideals of science differ in many ways from ideas in science. They indicate how a scientific community imagines science as it ought to be if ever completed; they express the ultimate criteria of rationality of their time….

“Ideas constitute science; ideals–Kant called them regulative ideas or principles–chart its goals. If we mistake constitutive for regulative ideas, he argues in a concluding chapter of his first critique, science may seem to us contradictory even where it is not.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. pp. 18-9.

“They [the ideals of unequivocation and homogeneity] were the most comprehensive ideals of rationality in the seventeenth century, but not the only ones. In their proximity, perhaps subordinate yet not identical, other ideals are clearly recognizable, notably the ideals of mathematization and mechanization.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 29.

“The ideal of mechanization, inasmuch as it calls for a monocausal explanation of nature, stands close to the ideal of uniformity although they are not altogether identical. It consists first and foremost of the demand to abolish final causes from the study of natural phenomena, to reduce all causes to mechanical causes….” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 30.

“The Scholastic universe [during the Middle Ages and the Renaissance] was Aristotelian: the cosmos of Renaissance philosophies of nature was, instead, Stoic, with interspersed Atomistic corrections. The former sought forms, the latter sought forces. The former considered their foremost task to be the purification of all ambiguities from scientific language–all the more so since the Nominalistic revolution. Renaissance philosophies of nature, on the other hand, abandoned the obsession with language but advanced the ideal of the homogeneity of nature in all its parts, a nature constructed of one matter and of one set of forces. Only in the seventeenth century were both ideals fused into one ideal: a science that has an unequivocal language with which it speaks and uniform objects of which it speaks. The infinite Euclidean space embodied and symbolized both aspects.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 41.

“Whether or not my guess that its origins were more Hellenistic than Judaic is correct, the question, of how God exists ‘in things’ seems to me to encapsulate, more than any other theological issue, the dialectics of divine immanence and utter transcendence. The attribute of omnipresence had to be differentiated from Christ’s presence and the presence of the Holy Ghost–but not too much. It had to be guarded from pantheistic interpretations, but also from elimination by excessive emphasis on God’s being nowhere. It had to be safeguarded against both too literal and too allegorical readings.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 49.

“We shall limit our discussion of Renaissance philosophies of nature to two examples almost a century apart: Nicolaus Cusanus and Bernardino Telesio. For very different reasons, both asserted the fundamental homogeneity of the universe; both exchanged the Aristotelian forms for forces.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 64.

“Like the Stoics, he [Telesio] wished to replace the Platonic or Aristotelian ‘forms’ (i.e., essences) with real forces, all of which are reducible to attraction and repulsion, or to heat and cold (as had Empedocles at one time). These forces operate on one, homogeneous, actual yet passive matter, the actuality of matter was already stressed by the Nominalists. Each body represents a balance of these forces and seeks to preserve that balance; each body possesses an instinct for self-preservation…. The war between the Aristotelian adherents of form and the new adherents of force was fought in Italian universities in the generation before Galileo, at times with bare fists.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 67.

“He [Hobbes] was, in this sense, a ‘mechanical philosopher,’ crusading against final causes, substantial forms, sensible or intelligible species, in short, anything that came from the despised vocabulary of Scholasticism.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 81.

“Eventually, the secular theologians of the seventeenth century (if indeed, they merit this name) gave way to a new generation of savants whose posture was often anti-theological, sometimes also anti-religious, occasionally even atheistic. It seems as though the secular theology of the seventeenth century was bound to dig its own grave, because it often stressed, however ambiguously, the self-sufficiency of the world and the autonomy of mankind. Immanuel Kant was neither the most radical not the most representative among the philosophers of the ‘Enlightenment.’ Yet his relentless endeavor to emancipate metaphysics and science from its theological baggage, and to develop an ethical theory in which human beings are their own supreme law-givers, was the most systematic and complex.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 346.

“The Enlightenment inherited from Christianity not its apocalypticism, but rather its social and pedagogical drive. The ideals of the Enlightenment were secularized, inverted Christian ideals through and through…. The Christian tenet that ‘there is no salvation outside the Church’ was matched by the new belief that there is no salvation except through the use of reason. Superstition and ignorance became the original sin of mankind.” Funkenstein, Amos. 1986. Theology and the Scientific Imagination: From the Middle Ages to the Seventeenth Century. Princeton UP. p. 357.

“The natural sciences often speak in the register of revelation, bringing transformative truths from outside the domains of ordinary human experience. Their preferred narrative mode is rupture, a history punctuated by grand paradigm shifts. Humanists by contrast retell the past to situate experience within storylines that neither erase our role as narrators nor absolve us of the responsibility to connect what is and what will be to what has gone before. Central to those stories is an interpretation of human nature and human purposes, an exploration of what human lives are for that builds on slowly accumulated archaeologies. This essay follows that humanistic tradition in a time when humanity, the fellow-feeling that lies at the heart of collective moral judgment, seems endangered by science’s disruptive and materialist thinking.” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. p. 2.

“A new ‘we’ has arisen, Chakrabarty argues, at the level of the species, with its history no longer separable from that of nature.” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. p. 6; reference: Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):197-222.

“The tension between humans morphing into nature and humans still dominating nature has reverberated through environmental thought in the intervening decades [since the naming of the Anthropocene].” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. p. 7.

“Put briefly, co-production calls attention to the integrated ways in which epistemic understandings of what the world is like, or consists of, evolve with normative understandings of how we think those worlds should be ordered and governed: ‘co-production is shorthand for the proposition that the ways in which we know and represent the world (both nature and society) are inseparable from the ways in which we choose to live in it. In this respect, co-production flies in the face of Enlightenment modernity’s signature achievement, the creation – through the ‘scientific method’ – of a space of objectivity from which the world can be perceived independently of any contaminating subjective beliefs, and the consequent separation of fact from value or nature from culture.” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. p. 8.

“The framework of co-production differs from these influential lines of critique [feminist, postcolonial, subaltern, Marxist etc.] in not taking any particular standpoint as the place from which to attack the presumption of scientific universalism, but rather to query how particular nature-culture orderings come into being and are sustained with relative stability over periods of time. This angle of vision leads to its own emphases in investigating some elements of order more intensively than others. Thus, the co-productionist theorist is likely to become more interested in how some subjects and standpoints originated in the first place than in the implications of being or thinking like a subject from some fixed position in society. Epistemologies and ontologies are of interest, then, mainly as windows onto the social arrangements that not only sustain them but that they reciprocally help sustain, including a society’s moral and political imaginaries. Nature on this account is always an arbiter of human values.” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. pp. 10-1.

“… how one tells the story of that disastrous period in the American West [the Dust Bowl] depends on whether one wishes to feature a ‘rising’ tale of individual human resourcefulness, grit, and technological ingenuity, or a ‘falling’, declensionist tale of greed, misunderstanding and overexploitation of nature. The former celebrates utilitarianism, whereas the latter deplores the excesses of capitalism….” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. p. 12.

“Time is to the historian what nature is to the scientist; a reservoir of meaning from which the diligent or impassioned excavator releases those findings that appear to possess the supreme quality of truth.” Jasanoff, Sheila. 2020. “Ours is the Earth: Science and Human History in the Anthropocene.” Journal of the Philosophy of History. 14:1-22. doi: 10.1163/18722636-12341447. p. 20.

“We have estimated the current economic value of 17 ecosystem services for 16 biomes, based on published studies and a few original calculations. For the entire biosphere, the value (most of which is outside the market) is estimated to be in the range of US$16-54 trillion per year, with an average of US$33 trillion per year. Because of the nature of the uncertainties, this must be considered a minimum estimate. Global gross national product total is around US$18 trillion per year.” Costanza, R., R. d’Arge, R. de Groot et al. 1997. “The value of the world’s ecosystem services and natural capital.” Nature. 387:253-260. doi? 10.1038/387253a0. p. 253.

“Without a guiding vision there is no road ahead; the science becomes an engineering discipline, concerned with temporal practical problems.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 173.

“By the end of the 20th century, however, the molecular vision of biology had in essence been realized; what it could see of the master plan of the living world had been seen, leaving only the details to be filled in. How else could one rationalize the strange claim by some of the world’s leading molecular biologists that the human genome (a medically inspired problem) is the ‘Holy Grail’ of biology? What a stunning example of a biology that operates from an engineering perspective, a biology that has no genuine guiding vision!” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 173.

“A society that permits biology to become an engineering discipline, that allows that science to slip into the role of changing the living world without trying to understand it, is a danger to itself. Modern society knows that it desperately needs to learn how to live in harmony with the biosphere.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 173.

“On the negative side, biology’s holistic problems, which were not commensurate with the new molecular perspective, would remain relatively or completely undeveloped. The result was a distorted growth of biology in the 20th century. The most pernicious aspect of the new molecular biology was it[‘s] reductionist perspective, which came to permeate biology, completely changing its concept of living systems and leading then to a change in society’s concept thereof.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 174.

“… biology today has hit the wall of biocomplexity, reductionism’s nemesis.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 174.

“A future biology cannot be built within the conceptual superstructure of the past. The old superstructure has to be replaced by a new one before the holistic problems of biology can emerge as biology’s new mainstream and define its future goals.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 175.

“Needless to say, classically trained biologists did not see it this way [that a gene was nothing more than its structure]: in that translation (the heart of gene expression) was not yet understood, ‘the problem of the gene’ could not possibly be completely (not to mention fundamentally) solved. No other single issue has exposed the difference between the molecular and classical perspectives more clearly than this one. Should the problem of translation be treated as just another (idiosyncratic) molecular mechanism (as it now is), or is that problem central, and thus fundamental, to the nature of the cell. As we shall see, biology today continues to live with this unresolved problem.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 176.

“From a theoretical point of view, one thing can be said about evolution with fair assurance: it is a complex, dynamic process. But it is only now, in the context of computer algorithms, fractals, and chaos mathematics, that we are beginning to get a useful feeling for what that means, and it means that evolution is a bumpy road to who knows where. ‘Bumpy’ implies that evolution, as a complex dynamic process, will encounter critical points in its course, junctures that result in phase transitions (drastic changes in the character of the system as a whole). ‘Who knows where’ implies that the outcomes of these transitions, saltations, are not predictable a priori.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 180.

“Next comes the evolution of the eucaryotic cell itself. While biologists have traditionally seen this as a step (saltation) beyond the stage of bacterial cells, I do not. The idea that eucaryotic cell structure is the product of symbioses among bacteria, and so represents a higher stage than that of the bacterial cell, goes back a good century and a half, but there has been no effort to seriously rethink the matter in the light of modern biological knowledge. Nowhere in thinking about a symbiotic origin of the eucaryotic cell has consideration been given to the fact that the process as envisioned would involve radical change in the designs of the cells involved. You can’t just tear cell designs apart and willy-nilly construct a new type of design from the parts. The cells we know are not just loosely coupled arrangements of quasi-independent modules. They are highly, intricately, and precisely integrated networks of entities and interactions…. To think that a new cell design can be created more or less haphazardly from chunks of other modern cell designs is just another fallacy born of a mechanistic, reductionist view of the organism.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 180.

“Evolving the mitochondrion through (endo)symbiosis is fundamentally different from evolving the eucaryotic cell in this way [per quotation above]. Whereas the latter process would involve a disruptive dismantling of the preexisting eucaryotic cellular design, acquisition of a mitochondrion does not significantly perturb the eucaryotic cell’s basic organization, which is in essence the same with or without the mitochondrion’s presence.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 180.

“But the physics and chemistry that entered biology (especially the former) was a Trojan house, 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 quashed. Biology would quickly become a science of lesser importance, for it had nothing fundamental to tell us about the world. Physics provided the ultimate explanations. Biology, as no more than complicated chemistry, was at the end of the line, merely providing baroque ornamentation on the great edifice of understanding that was physics–the hierarchy physics–>chemistry–>biology is burned into the thinking of all scientists, a pecking order that has done much to foster in society the (mistaken) notion that biology is only an applied science.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. pp. 184-5.

“In the last several decades we have seen the molecular reductionist reformulation of biology grind to a halt, its vision of the future spent, leaving us with only a gigantic whirring bio-technology machine. Biology today is little more than an engineering discipline.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 185.

“Thus, biology is at the point where it must choose between two paths: either continue on its current track, in which case it will become mired in the present, in application, or break free of reductionist hegemony, reintegrate itself, and press forward once more as a fundamental science. The latter course means an emphasis on holistic, ‘nonlinear,’ emergent biology–with understanding evolution and the nature of biological form as the primary, defining goals of a new biology.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 185.

“Society cannot tolerate a biology whose metaphysical base is outmoded and misleading: the society desperately needs to live in harmony with the rest of the living world, not with a biology that is a distorted and incomplete reflection of that world. Because it has been taught to accept the above hierarchy of the sciences, society today perceives biology as here to solve its problems, to change the living world. Society needs to appreciate that the real relationship between biology and the physical sciences is not hierarchical, but reciprocal: physics<–> biology. Both physics and biology are primary windows on the world; they see the same gem but different facets thereof (and so inform one another). Knowing this, society will come to see that biology is here to understand the world, not primarily to change it. Biology’s primary job is to teach us. In that realization lies our hope of learning to live in harmony with our planet.” Woese, Carl R. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. doi: 10.1128/MMBR.68.2.173-186. p. 185.

“Anthropogenic explanations of climate change spell the collapse of the age-old humanist distinction between natural history and human history.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 201.

“In unwittingly destroying the artificial but time-honored distinction between natural and human histories, climate scientists posit that the human being ha become something much larger than the simple biological agent that he or she always has been. Humans now wield a geological force.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 206.

“To call human beings geological agents is to scale up our imagination of the human. Humans are biological agents, both collectively and as individuals. They have always been so. There was not point in human history when humans were not biological agents. But we can become geological agents only historically and collectively, that is, when we have reached numbers and invented technologies that are on a scale large enough to have an impact on the planet itself. To call ourselves geological agents is to attribute to us a force on the same scale as that released at other times when there has been a mass extinction of species. We seem to be currently going through that kind of a period.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. pp. 206-7.

“The mansion of modern freedoms stands on an ever-expanding base of fossil-fuel use. Most of our freedoms so far have been energy-intensive.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 208.

“Geologists and climate scientists may explain why the current phase of global warming–as distinct from the warming of the planet that has happened before–is anthropogenic in nature, but the ensuing crisis for humans is not understandable unless one works out the consequences of that warming. The consequences make sense only if we think of humans as a form of life and look on human history as part of the history of life on this planet. For, ultimately, what the warming of the planet threatens is not the geological planet itself but the very conditions, both biological and geological, on which the survival of human life as developed in the Holocene period depends.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 213.

“The word that scholars such as Wilson or Crutzen use to designate life in the human form–and in other living forms–is species. They speak of the human being as a species and find that category useful in thinking about the nature of the current crisis. It is a word that will never occur in any standard history or political-economic analysis of globalization by scholars on the Left, for the analysis of globalization refers, for good reasons, only to the recent and recorded history of humans…. The task of placing, historically, the crisis of climate change thus requires us to bring together intellectual formations that are somewhat in tension with each other: the planetary and the global; deep and recorded histories; species thinking and critiques of capital.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 213; references: Edward O. Wilson. 1996. In Search of Nature; Paul J. Crutzen of Anthropocene naming.

“It is understandable that the biological-sounding talk of species should worry historians. They feel concerned about their finely honed sense of contingency and freedom in human affairs having to cede ground to a more deterministic view of the world.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 214.

“The crisis of climate change calls on academics to rise above their disciplinary prejudices, for it is a crisis of many dimensions.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. p. 215.

“Changing the climate, increasingly not only the average temperature of the planet but also the acidity and the level of the oceans, and destroying the food chain are actions that cannot be in the interest of our lives. These parametric conditions hold irrespective of our political choices. It is therefore impossible to understand global warming as a crisis without engaging the propositions put forward by these scientists. At the same time, the story of capital, the contingent history of our falling into the Anthropocene, cannot be denied by recourse to the idea of species, for the Anthropocene would not have been possible, even as a theory, without the history of industrialization. How do we hold the two together as we think the history of the world since the Enlightenment? How do we relate to a universal history of life–to universal thought, that–while retaining what is of obvious value in our postcolonial suspicion of the universal? The crisis of climate change calls for thinking simultaneously on both registers, to mix together the immiscible chronologies of capital and species history.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. pp. 219-220.

“Species may indeed be the name of a placeholder for an emergent, new universal history of humans that flashes up in the moment of the danger that is climate change. But we can never understand this universal. It is not a Hegelian universal arising dialectically out of the movement of history, or a universal of capital brought forth by the present crisis…. Yet climate change poses for us a question of a human collectivity, an us, pointing to a figure of the universal that escapes our capacity to experience the world. It is more like a universal that arises from a shared sense of a catastrophe.” Chakrabarty, Dipesh. 2009. “The Climate of History: Four Theses.” Critical Inquiry. 35(2):187-222. pp. 221-2.

“Take, for example, two very straight forward functional and structural uses of the Global Brain metaphor:

“Function: brains help organisms solve problems; a Global Brain would help the human superorganism solve problems too complex for any lower level of intelligent organization.

“Structure: neurons within neural networks process information in a parallel and distributed fashion transmitting information to connected neurons; this is the same basic structural pattern used by humans to transmit information via the internet.

“We can see these higher order functional properties in problem-solving abilities that transcend the ability of any one person (i.e., sending humans into outer space, constructing large stadiums or buildings), goals and aims that function for collectives of people (i.e., trying to end world poverty or instituting universal education programs), and phenomenal identification with experiences that affect society as a whole (i.e., collectively remembering horrors of World War 2, or collectively imagining a future world with higher possibility for everyone). Moreover, we can see these higher order structural properties in the emergence of large-scale social networking platforms that help people share information for a variety of different purposes (i.e., educational, transportation, hospitality, governance, etc.) in a parallel and distributed form.” Last, Cadell. 2020. “Global Brain: Foundations of a Distributed Singularity.” Korotayev, A.V. & D.J. LePoire (eds.) The 21st Century Singularity and Global Futures. pp. 363-375. doi: 10.1007/978-3-030-33730-8_16. pp. 365, 366.

“Global Brain refers to a phenomenon that has a planetary scale, exhibits system-level structure analogous to brain organization, and emergent brain-like properties (e.g., learning, problem-solving, information processing).” Last, Cadell. 2020. “Global Brain: Foundations of a Distributed Singularity.” Korotayev, A.V. & D.J. LePoire (eds.) The 21st Century Singularity and Global Futures. pp. 363-375. doi: 10.1007/978-3-030-33730-8_16. p. 366.

“In history human societies are composed of competing and cooperating ‘super-entities’ characterized by a specialized division of labor, making it difficult for individual humans to function and reproduce independently of the larger collective. Thus, although humans are of a totally other order than that of eusocial insects in regards to the symbolic medium of thought and communication, we share common superorganism-like cybernetic properties.” Last, Cadell. 2020. “Global Brain: Foundations of a Distributed Singularity.” Korotayev, A.V. & D.J. LePoire (eds.) The 21st Century Singularity and Global Futures. pp. 363-375. doi: 10.1007/978-3-030-33730-8_16. p. 367.

“In the case of its emergence, the Global Brain would be characterized not by the sum of its parts (human individuals and information-communication technologies) but as totally different than the sum of its parts (i.e., a superintelligence consuming the entire field of human activity). Thus, the Global Brain would technically exist everywhere and nowhere: it would be a total planetary phenomenon that is an effect of the collective interactions of human beings interconnected within a technological infrastructure supporting a virtual medium. We can contrast the nature of the Global Brain with the nature of historical ‘super-entities’ like corporations, nation-states, empires or kingdoms, which are not primarily distributed or self-organized but more-or-less controlled from a central location that was easily identified in physical reality.” Last, Cadell. 2020. “Global Brain: Foundations of a Distributed Singularity.” Korotayev, A.V. & D.J. LePoire (eds.) The 21st Century Singularity and Global Futures. pp. 363-375. doi: 10.1007/978-3-030-33730-8_16. p. 368.

“Ephemeralization is a concept that describes processes of reducing physical friction and stigmergy is a concept that describes processes of reducing social friction….

“Ephemeralization (the ability to do more with less) and stigmergy (the ability to reinforce synergistic interactions) are both processes driven by information-communication technologies.” Last, Cadell. 2020. “Global Brain: Foundations of a Distributed Singularity.” Korotayev, A.V. & D.J. LePoire (eds.) The 21st Century Singularity and Global Futures. pp. 363-375. doi: 10.1007/978-3-030-33730-8_16. pp. 369, 370.

“Now if the human system was ever capable of embodying or actualizing these concepts in their full ideality what would be the functional and structural nature of our system?… The hypothesis posited here is that such a system would represent qualities closely associated with the qualities of omniscience, omnipresence, omnipotence, and omnibenevolence.” Last, Cadell. 2020. “Global Brain: Foundations of a Distributed Singularity.” Korotayev, A.V. & D.J. LePoire (eds.) The 21st Century Singularity and Global Futures. pp. 363-375. doi: 10.1007/978-3-030-33730-8_16. p. 372.

“First, Jesus crucified; then, Jesus resurrected. Previously in antiquity, it was the patriarchal family that had been the agency of immortality. Now, through the story of Jesus, individual moral agency was raised up as providing a unique window into the nature of things, into the experience of grace rather than necessity, a glimpse of something transcending death. The individual replaced the family as the focus of immortality.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 58.

“Paul’s vision of the road to Damascus amounted to the discovery of human freedom – of a moral agency potentially available to each and everyone, that is, to individuals. This ‘universal’ freedom, with its moral implications, was utterly different from the freedom enjoyed by the privileged class of citizens in the polis.”

“What Paul did, in effect, was to combine the abstracting potential of later Hellenistic philosophy – in speculations about a universal or ‘human’ nature – with Judaism’s preoccupation with conformity to a higher or divine will. In order to do so, Paul ceases to think of that will as an external, coercive agency.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. pp. 60, 61.

“For there is no doubt that early Christian apologists associated the polytheism of paganism with misuse of the mind and the will. In deifying natural forces and creating local gods, paganism drew attention away from crucial questions about the individual will and man’s God-given responsibility. Even Judaism had fallen into the trap of largely identifying the will with external conformity to the law, which had led Paul, in reaction, to look ‘inward’, to motivation. This Christian awareness of the ‘love of God’ as the source of upright action was intensely practical.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 71.

“By recognizing mendicant orders in order to reach the poor and preserve orthodoxy, the reformed papacy achieved only a partial success. The development of the orders, especially the Franciscans, had a major unintended consequence: it laid the foundations for a radical critique of the role of the church in society, a critique which, drawing on the language of natural rights, began to emerge in the fourteenth and fifteenth centuries.

“Through the idea of natural rights, Paul’s emphasis on ‘Christian liberty’ acquired renewed life and potency. This was a moment of the greatest importance. For it was the moment when the egalitarian moral intuitions generated by the church began to be turned against the church itself, creating misgiving that eventually led to a principled rejection of any coercive or ‘privileged’ role for the church. In this way, these moral intuitions provided the basis for what would become the central project of secularism: the identification of a sphere resting on the ‘rightful’ claims of individual conscience and choice, a sphere of individual freedom protected by law. A commitment to ‘equal liberty’ was emerging from Christian moral intuitions.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 292.

“What stands out from fourteenth-century writings about both church and government is the extent to which the image of society as an association of individuals was gaining ground. It was becoming the shared basis for argument. This image of society had spread from the rhetoric of the ‘care of souls’ into canon and civil law, shaping first of all the claim of papal sovereignty and then the claims of secular rulers to a sovereign authority. By the fourteenth century it was also shaping arguments about the origin and nature of authority as such. The primary unit of subjection to authority was identified as the individual. A corporate conception of society was rapidly waning.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 293.

“While pregnant with further moral development, Judaism remained tribal. By contrast, Christianity held up the prospect of an essentially individual rather than a tribal relationship with divinity. It called individual wills into existence and gave them a glimpse of the transcendent It offered a relationship that informed social life rather than being determined by it. Franciscan arguments implied that neither pagan philosophy nor Judaism could fully emancipate the individual from conventional social roles. Both failed to reach the depths that only humility – illustrated by the life of Francis, who sought to imitate the Christ – could plumb. For Franciscans, that was the significance of the incarnation. The idea of ‘God with us’ linked human agency with a higher agency.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 301.

“Aquinas’ intellectual formation and that of Augustine resulted in each having a very different relationship with ancient philosophy. They had moved in opposite directions.

“Augustine had worked his way through the pagan schools and become dissatisfied with them before he became a Christian. Aquinas, on the other hand, was a believer before he discovered in Aristotle a range of speculation far exceeding that in previous Christian theology. So Aquinas sought to extend and strengthen Christian thinking with the help of ‘The Philosopher’.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 302.

“Ockham moved in that direction [of a ‘direct, intimate relationship between God’s will and individual wills’ that Augustine insisted upon and away from eternal ideas such as Aristotle espoused]. It is true that Aquinas’ references to eternal ideas in the mind of God were nuanced. But they were enough to convince Ockham that Greek rationalism – with its belief in the eternity of the world and essences – posed a threat to belief in God’s freedom as creator. That freedom was at the heart of Ockham’s voluntarist philosophy, the source of his defence of freedom against necessity.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 308.

“… Ockham, like Augustine, denies that intellect and will are entirely distinct faculties. Rather, they are companions. Human agency is a unity. Acts spring from the whole self or soul.

“That is how Ockham recast the role of reason. It is tempting to see his attack on the doctrine of eternal ideas as another stage in the prolonged struggle between polytheism and monotheism, for the rejection of essences and ‘final causes’ bears some resemblance to the attack on belief in ‘demons’ conducted by the early church. Both sprang from an aversion to populating the world with agencies intermediate between God and humans, agencies endowed with purpose or goals. In Ockham’s eyes, belief in such agencies obscured the direct relationship between the Creator and the created.

“That is the background to the principle of explanation associated with his name: ‘Ockham’s razor’. It calls for economy in explanation, avoiding the introduction of unnecessary entities or terms. Sharing with other nominalists the belief that ‘it is futile to work with more entities when it is possible to work with fewer’, Ockham argued that ‘a plurality must not be asserted without necessity’.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 310.

“Rather, ancient philosophers had emphasized fate, pride and shame, an entirely social matrix for morality. They took for granted the privileged life of the citizen in the polis.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 311.

“Ockham drew on the Augustinian tradition which portrayed a descent into the self as leading, paradoxically, to discovery of a higher will. That tradition presented the individual will, when properly directed, as a vehicle of divine agency.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 311.

“Ockham and his followers moved the analysis of causation from the model of ‘rational’ science to that of ‘empirical’ or ‘experimental’ science. In that respect Ockham considered himself the heir of Aristotle, but not an uncritical heir. He took up one type of cause identified by Aristotle – ‘efficient’ causes – and turned it into the paradigm of empirical explanation.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 318.

“Ockham and other nominalists did not renounce reason. Rather, they refined its uses. Their work amounted to a protest against the ‘domestication’ of reality, against a rationalism which claimed to contain God’s activity within a framework of human assumptions and definitions: what has been called ‘Greek necessity’. For Ockham and his followers, such claims to capture the world of experience in a system of essences or final causes was an example of hubris. So if we are to grasp the originality of nominalism, we must look both backward and forward.

“Looking backward, Ockham’s critique of essences and eternal ideas can be seen as the ultimate stage of a war which from its outset the Christian church had waged against polytheism. For polytheism survived as a temptation to multiply the non-material agencies at work in the world, agencies that interposed in the relations between God and man, Ockham wielding his ‘razor’ preserved something of the spirit of that war against ‘pagan’ superstition. Looking forward, there is little doubt that Ockham’s analysis of empirical reasoning – his understanding of causation in terms of regular succession or constant conjunction of events – contributed to developments in the following century which provided the bridge between Aristotle’s physics and modern physics. Ockham’s insistence on the difference between ‘reasons’ and ‘causes’ prepared the way for a kind of Christina positivism, and for the disenchantment of the physical world….

“Ockham would have been dismayed to see how, a few centuries later, his analysis of causation became joined to materialist assumptions directed against theism, a combination he would have dismissed as a new form of rationalist arrogance.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. pp. 319, 320.

“Its [liberalism’s] emergence was the result of a ‘civil war’ in early modern Europe, a war in which ‘liberal’ moral intuitions generated by Christianity were increasingly turned against attempts to ‘enforce’ belief.

“The civil war has distorted our understanding of the relationship between liberalism and Christianity. And that is because the proto-liberal beliefs which had developed within the church by the fifteenth century – the belief in moral equality and a range of natural rights, in a representative form of government and the importance of freer enquiry – only came together when they were deployed against the church’s claim to have a right to ‘enforce’ belief, with the help of secular rulers.

“Mounting opposition to that claim from the sixteenth to the eighteenth century – after the Reformation put an end to confessional unity in Europe – played a crucial part in the birth of modern liberalism. It shaped liberalism as a coherent doctrine directed against the idea of an authoritarian church, whether Catholic or Protestant. Liberalism became a doctrine which paved the way for a far more systematic separation of church and state – that is, for secularism.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 333.

“By the eighteenth century anti-clericalism had become so virulent in parts of Europe that it led to an onslaught on religious belief as such. The result was that liberal secularism in Europe came to be understood as essentially anti-religious. Its roots were interpreted in that light, with the help of the idea of the Renaissance. Any suggestion that the roots might be traced to Christianity became outlandish.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 335.

“But what I am maintaining is that as an historiographical concept the Renaissance has been grossly inflated. It has been used to create a gap between early modern Europe and the preceding centuries – to introduce a discontinuity which is misleading.

“If the fundamental feature of modernity is an individuated model of society – a model in which the individual rather than the family, clan or caste is the basic social unit – then it is important to distinguish that test from other criteria. Celebration of the Renaissance has confused the emergence of what is better called the pursuit of ‘individuality’ – an aesthetic notion – with the invention of the individual – a moral notion. This invention was the product of what philosophers call ‘ontological’ argument, argument about how reality is understood. And that was not the work of the humanists, though they too drew on its achievements. The humanists did introduce a new emphasis on cultivating the self, on the refinement of taste and self-expression. This was an emphasis that shaped what might be called the cult of individuality, depicting the individual as the ‘victim’ of social pressures and heroism as resistance to such pressures. Social institutions were presented as a threat to the self.

“This new sensibility contributed to developments in seventeenth- and eighteenth-century moral philosophy and political theory which are often ‘held against’ liberalism. They encouraged an ‘atomized’ picture of the world, separating the individual from a social context and obscuring the normative developments which had led to the emergence of liberalism. A kind of ‘physicalism’ did, it is true, invade liberal thinking during these centuries. It was reinforced by developments in the physical sciences which placed the individual mind in nature rather than culture, making the test of valid knowledge observable regularities rather than social norms. The philosophical tradition we call utilitarianism turned this into an ‘atomized’ model of society, a model in which individual wants or preferences are taken as given, with little interest in the role of norms or the socializing process.

“There is good reason for considering these later intellectual developments as a liberal heresy, because it deprives liberal secularism of its profoundly moral roots, cutting it off from the tradition of discourse which had generated it. Yet liberalism rests on the moral assumptions provided by Christianity. It preserves Christian ontology without the metaphysics of salvation.

“We have found that the ‘deep’ foundation for the individual as the organizing social role – a status which broke the chains of family and caste – was laid by lawyers, theologians and philosophers from the twelfth to the fifteenth century.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. pp. 337-338.

“The foundation of modern Europe lay in the long, difficult process of converting a moral claim into a social status. It was pursuit of belief in the equality of souls that made the conversation possible. A commitment to individual liberty sprang from that.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 339.

“… this revised view of the role of reason had other important consequences. It helped to reshape understanding of the physical world. It created a sharper distinction between an inner, moral life – ‘wrestling’ with the will – and the processes of the physical world. That emerges clearly in the direction taken by thought in the fourteenth and fifteenth centuries. For these centuries witnessed the almost irresistible spread of Ockham’s nominalist philosophy across Europe….

“Ockham’s emphasis on individual experience and observation as the only legitimate basis of empirical or ‘probable’ knowledge had distinguished such knowledge from deductive or ‘demonstrative’ truth, which did not provide factual knowledge of the world. This separation of two forms of knowledge worked against metaphysical speculation, in particular, ‘natural’ theology. For Ockham, the natural world became instead something to be investigated, in a search for the causes of things. The causes of external events could not, he held, be discovered by a priori reasoning, which produced certainty only in the sense that it drew the consequences of its own assumptions and definitions. This separation of contingent from formal truth created a threshold for much freer thinking.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 342.

“Thus, Ockham’s insistence on the difference between reasons and causes, the latter turning on observable sequences of events, liberated enquiry about the natural world by providing the conceptual basis for distinguishing ‘nature’ from ‘society’. This was a death blow to traditional teleological thinking, for it separated norms and the conditions of human action from the requirements for explaining external, physical events.

“So it was no accident that, by the fourteenth century, previous understanding of the physical world had come under review in the universities. A newly critical approach to Aristotle’s physics developed, an approach which noticed anomalies in the theory by relying on direct observation. The first response was to introduce additional assumptions to account for the anomalies and ‘rescue’ Aristotelian theory. Yet the multiplication of such assumptions in order to ‘save appearances’ gradually raised doubts about the fundamental assumption on which Aristotelian theory was based, that everything in the universe tends to find a resting place, its purpose or ‘final cause’.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 343.

“The idea that motion was as fundamental as rest in ‘nature’ was emerging. By the fourteenth century, it had begun to subvert the ancient model of the cosmos.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 343.

“But these assemblies [Estates-General in France, Cortes in Span, Imperial Diet in Germany] did not fail merely because of their diversity, their clinging to traditional privileges. There was a deeper reason. It was because the new idea of a ‘sovereign’ authority vested in monarchs projected a different image of society, an egalitarian image which now had a popular resonance that it had previously lacked. The appeal of royalty released and reinforced new aspirations. Popular attitudes had changed enough to deprive the traditional corporate model of society of its legitimacy. That is why ‘equal subjection’ to a sovereign was perceived not as loss but as gain. So we have to be careful when speaking of the ‘triumph’ of royalty in the fifteenth century. For, indirectly, it was also the triumph of moral intuitions generated by the church.

“The task of organizing Europe fell to monarchy because its way had been prepared by the church. It was not merely that the royal ambition to acquire a sovereign authority had been shaped by the papal revolution. At the deepest level – the moral and intellectual level – the church had won the struggle for the future of Europe. The church had projected the image of society as an association of individuals, an image which unleashed the centralizing process in Europe.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 346.

“If we look at the word ‘individual’ in historical dictionaries of the English or French languages, we will find that it first became current in the fifteenth century. The word ‘state’, with its stipulation of a sovereign authority, became current at about the same time. And that is no accident, for the meanings of these two words depend upon each other. It was through the creation of states that the individual was invented as the primary or organizing social role.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 347.

“… the Christian conception of God provided an ontological foundation for the individual, first as a moral status, and then, centuries later, as the primary social role. ‘The interiority of Christian belief – its insistence that the quality of personal intentions is more important than any fixed social rules – was a reflection of this. Rule following – the Hebraic ‘law’ – was downgraded in favour of action governed by conscience. In that way, the Christian conception of God provided the foundation for what became an unprecedented form of human society’ Christian moral beliefs emerge as the ultimate source of the social revolution that has made the West what it is.” Siedentop, Larry. 2014. Inventing the Individual: The Origins of Western Liberalism. Harvard UP. p. 353; subquote: Siedentop, Larry. 2000. Democracy in Europe.

“‘Care’ is also a social capacity and activity involving the nurturing of all that is necessary for the welfare and flourishing of life. Above, all, to put care centre stage means recognising and embracing our interdependencies. In this manifesto we therefore use the term ‘care’ capaciously to embrace familial care, the hands-on care that workers carry out in care homes and hospitals and that teachers do in schools, and the everyday services provided by other essential workers. But it means as well the care of activitists in constructing libraries of things, co-operative alternatives and solidarity economies, and the political policies that keep housing costs down, slash fossil fuel use and expand green spaces. Care is our individual and common ability to provide the political, social, material, and emotional conditions that allow the vast majority of people and living creatures on this planet to thrive – along with the planet itself.” Chatzidakis, Andreas, Jamie Hakim, Jo Littler, Catherine Rottenberg & Lynne Segal. 2020. The Care Manifesto: The Politics of Interdependence. London: Verso. pp. 5-6.

“One of the great ironies surrounding care is that it is actually the rich who are most dependent on those they pay to service them in innumerable personal ways. Indeed, their status and wealth are partly signified by the number of people they rely upon to provide constant support and attention, from nannies, house-maids, cooks and butlers to gardeners and the panoply of workers outside their households who service their every need and desire. Yet this deep-rooted dependency remains veiled and denied so long as the very wealthy retain their full sense of agency, having the capacity to dominate or sack and replace those who care for them. However, the affluent project their own dependency onto those they pay to care for them, altering the meaning of dependency to make it synonymous with the economic subordination of those reliant on the paltry wages of caring work, while refusing to admit their own enduring need for care.

“At the same time, in many countries those who should feel most entitled to care, such as the chronically ill, often report punitive humiliation when needing to make claims on the state, as though claimants must always be made to feel bad on some pretext or another.” Chatzidakis, Andreas, Jamie Hakim, Jo Littler, Catherine Rottenberg & Lynne Segal. 2020. The Care Manifesto: The Politics of Interdependence. London: Verso. pp. 22-3.

“Dependence on care has been pathologised, rather than recognised as part of our human condition.” Chatzidakis, Andreas, Jamie Hakim, Jo Littler, Catherine Rottenberg & Lynne Segal. 2020. The Care Manifesto: The Politics of Interdependence. London: Verso. p. 23.

“And that is the problem: academic intelligence offers virtually no preparation for the turmoil–or opportunity–life’s vicissitudes bring.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 36.

“Mayer finds that people tend to fall into distinctive styles for attending to and dealing with their emotions:

“Self-aware. Aware of their moods as they are having them, these people understandably have some sophistication about their emotional lives….

“Engulfed: These are people who often feel swamped by their emotions and helpless to escape them….

“Accepting: While these people are often clear about what they are feeling, they also tend to be accepting of their moods, and so don’t try to change them.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 48: reference: Mayer, John D. & Alexander Stevens. 1993. “An Emerging Understanding.” Unpublished manuscript. Mayer was at the U of New Hampshire.

“The idea of a ‘good cry’ is misleading: crying that reinforces rumination only prolongs the misery. Distractions break the chain of sadness-maintaining thinking; one of the leading theories of why electroconvulsive therapy is effective for the most severe depressions is that it causes a loss of short-term memory–patients feel better because they can’t remember why they were so sad.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 73.

“… depression is a low-arousal state, and aerobics pitches the body into high arousal. By the same token, relaxation techniques which put the body into a low-arousal state, work well for anxiety, a high-arousal state, but not so well for depression.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 74.

“The classical literature in psychology describes the relationship between anxiety and performance, including mental performance, in terms of an upside-down U. At the peak of the inverted U is the optimal relationship between anxiety and performance, with a modicum of nerves propelling outstanding achievement. But too little anxiety–the first side of the U–brings about apathy or too little motivation to try hard enough to do well, while too much anxiety–the other side of the U–sabotages any attempt to do well.

“A mildly elated state–hypomania, as it is technically called–seems optimal for writers and others in creative callings that demand fluidity and imaginative diversity of thought; it is somewhere toward the peak of that inverted U. But let that euphoria get out of control to become outright mania, as in the mood swings of manic-depressives, and the agitation undermines the ability to think cohesively enough to write well….” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. pp. 84-5.

“It is the combination of reasonable talent and the ability to keep going in the face of defeat that leads to success.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 88.

“Being able to enter flow is emotional intelligence at its best; flow represents perhaps the ultimate in harnessing the emotions in the service of performance and learning.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 90.

“And although people perform at their peak while in flow, they are unconcerned with how they are doing, with thoughts of success or failure–the sheer pleasure of the act itself is what motivates them.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 91.

“The spontaneous pleasure, grace, and effectiveness that characterize flow are incompatible with emotional hijackings, in which limbic surges capture the rest of the brain. The quality of attention in flow is relaxed yet highly focused. It is a concentration very different from straining to pay attention when we are tired or bored, or when our focus is under siege from intrusive feelings such as anxiety or anger.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 92.

“A strained concentration–a focus fueled by worry–produces increased cortical activation. But the zone of flow and optimal performance seems to be an oasis of cortical efficiency, with a bare minimum of mental energy expended.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 92.

“Because flow emerges in the zone in which an activity challenges people to the fullest of their capacities, as their skills increase it takes a heightened challenge to get into flow. If a task is too simple, it is boring; if too challenging, the result is anxiety rather than flow.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 93.

“More generally, the flow model suggests that achieving mastery of any skill or body of knowledge should ideally happen naturally, as the child is drawn to the areas that spontaneously engage her–that, in essence, she loves. That initial passion can be the seed for high levels of attainment, as the child comes to realize that pursuing the field–whether it be dance, math, or music–is a source of the joy of flow. And since it takes pushing the limits of one’s ability to sustain flow, that becomes a prime motivator for getting better and better; it makes the child happy.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. pp. 94-5.

“Stern is fascinated by the small, repeated exchanges that take place between parent and child; he believes that the most basic lessons of emotional life are laid down in these intimate moments. Of all such moments, the most critical are those that let the child know her emotions are met with empathy, accepted, and reciprocated, in a process Stern calls attunement….

“Attunement occurs tacitly, as part of the rhythm of relationship…. He finds that through attunement mothers let their infants know they have a sense of what the infant is feeling. A baby squeals with delight, for example, and the mother affirms that delight by giving the baby a gentle shake, cooing, or matching the pitch of her voice to the baby’s squeal… Such small attunements give an infant the reassuring feeling of being emotionally connected, a message that Stern finds mothers send about once a minute when they interact with their babies.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 100; reference: Stern, Daniel. 1987. The Interpersonal World of the Infant. Basic Books.

“Prolonged absence of attunement between parent and child takes a tremendous emotional toll on the child. When a parent consistently fails to show any empathy with a particular range of emotion in the child–joys, tears, needing to cuddle–the child begins to avoid expressing, and perhaps even feeling, those same emotions. In this way, presumably, entire ranges of emotion can begin to be obliterated from the repertoire for intimate relations, especially if through childhood those feelings continue to be covertly or overtly discouraged….

“Indeed, several theories of psychoanalysis see the therapeutic relationship as providing just such an emotional corrective, a reparative experience of attunement. Mirroring is the term used by some psychoanalytic thinkers for the therapist’s reflecting back to the client an understanding of his inner state, just as an attuned mother does with her infant.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. pp. 101-2.

“… the emergence of a crucial emotional aptitude: the ability to know another’s feelings and to act in a way that further shapes those feelings. Being able to manage emotions in someone else is the core of the art of handling relationships.

“To manifest such interpersonal power, toddlers must first reach a benchmark of self-control, the beginnings of the capacity to damp down their own anger and distress, their impulses and excitement–even if that ability usually falters. Attunement to others demands a modicum of calm in oneself…. Thus handling emotions in someone else–the fine art of relationships–requires the ripeness of two other emotional skills, self-management and empathy.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 112.

“One key social competence is how well or poorly people express their own feelings. Paul Ekman uses the term display rules for the social consensus about which feelings can be properly shown when….

“There are several basic kinds of display rules. One is minimizing the show of emotion–this is the Japanese norm for feelings of distress in the presence of someone in authority…. Another is exaggerating what one feels by magnifying the emotional expression…. A third is substituting one feeling for another; this comes into play in some Asian cultures where it is impolite to say no, and positive (but false) assurances are given instead.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 113; reference: Ekman, Paul & Wallace Friesen. 1975. Unmasking the Face. Englewood Cliffs, NJ: Prentice Hall.

“The more adroit we are socially, the better we control the signals we send; the reserve of polite society is, afer all, simply a means to ensure that no disturbing emotional leakage will unsettle the encounter (a social rule that, when brought into the domain of intimate relationships is stifling).” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 115.

“The degree of emotional rapport people feel in an encounter is mirrored by how tightly orchestrated their physical movements are s they talk–an index of closeness that is typically out of awareness. One person nods just as the other makes a point, or both shift in their chairs at the same moment, or one leans forward as the other moves back…. Daniel Stern found in watching the synchrony between attuned mothers and their infants, the same reciprocity links the movements of people who feel emotional rapport.

“This synchrony seems to facilitate the sending and receiving of moods, even if the moods are negative. For example, in one study of physical synchrony, women who were depressed came to a laboratory with their romantic partners, and discussed a problem in their relationship. The more synchrony between the partners at the nonverbal level, the worse the depressed women’s partners felt after the discussion–they had caught their girlfriends’ bad moods. In short, whether people feel upbeat or down, the more physically attuned their encounter, the more similar their moods will become.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 116; reference: Ekman, Paul & Wallace Friesen. 1975. Unmasking the Face. Englewood Cliffs, NJ: Prentice Hall.

“In general, a high level of synchrony in an interaction means the people involved like each other.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 116.

“In short, coordination of moods is the essence of rapport, the adult version of the attunement a mother has with her infant. One determinant of interpersonal effectiveness, Cacioppo proposes, is how deftly people carry out this emotional synchrony. If they are adept at attuning to people’s moods, or can easily bring others under the sway of their own, then their interactions will go more smoothly at the emotional level. The mark of a powerful leader or performer is being able to move an audience of thousands in this way. By the same token, Cacioppo points out that people who are poor at receiving and sending emotions are prone to problems in their relationships, since people often feel uncomfortable with them, even if they can’t articulate just why this is so.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 117; reference: Cacioppo, John. Social psychophysiologist at Ohio State U.

“Setting the emotional tone of an interaction is, in a sense, a sign of dominance at a deep and intimate level: it means driving the emotional state of the other person. This power to determine emotion is akin to what is called in biology a zeitgeber (literally, ‘time-grabber’), a process (such as the day-night cycle or the monthly phases of the moon) that entrains biological rhythms. For a couple dancing, the music is a bodily zeitgeber. When it comes to personal encounters, the person who has the more forceful expressivity–or the most power–is typically the one whose emotions entrain the other. Dominant partners talk more, while the subordinate partner watches the other’s face more–a setup for the transmission of affect.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 117.

“Apart from children who are spurned because they are bullies, those whom other children avoid are invariably deficient in the rudiments of face-to-face interaction, particularly the unspoken rules that govern encounters. If children do poorly in language, people assume they are not very bright or poorly educated; but when they do poorly in the nonverbal rules of interaction, people–especially playmates–see them as ‘strange,’ and avoid them. These are the children who don’t know how to join a game gracefully, who touch others in ways that make for discomfort rather than camaraderie-in short, who are ‘off.’ They are children who have failed to master the silent language of emotion, and who unwittingly send messages that create uneasiness.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. p. 122.

“Social ineptitude is perhaps most painful and explicit when it comes to one of the more perilous moments in the life of a young child: being on the edge of group at play you want to join. It is a moment of peril, one when being liked or hated, belonging or not, is made all too public….

“The two cardinal sins that almost always lead to rejection are trying to take the lead too soon and being out of synch with the frame of reference. But this is exactly what unpopular children tend to do: they push their way into a group, trying to change the subject too abruptly or too soon, or offering their own opinions, or simply disagreeing with the others right away–all apparent attempts to draw attention to themselves. Paradoxically, this results in their being ignored or rejected. By contrast, popular children spend time observing the group to understand what’s going on before entering in, and then do something that shows they accept it; they wait to have their status in the group confirmed before taking initiative in suggesting what the group should do.” Goleman, Daniel. 2005. Emotional Intelligence: 10th Anniversary Edition. NY: Bantam. pp. 123-4.

“Thus, the committee’s overarching recommendation is that the most effective leveraging of investments would come from a coordinated, interagency effort to encourage the emergence of a New Biology approach that would enunciate and address broad and challenging societal problems. The committee focused on examples of opportunities that cannot be addressed by any one subdiscipline or agency-opportunities that require integration across biology and with other sciences and engineering, and that are difficult to capitalize on within traditional institutional and funding structures. Fully realizing these opportunities will require the enabling of an integrated approach to biological research, an approach the committee calls the New Biology.” Committee on a New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. 2009. A New Biology for the 21st Century. Washington, D.C.: The National Academies Press. pp. 2-3.

“The careful work of biologists over millennia has produced a massive body of observations that illustrate a vibrant, intricate, causally complex world, in which products depend on processes, processes depend on products, wholes depend on parts, parts depend on wholes, and living beings depend on one another for our lives. The widespread interest in and acknowledgment of the interrelatedness of natural phenomena in biology thus creates the illusion of a coherent view of interdependence.

“Still, I contend, the ascendant view of interdependence at play in biology–as in popular culture–is not a view of interdependence at all. It remains a view of independence. By and large, we think that interdependence just means ‘independent objects interacting.’ We say that things interact strongly, weakly, reciprocally, sequentially, and so on, but their ultimate independence from one another remains intact.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 1-2.

“To get to a thoroughgoing view of interdependence, I argue that a second shift is required: one from considering things in interaction to considering things as mutually constituted, that is, viewing things as existing at all only due to their dependence on other things.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 2.

“However, it is as reasonable to ask, ‘How do new things come into being for organisms?’ as it is to ask, ‘How did new senses evolve?’ In other words, when cells begin to sense sugars, a new ‘thing’ comes into being for the cells. In a specific and important sense, the sugar did not exist as a thing before cells started to interact with it. Thus, organisms could be seen as ‘thing makers’ in a world that is not necessarily full of things prior to the thing-making activities of organisms.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 10.

“The dynamic, intricate, highly interdependent and highly ordered processes that give rise to the term ‘flower’ over and over again are precisely what make flowers appear so obvious, vivid, and stable as objects. The dubious essentialist assumption is thus a relatively simple one: it is that obviousness, vividness, and stability are properties that somehow inhere in objects, instead of experiences that arise at the nexus of active living bodies, percepts, and values. An alternative approach would be to carefully detail the processes by which objects come into being as objects–that is, as continuous, discrete, vivid, and efficacious–contra the essentialist assumption that continuity, discreteness, and so forth are properties that somehow inhere in objects.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 14.

“These are some of the general features of contingentism:…

“2. Contingent existence means existing dependent on other contingently existing things.

“3. Things exist contingently–dependent on other things, including, for example, observers that relate to them as things.

“4. Critically, however, observers themselves exist contingently (dependent themselves on bodily organization, objects, and lives) and do not exist inherently.

“5. If everything exists contingently, nothing exists inherently.

“6. Thus, the thoroughgoing interdependence of things and their lack of inherent existence are simply two sides of the same coin.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 15.

“Rather, contingentism is an attempt to understand reality in a way that accounts for the full interdependence of perceivers and perceived phenomena–which means, necessarily not taking either of them to be intrinsically existent.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 17.

“Indeed, the very idea of emergence suggests a kind of becoming, something appearing where it had not been present before. So when parts come together, it can seem like something novel emerges–hence the ‘greatness’ of the whole relative to its parts. Whatever is happening in this shift from an assemblage of parts to a greater whole, it is not necessarily a shift within the thing. It is a shift in perception, when the observer begins to relate with a whole as a whole. A clay pot may have different properties from individual clay particles, such as structure, semipermeability and curvature, such that that [sic] it can hold liquids. To say that these properties emerge at a larger scale is a kind of metaphor with the connotation that the clay particles themselves, when aggregated in a particular way, acquire a novel state. What has happened, however, is that observers experience clay pots as having different qualities from clay particles just because they now relate to a clay pot as a whole. If the clay pot were not related with as a whole, no ‘emergent’ property of structure, semipermeability, or curvature would be noted at all.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 26-7.

“A cause is never itself available to observation, but is rather an inference that is drawn after making repeated observations.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 30.

“In sum, knowledge validation is a set of intricate processes–none of which points to the existence of inherently existent objects, but all of which point to how objects come into being dependent upon these processes of sensory and social coordination. One such process is coordination among various bodily movements and sense perceptions, which greatly enhances the vividness of objects and increases our conviction of their self-presentedness. Another process is coordination between social members, where continuously enacted and interacted perceptual consensus mark which of the many and diverse experiences that arise throughout our lives count as ‘the real world.’” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 36-7.

“Thus, depending on one’s conceptual framework and explanatory goals, the responsiveness (or reactivity, activity, irritability, dynamism, behavior, and so forth) of cells can be thought of as an instantiation of some more general principle. For example, as suggested in the preceding list, cellular responsiveness is a kind of chemical reaction, or a kind of behavioral response, or a kind of information processing.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 48.

“We generally think of chlorophyll as involved in plants using light in this way, but not in sensing light, and certainly not in seeing light.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 52.

“The trick with the concept of signal transduction and of an object called a transducer is that it stabilizes the sense that whatever stays outside is different from what comes inside. To express this in more ‘process’ terms, whatever happens outside is not the same as what happens inside. A sugar that does not cross a cell membrane but binds a receptor (or sensor) on one side of the membrane is radically different from the changes in the receptor’s conformation following the binding, the chemical cascade initiated by the conformational change, and the cell locomotion that results from the cascade. We might ask, ‘What makes the magic happen? What is in the ‘black box’ of the transducer that keeps the external world on the outside, yet produces some effect on the inside?’

“There are many kinds of ways in which molecules come into cells: through ion channels, by binding to transporter proteins, by being incorporated into vesicles, and by diffusing through the membrane. In all of these processes, there is the sense that whatever was outside of the cell is the same as whatever comes into the cell. Interestingly, this may be true even in cases where a substance is modified in its entry into the cell, for example, in the case of certain glucose transporters that add a phosphoryl group to a glucose molecule as it enters the cell, thus creating glucose-6-phosphate. Glucose was a thing on the outside of the cell, and what enters the cell is the same thing, slightly changed.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 54.

“Why do we not see sensing as a process of assimilation [as chlorophyl’s absorption of life for growth] as well? Sensing is, after all, also a process that constitutes and builds organisms.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 55.

“However, in a nontrivial sense, the apple really does become a part of my body [upon looking at it]; upon seeing it, my physiology is not the same. Moreover, this act of seeing itself is not strictly a response to what is outside of me…. I am also responding to my own prior experiences, where this experience of ‘apple’ is not at all experienced as unique and unrepeated but is related to past experiences of apples (my stomach gives an involuntary turn and my throat constricts without warning, as my body re-experiences an apple I ate once–along with the worm in it). All of this arises from seeing what is ostensibly radically outside of me.

“The intuition that ‘information’ exists intrinsically and is transferred between things without itself being changed is part of what both creates and perpetuates the idea of sensing as ‘not assimilation.’” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 56.

“To return to the original motivating question of this discussion, do plants (merely) use light for energy, or do they sense light? These processes are only held in contrast with one another if one assumes that in the first case, the light is made the same as the organism, and in the second case, the light is kept separate from (outside of) the organism yet produces a change in the organism. That such divisions are commonly made reflects a long history in biology and cognitive science of taking bodily processes to be not only radically different from but also lower than cognitive processes.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 57.

“… we say that there are changes in the forms of energy–from light energy to chemical energy, in this case [when an electron absorbs a photon]–but continuity of energy itself. This is analogous to the idea that an object can change form, but remain the same object: It is assumed that energy can change form but remain the same energy. If energy is considered a substance, then this is a kind of essentialism. However, if energy is considered a number, there is no essentialism. The number is contingently existent, dependent on an observer to bound the system a certain way.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 59.

“If we see the world as things, objects will be ‘the same substance over time undergoing changes in form,’ and energy will be ‘what causes changes in object-forms.’ If we see the world as energy, energy will be ‘the same substance over time undergoing changes in form’, and objects will be ‘what cause changes in energy-form’ (for example, retinal molecules or solar panels which change light energy to chemical energy). In either case, the confusion is created by thinking of energy and form as separable from one another, when they are not. The relationship between energy and form can therefore be understood coherently only in contingentist terms.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 59.

“In the standard signal transduction account, ‘sensing and responding’ means ‘undergoing an ordered set of chemical reactions’–a signal transduction event. On the other hand, ‘sensing and responding’ can also mean ‘perceiving and acting–something that whole organisms (and not mere chemicals) are said to do. “Sensing and responding’ is thus a metaphor with two senses. In one use of the metaphor, sensing and responding is like materials undergoing transformation in a chemical reaction (like iron reacting with oxygen and transforming to rust, a physical-chemical phenomenon). In another use of the metaphor, sensing and responding is like unified agents with choice perceiving and acting (like our own experience of perceiving an intersection and deciding to go left or right, a psychological-behavioral phenomenon). In short, the metaphors we have for describing signal transduction are the physical language of objects causing transformation in other objects (chemical reactions), and the psychological language of agents sensing, deciding, and behaving (biological responses).” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 60.

“A similar cognitive process [to organisms’ reacting to a molecular signal versus assimilating a molecular feedstock] occurs in linking smaller-scale and larger-scale phenomena. A whole is caused by, or depends upon, its parts. Without the parts, there is no whole. Wooden chairs depend upon wood itself, copper wires depend upon copper atoms, cells depend upon molecules, and animals depend on cells. Yet, in the contingentist view, there is no link between the smaller-level and the larger-level phenomena, except for the cognitive process of linking the two. Whenever we observe a whole, we can always dissect it and discern an often predictable set of parts. Still, the assemblage of parts doesn’t somehow make the whole happen. That is, the parts have no inherent power to bring about the whole. This point was also discussed in a different context in the previous chapter, where the concept of ‘emergent properties’ as analyzed. The whole has different properties from the parts, yes, but not because some novel property intrinsic to the new whole suddenly emerges from the assemblage of parts. Rather, it is because a whole is related with as a whole that it is observed to have particular properties that are not present when it is related with as a set of parts.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 61.

“The idea of a ‘biological response’ in contrast to (mere) ‘chemical reactions’ is quite interesting because it is where the idea of agency arises in biological accounts. Agency is considered a kind of ‘larger-scale’ or higher-level phenomenon, contrasted with the smaller-scale and deterministic chemical reactions. Agency is the sense that an entity can make something happen in the world without itself being made to happen. We say a person has agency when she freely chooses, for example, the direction in which she will place her next step, where ‘freely chooses’ means that she was not somehow made (coerced, influenced, determined) to take that step in that direction. Agency is thus a kind of causal account–and, as it now familiar, a contingentist view of causal accounts does not involve anything making anything happen in the world.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp.62-3.

“The question of determinism versus agency has held Western philosophy in thrall for centuries, but this does not mean that biology needs to somehow answer that problem–or rather, it does not mean that biology even has to accept it as a problem. Biologists have taken on the problem or seen it as a compelling one, but this is not a necessary endeavor. The problem of determinism versus agency does not arise as a problem within a contingentist framework, just because neither agents nor causal powers are taken to be intrinsically existent from the start. If agency and causation have a place in contingentist accounts, it is as a pragmatic matter of being able to give more or less satisfying causal accounts, not as a self-presented problem of how and where agency has arisen from an otherwise deterministic universe.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 63-4.

“If a living organism is not quite like the physical idea of an assemblage of chemical reactions, and not quite like the psychological idea of the unified behaving agent, then what else is it like? Because physical and psychological metaphors depend upon one another and operate in opposition to one another, there are various ways in our language of relating them with the use of various prepositions. Life is considered what is either both physical and psychological, in between the physical and the psycholgical, either physical or psychological, in between the physical and the psychological, either physical or psychological, or transformed from the physical into the psychological (or vice versa). Another metaphor for life may also be that which is beyond the physical and psychological altogether. By ‘beyond,’ what is suggested is not the sense of somehow ‘independent of,’ but simply the sense that biological phenomena do not have to operate only in relation to this dichotomy, even if to mediate between them.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 65.

“The ‘reactivity’ view suggests that organism and environment are transformed simultaneously, and at each moment.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 67.

“The organism, sensing apparatus, and external object do not interact with or react with one another (that is, they do not cause changes to each other by virtue of some intrinsically existent causal power). Neither do they remain the same objects that change (or are transformed) over time. Rather, they arise new in each instant.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 68.

“One narrative of grief is that one day we will ‘go back to feeling like our old selves again.’ But the experience of grief can also reveal that afer the loss of a loved one, one is not the same. ‘A contingentist account,’ so to speak, of grief and its healing might not advocate for the return to an intrinsically existent self, but for a recognition that, yes, the self will now have to be made anew–as it always has been.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 78.

“Even vast swaths of what is ostensibly your own life are utterly opaque to you–everything from gestation through infancy, and the countless unconscious processes that allow you to live at all. To the extent that we think that this is what it means to know what is–to experience the sum of all theoretically possible experiences–of course, we will always fall short. This ‘theoretically possible,’ this imagined space, then keeps us separate from what is. We are then likely to see ourselves as beings with inherently limited knowledge in a world populated by the same infants who experience bottomless abandonment when they’re left alone in a room, rodents who eat their young when their scent is changed, and baffled goldfish swimming around the same little bowl.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 95-6.

“Considering the myriad things upon which our knowledge depends, we may feel trapped, doomed: ‘Help! I can’t get out of my body, my senses, my thoughts, my language, my culture, my society, my environment!’ But we can ask ourselves, was it supposed to be some other way? Aren’t these exactly what allow anything at all to happen for us? Don’t our experiences depend completely upon these? Another possible response is, ‘Thank goodness! Here are my body, my senses, my thoughts, my language, my culture, my society, my environment! And therefore, here I am, here it all is!’ In other words, instead of experiencing these processes as constraints upon some abstract and imaginary theoretical space–a picture that, despite good intent and limited usefulness, becomes easily reified and used to torture ourselves and others into both lifelong separation from and desperation for the really, really real world–we can experience these processes as precisely what allow us to live and to live in a world that is, yes, plenty vast, plenty vivid, and changing endlessly as the processes themselves change.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 97.

“This book thus far has been a reckoning with many absences:

“the absence of referents independent of terms,
“the absence of objects independent of perceptions,
“the absence of essences within things,
“the absence of causal powers between regularities,
“the absence of subjects independent of experiences and actions,
“the absence of laws independent of concepts and cognitive consonances, and
“the absence of gaps between subjects and reality independent of the experience of such.

“There is also the absence of absence itself, insofar as ‘absence’ is itself a term which brings us full circle back to the absence of referents independent of terms. That is, there is no intrinsically existent referent to the term ‘absence’….” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 99.

“Objects exist as objects dependent on subjects and processes. Subjects through perceptual-conceptual-behavioral processes (sensing, feeling, thinking, acting) unify phenomena and differentiate them from other phenomena, thus giving rise to objects….

“Perceptual-conceptual-behavioral processes exist dependent on subjects and objects. Subjects narrate these processes as links between themselves and objects from which they are separate. A complex network of terms and concepts (‘object,’ ‘energy,’ ‘information,’ ‘form,’ ‘transformation,’ ‘ assimilation’, ‘transduction’) sustains both the sense of separateness of objects from subjects and the sense of interaction of objects with subjects.

“In short, not the object or the subject or the process that links them is firm ground. None of them exists intrinsically, so none of them can be the fundamental support for the others. Their stability arises precisely from their interdependence–they keep each other in place contingently.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 100.

“Like all scientists, biologists seek patterns and describe them. Patterns relate to other patterns, and biology becomes an increasingly intricate, beautiful, regular, and dense net of relationships. It is easy to imagine that the net is grounded somewhere…. it is easy to assume that the dense net of experiences is anchored somewhere–in a world of objects, or in a body, brain, or soul. We often believe that the regularities we experience must be grounded in some kind of substance beyond them–material, spiritual, or mental. However, it is entirely possible that the net is aloft, that it is not tethered to anything outside of it. In fact, as far as anyone can tell, the net is all there is, so there can be nothing outside of it that could serve as a tether.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 100-1.

“Why ‘contingentism,’ when other terms have already done a great deal of work detailing the interdependence of objects and subjects? After all:

“Doubtfulness about the status of truth claims as correspondence to intrinsically existent categories is already ‘skepticism’ (Sextus Empiricus, Pyrrho).

“Justification of claims and practices with reference to their usefulness (instead of with reference to correspondence to any intrinsically existent category) is already ‘pragmatism’ (William James, Richard Rorty).

“The interpenetration of parts and wholes is already ‘dialectics’ (Karl Marx, Richard Lewontin, Richard Levins).

“The specific tracing of the coming-into-being of things at the nexus of myriad occurrences is already ‘genealogy’ (Friedrich Nietzsche, Michel Foucault).

“The co-construction of object and subject is already ‘constructivism’ (Ludwik Fleck, Barbara Herrnstein Smith).

“The process by which objects and subjects come into being at all is already “ontogenesis’ (Gilbert Simondon).

“The ‘bringing forth of a world by living’ is already ‘autopoeisis’ (Humberto Maturana, Francisco Varela, Evan Thompson).

“The development of organisms as contingent and inseparable into intrinsically existent categories like ‘nature’ and ‘nurture’ is already ‘developmental systems theory’ (Susan Oyama).

“The refusal to reify the difference between matter and mind is already ‘nondualim’ or ‘dependent arising’ (Nagarjuna, Jay Garfield).

“The analysis of metaphysical entities to reveal what they themselves depend on is already ‘deconstruction’ and ‘rhizomatics’ (Jacques Derrida, Gilles Deleuze).

“The absence of an intrinsically existent fundament upon which all else depends is already ‘irreductionism’ (Bruno Latour).

“What, then, is the use of ‘contingentism’ in this already large family of terms?

“First, ‘contingentism’ is one way of bringing the family together by emphasizing an important common thread between them (a family resemblance, perhaps)….

“Second, by drawing attention to this common thread of mutual dependence, we can see its relative simplicity. To put it very simply: Yes, everything does depend. and by everything, we mean everything, without remainder….

“Third, and finally, ‘contingentism’ also suggests natural alliances with the biological sciences. There are already several concepts of contingency-as-dependence in circulation in biology:

“1. Soil and sun produce grass, which is eaten by deer, who are eaten by wolves. All of these are decomposed by microbes, which make nutrients available to grass. Living beings depend on each other and on nonliving factors in order to continue living. This is an example of the interdependence of living beings, and of living beings and nonliving entities, or ecological interdependence.

“2. An enzyme is produced dependent upon the presence of the molecule that it cleaves. The enzyme lactase, for example, is produced in the presence of the sugar lactose, which it digests. When the lactase has cleaved all of the lactose, it is no longer produced, thereby effectively ‘shutting off’ the cycle. This is an example of the interdependence of products and processes, or regulatory interdependence.

“3. A cell population metabolizes and excretes chemicals in a way that acidifies the local environment, producing changes in the composition of the cells themselves. A smaller-scale entity influences a larger-scale entity, which in turn influences the smaller-scale entity. This is an example of the interdependence of parts and wholes, or hierarchical interdependence. This kind of interdependence is also at play in human and animal physiology, and in the medical sciences–for example, the heart circulates blood throughout the entire body, which in turn provides oxygen and nutrients to the heart.

“To this (nonexhaustive) set, the use of contingency employed in this book adds and explores a fourth type of interdependence, one which has historically not been emphasized in most biological accounts. This is mutual constitution, or ontological interdependence–the view that things only exist as things dependent upon other things.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 101-3.

“Many biologists are ecological thinkers, acknowledging the constant interaction of organisms and environments, and their close interdependence. Standard interactionism, however, divides the world into objects and subjects, and then says, ‘They’re always interacting.’ This division need not necessarily be taken as an inherently existing prior. Contingentism in the sense of ontological interdependence is a more thoroughgoing ecological worldview, one that acknowledges the total interdependence of phenomena, and thus the absence of the inherent existence of either subject or object, either organism or environment. In this sense, contingentism simply follows down the full implications of a way of thinking that is already familiar to many biologists.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. p. 103.

“There are two common ways of compartmentalizing mystery so that it doesn’t enter our comfortable, predictable, everyday world. One is to put it in the realm of ‘inexplicable things that no one will every know,’ as dualists tend to do. Another is to put it in the realm of ‘currently inexplicable things that we may know some day in the future,’ as physicalist monists tend to do. Both approaches take the mystery out of mundane existence, the latter by eliminating it altogether, the former by relegating it to a separate, sacred sphere.

“But we do not need to separate the material from the mystical, nor do we need to eliminate either the material or the mystical from existence. The material world and the mystical world could be exactly the same place in every respect. For one, the world of cold, unfeeling, and inanimate matter is already vibrantly animated by our instinct that matter is, by itself, capable of being cold, unfeeling, and inanimate.” Sharma, Kriti. 2015. Interdependence: Biology and Beyond. NY: Fordham UP. pp. 104-5.

“There is a further crucial feature of the religions in this situation of multiple overwhelming. Most of them are themselves about being overwhelmed–by God (or however we name the transcendent present to humanity); by revelations and imperatives from beyond ourselves which invite us into radical transformation; by worship, prayer, meditation, service, and other activities which call for all we have and are. They have centuries of premodern experience in coping with being overwhelmed in multiple ways–not only by God, but also by other overwhelmings that have always been part of the human condition, such as disease, famine, war, wickedness, sexual passions, love of money, fame and power, overdrinking and overeating; and, among the more positive overwhelmings, by the passionate pursuit of beauty, truth, and goodness.” Ford, David F. 2013. Theology: A Very Short Introduction, 2nd Edition. Oxford UP. p. 9.

“Two core criteria [of good theology and theologians] are wisdom and creativity….

“Four elements in particular might be seen as a sort of ‘DNA’ of the best theology:

“1. Wise and creative retrieval of the past….

“2. Wise and creative engagement with God, church, and world now….

“3. Wise and creative thinking….

“4. Wise and creative expression.” Ford, David F. 2013. Theology: A Very Short Introduction, 2nd Edition. Oxford UP. pp. 11, 12.

“As I look around in Europe, North America, China, and elsewhere at what I would consider examples of ‘best practice’ in universities and colleges, the advantage seems to be with those which try to combine theology and religious studies–or, even better, refuse to recognize any simple splitting of the field into two. What seems to be happening is that in the best centres of religious studies they do not now usually pretend that a scholar can neutrally stand nowhere. They also see that it is arbitrary to draw a line which says that in the academic study of religion you may not pursue questions of truth and practice beyond a certain point. Once this is granted, then religious studies must allow scope for intelligent faith leading to constructive and practical theologies.” Ford, David F. 2013. Theology: A Very Short Introduction, 2nd Edition. Oxford UP. p. 15.

“In the best centres of theology a complementary movement in the other direction can be seen. They recognize that, if God is really related to the whole of reality, then they need to engage with not only what usually comes under religious studies but also with many other disciplines–such as economics, medicine, the natural sciences, law, and the creative arts. The great questions of beauty, truth, and practice in theology need to be informed as thoroughly as possible by a range of disciplines.” Ford, David F. 2013. Theology: A Very Short Introduction, 2nd Edition. Oxford UP. p. 16.

“In the seventeenth century–the century of the ‘Scientific Revolution’–the public reception of science, natural philosophy as it was then, was decidedly hostile.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 1.

“…we see how the question of the unity of science was a pivotal issue from the beginning of the nineteenth to the middle of the twentieth century, and how in crucial respects it represents a failed attempt to recapture a notion of unity that collapsed with the demise of a pre-modern idea of Christian unity of understanding.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 9.

“…we need to realize that it was not science as a model of truth that placed it at the centre of modern culture, but science as a model for the future.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 9.

“The association of science and civilization, crucial to the standing of science in the modern era, would simply not be possible without popular science–popular natural history books, children’s science books, museums, science fiction–because science doesn’t have the resources to effect this association in its own right. In order to meet the expectations of the vastly expanded role that it had assumed from the end of the eighteenth century, one in which it was displacing religion as the key to understanding our place in the world for example, it was crucial that science be extended into the non-propositional realm, engaging with the world in terms of desires, expectations, anxieties, fears, hopes, goals, raw beliefs, etc. Only popular science could do this, but it could never have just been a promotional exercise, however much scientists may have wished for this. It raises both expectations and anxieties about the standing of science in the modern era.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 14.

“‘Civilization’, for example, shifts in the late eighteenth century from something atemporal to something that, like science, progresses over time by stages; and, for reasons that have to do with its standing as a bearer of civilization, the understanding of ‘science’ comes to incorporate technology in the early decades of the nineteenth century, only for attempts to be made to dissociate technology form science in the wake of the First World War.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 19.

“Civilization itself, in anything resembling a modern understanding, is a relatively recent idea, and it appears at much the same time in the commercial societies of France and Britain. There had been no word for ‘civilization’ in Latin (Leibniz uses the term cultus as an antonym for barbarism but it hardly corresponds in meaning), or in the European vernaculars before the second half of the eighteenth century. Moreover, what had traditionally been the contrast class for civilization, namely barbarism, was thought of in a rather different way prior to then…. The contrast was between the demands of Christianity and barbarism, and the role of classical education was to bolster the former….

“The association with Christianity is retained in an early appearance of the term ‘civilisation’ in French, in 1756 in Mirabeau’s L’Ami des hommes.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 23.

“Science’s claim to universality is different from its claim to progress in a crucial respect. Progress is a distinctively Enlightenment notion. Christianity had made no claims to progress, and the notion was alien to it. By contrast, universality had been a cornerstone of medieval Christianity, and a claim to universality had been central to the standing of Catholicism from the Reformation onwards. By the eighteenth century, it had become central to the standing and legitimacy of science. Unlike in the arts, where one can appreciate wide diversity, and correlatively where on can grasp and see the point of different kinds of aesthetic judgement, the value of scientific laws is unvarying and absolute.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 46-7.

“With regard to the question of progress, the critical characteristic of science is that it undergoes a type of development that is quite different from that in the arts, one that comes to be central to the understanding of civilization. It exhibits cumulative progress, whereas the arts do not….” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 49.

“The Greek ages were divided into the gold, silver, copper, and earthen, while the biblical myth offers a stadial understanding of history along the lines of perfection, fall, and redemption.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 50.

“One significant feature of the reception of Darwin in the East was that the Western notion of a conflict between science and religion was not exported.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 66.

“With the demise, in the thirteenth century, of a Christian-Platonist conception of the world that had integrated the natural and the supernatural, the organizing thread was ripped out of the natural realm. It was with this epochal separation of the natural and the supernatural that modernity began to emerge in the Christian West. The aftershock was felt for centuries, and John Donne’s 1611 lament for a pre-mechanical world. ‘Tis all in pieces, all coherence gone’, captures the continuing sense of loss of unity of understanding that marks out the modern era.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 77.

“It is not that there is a unity of science, it is that there must be a unity of science [in the nineteenth century].” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 79.

“The term ‘scientist’… was not generally adopted until the early decades of the next century, being the subject of an inconclusive debate in Nature as late as 1924. In the nineteenth century the resistance was significant, in part because as Richard Yeo notes, ‘some of the important men of science, such as Michael Faraday and T.H. Huxley, preferred to think of their work as part of broader philosophical, theological, and moral concerns’.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 81; reference: Yeo, Richard. 1993. Defining Science: William Whewell, Natural Knowledge and the Public Debate in Early Victorian Britain. Cambridge. p. 5.

“We must also bear in mind that in the nineteenth and early twentieth centuries science was increasingly seen by many as an alternative to religion (i.e. to Christianity)…. But the unity of science did not just provide a means of bringing a comprehensive ordering to scientific understanding for those who saw its replacement of religion as legitimate. It was also crucial for those who believed that such replacement was illegitimate. For such critics, it was important to establish the unity of science as a form of understanding that had strict limits, and to secure the boundaries of scientific understanding, preventing it from straying beyond these limits. In both cases, the unity of science lay at the core of the understanding of science in the nineteenth century, binding together cultural, political, religious, and technical issues in a distinctive fashion, one that bears directly on the question of how the relationship between science and civilization was envisaged.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 94.

“In particular, once we take seriously the roles of experimental practice, and the role of models–particularly physical, experimental models–it becomes evident that physical enquiry deploys a range of explanatory resources that fail to fit into the category of theory. At the same time, because reduction programmes tend to work in terms of the reduction of one kind of theory to a more ‘fundamental’ kind, the fact that theories do not remotely exhaust–and in some cases do not even capture–what physical enquiry and physical explanation consist in, means that reduction as traditionally conceived is simply not an appropriate or fruitful way to think about the relationship between the various forms of physical enquiry….

“…from the seventeenth century onwards, there have always been forms of experimental investigation that have been independent of theoretical enquiry.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 104, 105.

“In the early 1840s, he [James Joule of electrical theory fame] had moved from the role of ‘ingenious inventor’ to that of ‘experimental natural philosopher’, and the transition illustrates the gap between a practical, and in an important respect extra-scientific, interest in machinery and a scientific one. His first publication, in 1838, was a proposal for an engine powered by electromagnetism, and appeared in a magazine edited by the popular electrical showman William Sutgeon…. But by 1839 Joule was beginning to dissociate himself from the role of inventor, and in subsequent communications to Sturgeon’s Annals we find a shift, as Smith puts it, ‘away from ingenious apparatus to experimental natural philosophy…. Faraday, not Sturgeon, had now become his [Joule’s] role model…. This approach to experimentation was very different from that of Faraday, who went out of his way to present his results as disembodied facts, abstracted from the machines and the labor that had made them. He directed attention away from the material artifacts on his lecturing table because he argued that nature lay elsewhere.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 113, 114; reference: Smith, Crosbie. 1998. The Science of Energy: A Cultural History of Energy Physics in Victorian Britain. p. 58.

“Here my limited aim is twofold: to draw attention to the criteria for what was deemed to be science, by contrast with a process of invention; and to register the idea that rather than simply seeing technology as applied science, from the nineteenth century onwards there is a case to be made that science is in many respects best treated as theorized technology. Science does not generate its own problems but starts from technological problems and reworks them, attempting to give them a different kind of standing.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 115.

“In other words, unification in terms of energy is a matter of intertranslatability, not the identification of some single hypostatized power or force.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 120.

“The physicist Paul Dirac, for example, suggested that the appropriate goal in making fundamental connections between disciplines in physics was that of removing inconsistencies, not attempting to unite theories that were previously disjoint. The former, he argued, led to brilliant successes, as in Maxwell’s investigation of an inconsistency in the electromagnetic equations, Planck’s resolution of inconsistencies in the theory of black-body radiation, and Einstein’s resolution of inconsistencies between his theory of special relativity and the Newtonian theory of gravitation. By contrast, the ‘top down’ method of attempting to unify physical theories that were previously disjoint, he noted, had produced nothing of significance.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 120-1.

“It is worth reminding ourselves from the outset [of considering chemistry, just below physics in the hierarchy of science, at the outset of the nineteenth century] that a hierarchy of the sciences based in mathematics or mechanics as not the only option on offer in the eighteenth and early nineteenth centuries. At the turn of the century, proponents of Naturphilosophie, for example, adopted a model of polarities that put the life sciences at the centre of the natural realm. Schelling explicitly subordinated chemistry to the life sciences, writing that ‘the purposeful formation of animal matter … can be explained only by a principle that lies beyond the sphere of chemical processes’, which are ‘incomplete processes of organization’.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 122.

“The basic difficulty in thinking of chemistry in terms of the resources of physics was that the kinds of physical entities with which mechanics works are quite distinct from material substances. Mass points do not behave remotely like the material components of things, for example, and provide no basis on which to account for the behaviouir of substances of interest to chemists: the persistent identity of certain substances, why their properties are typically quite different from any of their components, why they cannot be broken up by mechanical means into their original components, why substances combine in definite simple proportions, or even how they can combine in the first place. The nature of reactivity was probably the most central concern of chemistry, yet it was something that atomism was unable even to address.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 123.

“As Nye notes: ‘At the beginning of the nineteenth century, Physik was taught in the Gernam university philosophical faculty, and Chemie in the medical faculty…. At this time the idea of a physics laboratory hardly existed; the word laboratory implied research in chemistry.’ This character of chemistry as an empirical discipline was set from the 1720s onwards, as attention came to be directed exclusively to the phenomenal level of chemical behaviour.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 125; subquote: Nye, Mary Jo. 1996. Before Big Science: The Pursuit of Modern Chemistry and Physics, 1800-1910. p. 9.

“In chemistry, by contrast, the paradigm form of material substances was liquids, not solids…. Eighteenth-century chemists did not start from a conception of what the ultimate constituents of substances must be and try to account for the properties of these substances in terms of the pre-identified constituents. They moved in the opposite direction, taking chemically characterized substances and asking how they could be treated, for example through heating or by being dissolved, so as to yield constituents.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 126.

“But there is a crucial feature of organic chemistry that propelled it to the forefront of theoretical chemistry in the nineteenth century. As far as the kinds of reactions that are investigated in inorganic chemistry are concerned, for the most part one can get by perfectly well by providing what are in effect recipes that tell you how to identify and mix ingredients: how much of which elements a comp0ound contains (ideally a simple ratio), and how much of each element one has to combine to produce a new compound. But the ingredients are very limited in organic compounds, and many different compounds have exactly the same ingredients in exactly the same proportions. What organic chemistry requires, therefore, is an account of the internal structure of the compound, since that is where the difference lies.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 128.

“Bergman, for example, had been particularly alert to the role of the environmental condition in which a chemical reaction takes place, noting that it can alter and direct the specific form of the product….

“‘Berthollet’s approach virtually transformed chemistry into a form of natural history, whereby the chemist had to deal with each reaction both as a type, illustrating a general law, and as a specific event in which individual conditions play a major role. Not only was the chemical universe made up of many unique individuals whose number was being multiplied enormously through chemical research, but the individuals themselves were influenced directly by the conditions under which they were formed and existed. Thus, as in natural history, chemical genera, species, and varieties could be grasped only through a procedure combining diachronic and synchronic understanding.’” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 130-1; subquote: Reill, Peter. Hanns. 2005. Vitalizing Nature in the Enlightenment. p. 87; references: Bergman, Torbern – 18th century chemist; Berthollet, Claude Louis – late 18th and early 19th century chemist.

“In sum, once we get down to the details of nineteenth-century and early twentieth-century chemistry, it becomes evident that there are no grounds for simply assuming either the unity of chemistry and physics, or even the unity of chemistry…. At a general level, one way to describe what is at issue here is in terms of the modularity of science. It consists of relatively discrete areas, some of which may resist connections with others. By contrast, unity imposed through a philosophical/metaphysical homogenization of science loses explanatory richness and a sense of how results are generated in the first place.

“One of the problems that arises from thinking in terms of unification is that it distracts us from what the concrete aims of scientific investigation in the period were. In the case of chemistry, for example, Alan Rocke identifies the actual concerns in these terms:

“‘… for those who actually lived through the period, the dominating story in chemistry of the 1860s, 1870s, and 1880s was neither the periodic law, nor the search for new elements, not the early stages of the study of atoms and molecules as physical entities. It was the maturation, and demonstration of extraordinary scientific and technological power, of the ‘theory of chemical structure’–loosely defined, a set of ideas that enabled one to succeed in tracing and portraying the exact way in which atoms are connected up with each other to form molecules.’” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 140-1; subquote: Rocke, Alan J. 2010. Image and Reality: Kekule, Kopp, and the Scientific Imagination. p. xiv.

“There are a number of difficulties with the resort to fundamental particles. As things stand at present, for example, the ‘Standard Model’ of elementary particle physics tells us that there are twelve particles (six quarks and six leptons) and four forces (electromagnetism, strong force, weak force, and the Higgs field) at the most fundamental physical level. But a little probing reveals the explanatory economies that one might expect from ‘fundamental’ particles are illusory. As regards the particles themselves, the Standard Model count does not include the eight different ‘colours’ of gluons, or currently undetected partners for all elementary particles, such as sfermions, postulated by supersymmetry theory. Nor does it include the many different extra particles that have been postulated in an effort to overcome difficulties in the Standard Model, such as axions, branons, cornucipons, cuscutons, dyons, erebons, flaxions, giant magnons, macros, magnetic monopoles, maximons, planckons, preons, simps, skyrmions, sterile neutrinos, wimps, wimpillas, and so on.

“More importantly, confining our attention to the particles of the Standard Model, once we ask how these interact, we need to invoke some twenty free (or ‘adjustable’) parameters specifying the properties of the particles (masses, phases, and mixing angles) and the strengths of the particles’ interactions (the ‘coupling constants’). The Standard Model itself furnishes us with no clues as to why these parameters have the values they do: they are simply the values that experiments reveal….

“In the light of these considerations, recourse to the properties of fundamental particles hardly provides a model of complete and comprehensive explanation even for those macroscopic phenomena with which we are familiar (which make up less than 5 per cent of the total energy-matter content of the universe). Indeed, the search for an absolute ‘fundamental’ level, a carry-over from Democrateanism where atoms were deemed to have a few simple intrinsic properties on which everything else tested, begins to look more and more like a metaphysical dead end.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 152-3.

“It would seem that the natural sciences have always been favoured over the life sciences in this respect in the West, particularly since the seventeenth century, but not necessarily elsewhere: not in China for example. And one significant difference between these two is the lack of a conception of ‘nature’ in the latter. As Geoffrey Lloyd, in a comparison of ancient Greek and ancient Chinese science, notes, there is no straightforward equivalent to the classical Greek term for nature, phusis, in classical Chinese:

“‘Of course, a variety of terms tian (heaven), wu (things), xing (character), li (pattern), dao (the way), zi ran (spontaneity…), do survive perfectly adequately, in different contexts, to express ideas where the English translation would be in terms of nature, the Greek in terms of phusis, or their cognates. Yet that is still not to say that there is a concept of nature in classical Chinese, just the one, not that it was a major preoccupation.’” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 155; subquote: Lloyd, G.E.R. 1996. Adversaries and Authorities: Investigations into Ancient Greek and Chinese Science. Cambridge UP. p. 6.

“From as early as Aristotle’s account of the sciences, natural history had always been treated as a merely descriptive form of classification, with no legitimate aspirations to scientific standing. Such classifications tended to vary locally….” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 156.

“At the same time [early nineteenth century], as apart of a repackaging of the life sciences, there was a reduction of the scope of natural history, which had traditionally included animals, plants, and rocks, classified along the same general lines into families, genera, and species. The study of rocks was gradually being separated from the other areas of natural history classification, and by the early decades of the century animals had become the focus of enquiry, marginalizing botany from theoretical developments, despite the fact that at a practical level the identification of plants remained crucial since botany was one of the most commercially important scientific enterprises of the century.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 157.

“Chemistry could conceivably be dismissed as being incomplete without a mechanist reduction, but if the life sciences were treated non-mechanically they were in direct conflict with any reductionist aspirations that physics may have harboured. This is because, by contrast with chemistry, anti-mechanist advocates in biology had at least one clear alternative, a form of teleological holism.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 160.

“‘That a meeting point between biology and physical science may at some time be found, there is no reason for doubting. But we may confidently predict that if that meeting-point is found, and one of the two sciences is swallowed up, that one will not be biology’….

“Conceptions of the unity of science can vary radically, depending on the hierarchy that they deploy: in the simplest case, whether it is bottom up as in atomism, or top down as in holism.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 160; subquote: Bernal, J.D. quoted in: Haldane, J.S. 1908. “An Address on the Relation of Physiology to Physics and Chemistry, Delivered before the Physiological Section of the British Association for the Advancement of Science, Dublin, 1908.’ The British Medical Journal. 693-6. p. 696.

“At the end of the eighteenth century Kant, in his Kritik der Urtheilskraft, had set out the options for how we conceive of an apparently non-mechanical teleologically guided living realm in terms of four alternatives: life can be accounted for in terms of a Spinoza-like conatus in matter; a divine teleology regulating the world; a purely mechanical world in which teleology is a feature of the way in which we must conceive of living things and not something inherent in them; and finally hylozoism, the doctrine that living powers inhere in matter. To these we might add a straightforward mechanical reduction that made no explanatory concessions to teleology at all.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 162.

“To have it shown that in muscular action–the paradigm case of the expendiutre of force/energy in a living thing–nothing more than a mechanical process was involved, was a severe blow to the idea that the matter of living things exhibited irreducibly vital forces.

“The second development was the emergence of cell theory. Throughout the eighteenth century, in disputes between mechanists, hylozoists, and others, the question of life was located in the terrain of matter theory. As I have indicated, many of those working in the life sciences in the eighteenth century took the irreducibility of the phenomenon of life to indicate that it was an intrinsic property of matter, and argued that the study of lifeless matter was simply a sub-species of matter theory, not a model for it….

“This changed in the early decades of the nineteenth century, with the elaboration of cell theory…. … cells, bolstered by the growing realization that all cells had nuclei, took on a physiological role, as the basic units of metabolic exchange. Tissues, which had played such a crucial role in physiology up to this point, gradually gave way to cells as the ultimate units of life.

“Cell theory meant that the question of where the separation between the living and the non-living lies could be taken out of the realm of matter theory of the type envisaged by writers of Kant’s generation, thereby transforming the kinds of resources to which those studying living things could appeal. At the same time, because cell theory arose from a generalization from similarities between the constituents of animals and plants, it produced a new form of unification of the study of living things, establishing a significant degree of autonomy for the life sciences.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 166-7.

“… from the 1830s onwards physiology was increasingly cell physiology. Neither mechanist dreams of reducing physics to atomistic point masses, nor those of chemists such as Dalton of reducing chemistry to hard, spherical chemical atoms, had borne fruit, but finally here was a discipline that made a plausible claim to identifying its functionally basic constituents. Moreover, unlike contemporaneous physical and chemical atoms, the understanding of cells did real work: all the various healthy and morbid functions of the body were the outward expressions of the activities of cells. Physiology and pathology were transformed forthwith.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 168.

“But the strengths of an experimental physico-chemical approach in areas such as respiratory physiology were not matched in developmental physiology, which had always presented a dilemma for physico-chemical explanation. Descartes, for example, in offering a strictly mechanist account of the development of the foetus, had been faced with the problem of how, if the foetus is formed from inert undifferentiated matter which is the same in every animal, it can develop into one kind of animal in one case and a completely different kind in another. The answer on his account, lay in the physically characterizable environment of the womb, which differs from one species to another, and causes variations in development.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 174.

“They [chemists and physicists trying to explain life phenomena] offer explanations or systems of life which tempt us at times by their false simplicity, but which harm biological science in every case, by bringing in false guidance and inaccuracy which it then takes long to dispel. In a word, biology has its own problems and its definite point of view; it borrows from other sciences only their help and their methods, not their theories.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 181.

“Leaving to one side the problems that arise for reductionism once we take seriously the fact that it is models, not theories, that do much of the explanatory work in physics from the nineteenth century onwards, there are significant difficulties involved in the reconciliation of conflicting theories within the discipline of physics, and these are compounded and effectively made irresoluble [sic] once projects for the unity of science are mapped on to them. The problem is that such metalevel unification projects envisage something that operates at a level of abstraction where any empirical difficulties are treated as mere temporary obstacles on the route to unification. There are two (unstated) assumptions of the metalevel conception that are crucial to its resilience in the face of the failures of reductionism. The first is the assumption that there must be a unity of science: that it is not just an empirical matter of fact that science is a unified enterprise. This effectively gives the unity of science an a priori status, meaning that failures to unify have no evidential bearing on its general standing. The second assumption provides the rationale for the first. It is that the natural realm itself is unitary: as if there were some master plan behind nature that makes unification a universal requirement of a complete explanation.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 182-3.

“Without reduction, can we still have the unity of science? The doctrine of emergent properties has been supposed to fill in the gaps where reduction ceases to work. The claim is that as one moves from one tier or level to the next, one moves to a new level of ‘complexity’, and new properties emerge which are not reducible to the supposedly more fundamental properties but which in some way still result from them. In his discussion of the prospects for reduction in the life sciences, Ernst Mayr writes that his discussion of reductionism ‘can be summarized by saying that the analysis of systems is a valuable method, but that attempts at a “reduction” of purely biological phenomena or concepts to laws of the physical sciences has rarely, if ever, led to any advance in our understanding. Reduction is at best a vacuous, but more often a thoroughly misleading and futile approach. This futility is particularly well illustrated by the phenomenon of emergence.’ Emergence, he continues, ‘is a thoroughly materialist notion. Those who deny it … are forced to adopt pan-psychic or hylozoic theories of matter.’” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 183; subquote: Mayr, Ernst. 1992. The Growth of Biological Thought: Diversity, Evolution, and Inheritance. p. 63.

“The doctrine of emergent properties has become the preferred option in explaining why we need to keep in place the hierarchy of sciences–something that is constitutive of the unity of science–while acknowledging the failure of strict reductionism.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 183.

“Emergent properties are offered as an alternative to reductionism, an alternative that promises the benefits of reductionism without any of the costs. The shared assumption is that it is because physics is as it is that everything else is at it is: the ultimate constituents from which everything is composed are just the kinds of things described in physics, and it is the peculiarities of the arrangements and states of these constituents that give rise to the contents of the different disciplines.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 183.

“… materialism in a literal sense has been left behind in the course of the twentieth century as developments from geometrodynamics to string theory have postulated very unmaterial-looking constituents of the physical universe. It is the physical sciences, not the material sciences, that bear the ontological load, and as a consequence materialism has become physicalism. In other words, the commitment to materialism translates into an open-ended commitment to the physical sciences. But what does this open-ended commitment amount to? It can only be a commitment to the priority of the physical sciences, and this in turn can only be an explanatory priority.

“But if we need different kinds of explanations for these different kinds of phenomena, we can ask what the rationale is for labelling them ‘emergent’, as opposed to autonomous. The term suggests that, even though everything is ultimately just physics, the natural realm is layered in a way not describable in physics…. The core problem for emergent properties is the suggestion that the new properties come into existence in a way not describable either by physics or by the ‘emergent’ disciplines, which simply take the new properties as given. The way in which these new phenomena ‘emerge’ out of purely physical ones should surely appear problematic to advocates of materialism or physicalism. But the crucial point is that what generates these emergent properties is not an explanatory requirement but an ontological one.

“The ontological requirement is physicalism: the doctrine of emergent properties assumes the truth of physicalism, as a statement of ontological faith, and then sets out cases where it deems the resources of physicalism to be insufficient. The term ‘emergent properties’ may be relatively recent, but the phenomenon of hierarchical ordering and the appreciation of its problems isn’t. The doctrine resembles a certain kind of property classification that was abandoned in the early modern period, namely the hierarchical classification of things into plants, animals, and humans in terms of the emergence of various kinds of ‘soul’: vegetative souls, responsible for lower functions such as nutrition; sensitive souls, conferring the power of sensation; and rational souls. Descartes was one of the most effective critics of this kind of approach, pointing out that it was no more than an exercise in labelling. The vegetative and sensitive ‘souls’ are merely names invented for what are considered to be significant qualitative differences. These labels have no explanatory value, but they were presented as if they furthered our understanding in some way.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 184-5.

“If it were the case, as modern proponents of ontology evidently believe, that science sets out ultimately to tell us about the nature of reality, identifying the basic kinds of things that exist in the world, then ontology might provide some guidance in understanding the relations between the sciences. But how seriously can we take this view of what science does? Note that the strategy it relies upon is not new, but, conceptually speaking, a reworking of scholastic metaphysics, where it was developed most fully in the context of exploring the relation between natural-philosophical and theological theories, which had different sources and employed different procedures, and which occasionally seemed to conflict. It was considered that the conflict could not be real, however, for surely there must be a unity of understanding, a unity that reflected the fact that the natural world had been created by a single creator with consistency of purpose. The approach worked reasonably well in that context, at least before the sixteenth century, but its revival in a secularized form as a theory about the relation between the sciences does its greatest damage–whatever other misconceptions it engenders, and whatever other dead ends it leads us to–by locking us into a conception of the unity of the science as an unquestioned assumption behind the whole project, because the unity of science, which is contentious, is treated as if it were a reflection of the unity of ‘reality’, which is supposedly uncontentious. But the latter is neither contentious nor uncontentious; it is simply meaningless in a secular context, for what on earth could the ‘unity of reality’ refer to? What would a ‘disunity of reality’ look like? This misconceived way of proceeding simply begs the question of the unity of science, at the same time indicating why it could have been treated as something with a virtually a priori standing. The whole point of the historical approach that we are taking is to bring to light just how contingent the emergence of the idea of the unity of science has been in the modern era, and how the motivations behind it, and the forms of legitimation that have been used to defend and encourage it, turn out, with a little probing, to have been anything but the kinds of thing that we would expect of something a priori or conceptually fundamental.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 186.

“If the life sciences don’t use resources developed in the domain of physical-mechanical problems, it is not because they are ‘more complex’ (particle physics is at least as complex as anything in the life sciences) or because they involve emergent properties, but because these are inappropriate to their subject matter.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 187.

“Once we have abandoned reductionism, there is no mystery that emergent properties must be invoked to resolve.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 187.

“… Wallace himself was subsequently to become one of the most prominent defenders of the discontinuity between human beings and other animals, advocating a form of spiritualism to account for the distinctiveness of human beings.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 201.

“Huxley was not the only evolutionist to uphold the doctrine of evolutionary progress in the 1940s: Dobzhansky, Mayr, Simpson, and Stebbins all addressed the question of ‘the future of mankind’ in evolutionary terms.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 216.

“There has in fact always been a good claim for pluralism in the life sciences.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 219.

“Reversing Smart’s assessment [that biology is intrinsically heterogeneous and therefore unable to help scientific unification], I suggest that the biological sciences, conceived not as part of a unified enterprise but as harbouring an inevitable element of unruliness by comparison with the physical ‘core’, might act as a better model for science generally, and the physical and material sciences more particularly. The choice is not so much between unity and pluralism as between homogenization and pluralism. Pluralism allows us to make links where appropriate, but there is no a priori requirement (explanatory or otherwise) that everything must ultimately be connected, and a fortiori there is no requirement that the links established must ultimately take a form of reduction.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 220; reference: Smart, J.J. 1963. Philosophy and Scientific Realism. ch. 3.

“Comte, for example, was openly hostile to experimental research because it could lead to awkward discoveries that could only result in further uncertainties. His terminology is revealing because what such unity of science projects share is a concern with certainty, as opposed to understanding for example, and certainty is something that can militate against revision, as the history of religious belief amply testifies.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 221.

The question now arises: once we rid ourselves of the hierarchical assumptions that the unity of the sciences carries with it, is there some more fruitful way of characterizing scientific practice, of the kind that we have encountered in this and earlier chapters?

“The alternative, pluralism, has a number of varieties in the literature on physical and biological explanation. Some argue, for example, that a preference for micro-explanations cannot be justified, and does not capture how explanations in physics work, whereas others hold that macro- and micro-explanations when integrated give a better explanatory account of the phenomenon of interest than they would if taken separately.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 221.

“What I want to suggest is that there arose an expectation that science would take over a task for which Christianity had been found wanting, namely that of providing a cohesive unit of understanding, without any thought being given as to whether such an aim could stand up to scrutiny. Nevertheless, considerable fine-tuning is needed if we are to understand how science took on this new role. Everything hinges on the naturalization of human behaviour, that is, on science taking over from religious conceptions in accounting for human behaviour, with the focus in the initial stages on economic and moral behaviour. But it also depends crucially on the transformation of philosophy into a metatheory of science, something that provides a means of placing science at the centre of any form of understanding.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 224-5.

“The problem was that, as a scientific culture developed, the issues turned not just on understanding the world, but increasingly on understanding our place in the world. The human sciences bore directly on the latter, and it was here that the conflicts with religious and philosophical forms of understanding were greatest. What resulted from these conflicts–which included, among other things, intractable perennial questions about the nature of morality and the nature of consciousness–was the emergence of comprehensive metascientific theories.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 229.

“Whereas in Britain [for the appearance of metascientific trends in philosophy like Mill in the third quarter of the nineteenth century] the catalyst had been a scientific political economy, however, in Germany it was ‘scientific materialism’. The claim of scientific materialism was that, with the emergence and consolidation of science, there are no longer any genuine philosophical problems: the speculative approach of philosophy can be replaced entirely by the empirical methods of science. The principal response to scientific materialism in Germany was Neo-Kantianism, which radically reshaped the aims of philosophy, transforming it into a metatheory of science.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 259.

“The continuity between animals and humans as established in evolutionary theory meant not only that the strict separation between the two that had been a premise of Christian thinking had to be abandoned, but also that the systems of morals based on them had to be discarded.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 260.

“Comte’s conception of the unity of science placed the human sciences firmly within a hierarchy, so that they were construed as a continuation, via biology, of the natural sciences, and indeed, the human sciences stood at the head of the unified system, and were treated by Comte as its culmination. Mill, by contrast, rejected both the single hierarchy of Comte and the kind of bifurcation that Whewell had demanded. Although initially influenced by Comte, in his explicit engagement of questions in ethics he abandoned the idea of single hierarchy of understanding because, as we have seen, he believed that, while objectivity requires that all forms of enquiry must appeal to external quantitative standards, natural science and ethics appeal to different external standards: inductive evidence and observable consequences respectively.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 276-7.

“The epistemology/metaphysics division, in the form it takes in this reworking of Kantian questions, is a deep one, and it comes to a head decades later, in 1929, in the famous ‘working session’ (Arbeitsgemeinschaft) at Davos with Cassirer and Rickert’s one-time pupil, Heidegger….

“The issues are whether propositional understanding is the only genuine form of understanding, and if not whether propositional and non-propositional forms of understanding are independent of one another. From the Enlightenment onwards, there was much dispute about these questions…. Simplifying considerably, these are whether (as Cassirer believed) propositional understanding can be radically revised so as to include what had traditionally been taken to be non-propositional forms, without losing the centrality of scientific understanding; or whether (as Heidegger believed) non-propositional understanding is not just our only possible starting point in engaging with the world, but our only means of engaging with the world per se.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 282-3.

“… the crucial point is that none of the earlier successful scientific cultures engaged in the legitimatory venture of consolidating scientific gains in such a way as to establish sciences as a model for all forms of understanding. Large-scale consolidation of this type was never part of the programmes of Alexandrian, Arab-Islamic, or Chinese science, for example…. the idea of large-scale consolidation is not something inherent in the scientific enterprise as such, but it is inherent in Western scientific enterprise after the Scientific Revolution.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 424.

“The origins of Western scientific culture lay in fact not in scientific developments as such but in a particular set of political and religious problems, and it was thought of and defended in the context of a Christian understanding of the world until the middle of the eighteenth century. By the nineteenth century, science was becoming dissociated from Christianity, but taking its cue from Christianity it began to be presented as an autonomous enterprise representing truly universal values, by contrast with those of Christianity, now increasingly considered dogmatic and parochial.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 424.

“… it is crucial to distinguish as far as possible between the consolidation of scientific enquiry and the consolidation of a scientific culture, especially since it is the latter–not the former–that marks out what happened in Europe as quite different from the development of science elsewhere.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 425.

“On this integrated conception [studying the origin of scientific inquiry and culture back to the twelfth century], philosophy was a tool of theology, and there was no division into autonomous secular and ecclesiastical realms. It was with the Investiture Controversy (1050-1122) that this conception first came apart in a politico-theological context. The Controversy hinged on the appointment of clergy by monarchs and nobles, which was condemned by Pope Gregory VII, whose first target was the removal of the monarch’s power to appoint popes. Asserting papal supremacy over the entire Western church, he declared its independence from secular control. The resolution of the Controversy resulted in the church achieving a legal identity independent of emperors, kings, and feudal lords. But the relevant upshot of this for our purposes was a separation of the ecclesiastical and secular realms.

“The bifurcation into ecclesia and mundus gradually covered every aspect of political and intellectual life, and its first manifestation was the legal division into autonomous ecclesiastical and secular legal systems, initiating a tradition of reconciling the two legal systems so that they did not conflict. These procedures provided a model for the various forms of bifurcation that followed, not least in the realm of understanding, and this brings us to a formative development in the establishment of a scientific culture: the revision of the Aristotelian conception of metaphysics, one that enabled it to play a mediating role between what became two independent sources of knowledge, natural philosophy on the one hand, and revelation and Christian teaching on the other. Aristotelianism made sense perception the sole source of knowledge of the natural world, and allowing an understanding of the natural world that deployed purely natural resources was a fundamental concession.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 426-7.

“I stress that this [the turn to natural philosophy for the natural world by theologians around the twelfth century] was a theologically motivated move: the adoption of Aristotelian metaphysics provided resources for dealing with pressing theological issues in a far more satisfactory way than the alternatives. But Aristotelian metaphysics came as part of a package in which natural philosophy provided exclusive access to the natural world. In adopting it, Christianity took on a unique feature: a fundamental engagement with science, which set it apart from all other religions, transforming it radically and giving it a distinctive identity. Islam was the only other religion which had had a full-scale engagement with science, and Aristotelianism had also provided the route for this engagement: indeed the scholars of thirteenth-century Paris were deeply indebted to the Arabic Aristotle tradition.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 427.

“These developments [the inclusion of natural philosophy for the natural world] have occasionally been resisted: nineteenth-century Catholicism retreated into a staunchly anti-science form of dogmatism, struggling vainly to institute a form of theocracy, and twentieth-century evangelical Protestantism attempted to subordinate science to a biblical literalism.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 428.

“From the 1750s on, there were three sets of questions that dominated debate about the relations among science, religion, and metaphysics. The first was the assessment of the merits and drawbacks of systematic and non-systematic understanding. The second was the contrast between propositional understanding–the kind of understanding traditionally associated with scientific inquiry, where all understanding is construed in terms of knowing that something is the case–and non-propositional understanding, that is, approaching the world in terms of aspirations, fears, anxieties, plans, raw beliefs, desires, etc. The third concerned the respective roles of reason and sensibility in understanding the world and our place in it. System, propositional understanding, and reason were, as one might expect, defended together, as were anti-system arguments, non-propositional understanding, and sensibility.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 430.

“What emerges from this [that technical innovations were not just dependent on scientific theorizing and popular science was not just a promotional exercise for science] is a conception of science as a mixture of theory, experiment, and theory-free invention, articulated through a number of channels, including popular science, and resulting in both discursive products (theoretical understanding) and non-discursive products (machines and complex systems). These factors interact in ways that are highly dependent on context, and the outcome of the interaction cannot be discerned in advance. ‘Science’ emerges from this as an unstable mixture, and this reinforces its modular character, and the need for pluralism in its explanations.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 433.

“But by the late nineteenth century, the modular pluralistic factors have entered the core of scientific programmes, leaving behind the idea of the unity of science, inducing a unification panic among many scientists and philosophers, and giving science as a whole an unruly character if viewed from the perspective of ‘pure theory’.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 434.

“It is not possible to make sense of these developments [that technological and engineering developments forced science to see itself as other than essentially scientific theory] without abandoning the idea of the unity of science, an idea that has been premised on two things: a secularized religious model of nature in which nature is the result of a single coherent act of creation; and that of science as an essentially abstract enterprise, a body of theory open to application and popularization, neither of which have a bearing on its essential characteristics. In the circumstances, it is unsurprising that science took on an aura of religious authority from the late eighteenth century onwards. But the integration of science, technology, invention, and engineering, and the need to articulate scientific values in a wide variety of ways, including in terms of popular science if they are to be effective, have resulted in something that the traditional understanding of science wholly fails to capture. In particular, the idea that science could take on the mantle of a unity of understanding, that it could replace Christianity in a role for which the latter had been found wholly inadequate, without asking why Christianity encountered the problems that it did in the first place, shows an egregious lack of will to confront the issues.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. pp. 434-5.

“Since the middle of the nineteenth century, science has shed the last remnants of its purity and come of age, its inherent unruliness and pluralism brought to the surface for all to see. As a result, its standing as the bearer of the values of civilization has now begun to look mysterious at best. Accordingly, the question of what exactly we want out of science becomes an urgent one.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 435.

“Above all, it [scientific unification] cannot lie in some quasi-religious, quasi-metaphysical quest for the ultimate truth about the world. To the extent to which a general model can be illuminating, I admit to being tempted by medicine, by contrast with physics, as a way of thinking through how the sciences operate. Human anatomy, physiology, pathology, etc. are not theories [derived previously such as from physics] which happen to find application in the prevention and treatment of illness. This is to get things the wrong way around. These theoretical and experimental disciplines have been brought into existence and shaped by a medical agenda, and their standing is subservient to the social and other goods that medicine sets out to achieve. The physical sciences are not quite like this, but it might perhaps be possible, with care to model the physical sciences on this basis, in terms of providing the means of transforming living and working conditions.” Gaukroger, Stephen. 2020. Civilization and the Culture of Science: Science and the Shaping of Modernity 1795-1935. Oxford UP. p. 435.

“Since our supreme object is to measure and master the world, we can make relatively little use of theology, philosophy, and deductive logic–the three stately entrance ways to knowledge erected in the Middle Ages. In the course of eight centuries these disciplines have fallen from their high estate, and in their place we have enthroned history, science, and the technique of observation and measurement…. Its [theology’s] functions… have been taken over, not as is often supposed by philosophy, but by history–the study of man and his world in the time sequence.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 17.

“Theology in the thirteenth century presented the story of man and the world according to the divine plan of salvation. It provided the men of that age with an authentic philosophy of history, and they could afford to ignore the factual experience of mankind since they were so well assured of its ultimate cause and significance.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 17.

“As history has gradually replaced theology, so science has replaced philosophy.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 20.

“The atmosphere which sustains our thought is so saturated with the actual that we can easily do with a minimum of the theoretical….

“So long as we can make efficient use of things, we feel no irresistible need to understand them. No doubt it is for this reason chiefly that the modern mind can be so wonderfully at ease in a mysterious universe.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. pp. 27, 28.

“… the Philosophes betray their debt to medieval thought without being aware of it. They denounced Christian philosophy, but rather too much, after the manner of those who are but half emancipated from the ‘superstitions’ they scorn. They had put off the fear of God, but maintained a respectful attitude toward the Deity. They ridiculed the idea that the universe had been created in six days, but still believed it to be a beautifully articulated machine designed by the Supreme Being according to a rational plan as an abiding place for mankind. The Garden of Eden was for them a myth, no doubt, but they looked enviously back to the golden age of Roman virtue, or across the waters to the unspoiled innocence of an Arcadian civilization that flourished in Pennsylvania. They renounced the authority of church and Bible, but exhibited a naive faith in the authority of nature and reason. They scorned metaphysics, but were proud to be called philosophers…. They defended toleration valiantly, but could with difficulty tolerate priests. They denied that miracles ever happened, but believed in the perfectibility of the human race….

“I shall attempt to show that the Philosophes demolished the Heavenly City of St. Augustine only to rebuild it with more up-to-date materials.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. pp. 30, 31.

“Some sure instinct warned them [the philosophers of the 18th century] that it would be dangerous to know too much, that ‘to comprehend all is to pardon all.’” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 43.

“To be enlightened was to understand this double truth, that it was not in Holy Writ, but in the great book of nature, open for all mankind to read, that the laws of God had been recorded….

“Nature and natural law–what magic these words held for the philosophical century!” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 51.

“In the eighteenth-century climate of opinion, whatever question you seek to answer, nature is the test, the standard: the ideas, the customs, the institutions of men, if ever they are to attain perfection, must obviously be in accord with those laws which ‘nature reveals at all times, to all men.’” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 53; subquote: Voltaire, Oeuvres. XXV. P. 560.

“In earlier centuries the ideal image of nature was, as one may say, too ghostly ever to be mistaken for nature herself. Nature herself had hitherto seemed to common sense intractable, even mysterious and dangerous, at best inharmonious to man. Men therefore desired some authoritative assurance that there was no need to be apprehensive; and this assurance came from theologians and philosophers who argued that, since God is goodness and reason, his creation must somehow be, even if not evidently so to finite minds, good and reasonable. Design in nature was thus derived a priori from the character which the Creator was assumed to have; and natural law, so far from being associated with the observed behavior of physical phenomena, was no more than a conceptual universe above and outside the real one, a logical construction dwelling in the mind of God and dimly reflected in the minds of philosophers.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 55.

“Hidden away in the elaborate structure of Locke’s Essay was a most disconcerting corollary. It was this: if nature be the work of God, and man the product of nature, then all that man does and thinks, all that he has ever done or thought, must be natural, too, and in accord with the laws of nature and of nature’s God…. But if all is natural, then how could man and his customs ever be out of harmony with nature?” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 66.

“Before the middle of the century Hume had taken up this world-old problem, had looked at it straight, had examined it attentively round and round about; and then, in his Dialogues Concerning Natural Religion, with all the dialectical resources of the new philosophy, with a penetrating insight matched only by the serene urbanity with which he displayed it, had remorselessly exposed the futility of reason to establish either the existence or the goodness of God. ‘Epicurus’s old questions are yet unanswered. Is he [God] willing to prevent evil, but not able? Then he is impotent. Is he able, but not willing? Then he is malevolent. Is he both able and willing? Whence then is evil?’…

“Well, we know what the Philosophers did in this emergency. They found, as we all find when sufficiently hard pressed, that reason is amenable to treatment. They therefore tempered reason with sentiment, reasons of the heart that reason knows not of….” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. pp. 68, 69.

“… Diderot was typical of his generation; generally speaking, the Philosophers were all, like Hume and Diderot, ambitious to be esteemed ‘men of virtue.’ The reason is precisely that they were, from the point of view of their opponents, enemies of morality and virtue; and what, indeed, could justify all their negations, all their attacks on Christian faith and doctrine, if they were unable to replace the old morality by a new and more solidly based one?” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 80.

“There is a profound significance in Diderot’s feeling that it would be better not to defend virtue at all than to fail in the attempt….” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 81.

“… the soul that Cartesian logic had eliminated from the individual had to be rediscovered in humanity. The soul of the individual might be evil, it might be temporary, it might even be an illusion. But the soul of humanity, this something ‘essential to’ human nature, this ‘common model of ourselves’ (and what was this but the old medieval ‘realism’ come to life again?) Was surely immortal because permanent and universal. What the Philosophers had to do, therefore, was to go up and down the wide world with the lamp of enlightenment looking, as Montaigne did before them, for ‘man in general.’ They had to identify and enumerate and describe the qualities that were common to all men in order to determine what ideas and customs and institutions in their own time were out of harmony with the universal natural order.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. pp. 87-8.

“With this creed the ‘constant and universal principles of human nature,’ which Hume tells us are to be discovered by a study of history, must be in accord, and ‘man in general’ must be a creature who would conveniently illustrate these principles. What these ‘universal principles’ were the Philosophers, therefore, understood before they went in search of them, and with ‘man in general’ they were well acquainted, having created him in their own image.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. p. 103.

“The importance of the Christian story was that it announced with authority that the life of man has significance, a universal significance transcending and including the temporal experience of the individual. This was the secret of its enduring strength, that it irradiated pessimism with hope: it liberated the mind of man from the cycles in which classical philosophy had inclosed it as in a prison, and by transferring the golden age from the past to the future substituted an optimistic for a disillusioned view of human destiny.

“The eighteenth-century Philosophers might therefore rewrite the story of man’s first state, relegating the Garden of Eden to the limbo of myths; they might discover a new revelation in the book of nature to displace the revelation in Holy Writ; they might demonstrate that reason, supported by the universal assent of mankind as recorded in history, was a more infallible authority than church ad state–they might well do all this and yet find their task but half finished. No ‘return,’ no ‘rebirth’ of classical philosophy, however idealized and humanized, no worship of ancestors long since dead, or pale imitations of Greek pessimism would suffice for a society that had been so long and so well taught to look forward to another and better world to come. Without a new heaven to replace the old, a new way of salvation, of attaining perfection, the religion of humanity would appeal in vain to the common run of men.” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. pp. 128-9.

“… for the worship of God, Diderot has substituted respect for posterity; for the hope of immortality in heaven, the hope of living in the memory of future generations…. The essence of the matter Diderot managed to reduce to an epigram: ‘Posterity is for the Philosopher what the other world is for the religious.’” Becker, Carl. 1932[2003]. The Heavenly City of the Eighteenth-Century Philosophers; Second Edition. Yale UP. pp. 149, 150.

 

“Matsutake are wild mushrooms that live in human-disturbed forests. Like rats, raccoons, and cockroaches, they are willing to put up with some of the environmental messes humans have made. Yet they are not pests; they are valuable gourmet treats–at least in Japan, where high prices sometimes make matsutake the most valuable mushroom on earth.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. Pp. 3-4.

“Neither tales of progress nor of ruin tell us how to think about collaborative survival. It is time to pay attention to mushhroom picking. Not that this will save us–but it might open our imaginations.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 19.

The concept of assemblage is helpful. Ecologists turned to assemblages to get around the sometimes fixed and bounded connotations of ecological ‘community’…. Assemblages are open-ended gatherings. They allow us to ask about communal effects without assuming them. They show us potential histories in the making. For my purposes, however, I need something other than organisms as the elements that gather.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. pp. 22-3.

“Assemblages don’t just gather lifeways; they make them. Thinking through assemblage urges us to ask: How do gatherings sometimes become ‘happenings,’ that is, greater than the sum of their parts? If history without progress is indeterminate and multidirectional, might assemblages show us its possibilities?

“Patterns of unintentional coordination develop in assemblages.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 23.

“… it might be useful to imagine the polyphonic assemblage in relation to agriculture. Since the time of the plantation, commercial agriculture has aimed to segregate a single crop and work toward its simultaneous ripening for a coordinated harvest. But other kinds of farming have multiple rhythms. In the shifting cultivation I studied in Indonesian Borneo, many crops grew together in the same field, and they had quite different schedules. Rice, bananas, taro, sweet potatoes, sugarcane, palms, and fruit trees mingled; farmers needed to attend to the varied schedules of maturation of each of these crops. These rhythms were their relation to human harvests; if we add other relations, for example, to pollinators ord other plants, rhythms multiply. The polyphonic assemblage is the gathering of these rhythms, as they result from world-making projects, human and not human.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 24.

“Factory labor is an exemplar of coordinated progress time. Yet the supply chain is infused with polyphonic rhythms. Consider the tiny Chinese garment factory studied by Nellie Chu; like its many competitors, it served multiple supply lines, constantly switching among orders for local boutique brands, knock-off international brands, and generic to-be-branded-later production. Each required different standards, materials, and kinds of labor. The factory’s job was to match industrial coordination to the complex rhythms of supply chains.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 24; reference: Chu, Nellie. 2014. “Global supply chains of risks and desires: The crafting of migrant entrepreneurship in Guangzhou, China.” PhD dissertation, UCSC.

“This book argues that staying alive–for every species–requires livable collaborations.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 28.

“Thinking through self-containment [of economic man for example] and thus the self-interest of individuals (at whatever scale) made it possible to ignore contamination, that is, transformation through encounter.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 28.

“The ability to make one’s research framework apply to greater scales, without changing the research questions, has become a hallmark of modern knowledge….

“Scalability, in contrast, is the ability of a project to change scales smoothly without any change in project frames…. Scalability requires that project elements be oblivious to the indeterminacies of encounters; that’s how they allow smooth expansion….

“Scalability is not an ordinary feature of nature…. Yet, despite the contributions of thinkers such as Braudel and Bohr, the connection between scaling up and the and the advancement of humanity has ben so strong that scalable elements receive the lion’s share of attention.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 38.

“The challenge of thinking with precarity is to understand the ways projects for making scalability have transformed landscape and society while also seeing where scalability fails–and where nonscalable ecological and economic relations erupt.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 42.

“One of the strangest projects of privatization and commodification in the early twentieth-first century has been the movement to commoditize scholarship. Two versions have been surprisingly powerful. In Europe, administrators demand assessment exercises that reduce the work of scholars to a number, a sum total for a life of intellectual exchange. In the United States, scholars are asked to become entrepreneurs, producing ourselves as brands and seeking stardom from the very first days of our studies, when we know nothing. Both projects seem to me bizarre–and suffocating. By privatizing what is necessarily collaborative work, these projects aim to strangle the life out of scholarship.

“Anyone who cares about ideas is forced, then, to create scenes that exceed or escape ‘professionalization,’ that is, the surveillance techniques of privatization. This means designing research that requires playgroups and collaborative clusters: not congeries of individuals calculating costs and benefits, but rather scholarship that emerges through its collaborations. Thinking through mushrooms, once again, can help.

“What if we imagined intellectual life as a peasant woodland, a source of many useful products emerging in unintentional design? The image calls up its opposites: In assessment exercises, intellectual life is a plantation; in scholarly entrepreneurship, intellectual life is pure theft, the private appropriation of communal products. Neither is appealing. Consider, instead, the pleasures of the woodland. There are many useful products there, from berries and mushrooms to firewood, wild vegetables, medicinal herbs, and even timber. A forager can chose what to gather and can make use of the woodland’s patches of unexpected bounty. But the woodland requires continuing work, not to make it a garden but rather to keep it open and available for an array of species. Human coppicing, grazing, and fire maintain this architecture; other species gather to make it their own. For intellectual work, this seems just right. Work in common creates the possibilities of particular feats of individual scholarship. To encourage the unknown potential of scholarly advances–like the unexpected bounty of a nest of mushrooms–requires sustaining the common work of the intellectual woodland.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. pp. 285, 286.

“In ‘The Carrier Bag Theory of Fiction,’ Ursula K. Le Guin argues that stories of hunting and killing have allowed readers to imagine that individual heroism is the point of a story. Instead, she proposes that storytelling might pick up diverse things of meaning and value and gather them together, like a forager rather than a hunter waiting for the big kill. In this kind of storytelling, stories should never end, but rather lead to further stories.” Tsing, Anna Lowenhaupt. 2015. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton UP. p. 287.

“The basic problem with the Newtonian idea of fluids as collections of hard particles imparting resistance through inelastic collisions, was that there was no way, on this basis, to treat a fluid as a deformable mass.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 319.

“[Buffon] was forthcoming on the defining feature of living things: it was ‘the capacity to reproduce’, a capacity which, he considers, makes animals and plants ‘practically of the same order’…. Buffon rejects morphological criteria entirely and defines an animal species in these reproductive terms…. But the crucial thing to remember here is that, for Buffon, ability to interbreed is a function criterion, not one that mirrors essential similarities and differences. Indeed, there seem to be no essential similarities and differences of any kind. God has not put any fixed differences between animals and plants, we are told, and ‘the living and the animate, far from being a metaphysical quality of beings, are physical properties of matter.’” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. pp. 378-9; subquote: Buffon, George Louiis Leclec, Comte de. 1827. Oeuvres completes de Buffon…. (34 vols.) “Histoire des animaux. ch. 1: X. 276-7, 285.

“The developmental role of sensation plays a pivotal role in Buffon’s account, and indeed there was something of a priority dispute with Condillac over the use of the thought experiment of the statue receiving various sensory faculties, although it is an image that originates much earlier, in Descartes’ Le Monde. Buffon and Condillac use the thought experiment in the same way, and reach much the same conclusions. In particular, Buffon argues that the statue at first believes all its sensations to refer to internal experiences, and it [is] only when a tactile faculty is provided [that] it realizes, ‘in horror’, that there is something outside it. Only touch can provide a sense of an external world, and with this sense effectively comes a precondition for morality, in that with it comes a recognition of the existence of others, and a love for them replaces the earlier narcissism. Sensibility and a recognition of an external world come simultaneously, and this is important for the Lockean tradition in France.

“Its importance lies in the fact that it is intended as a replacement for an inadequate innate ideas tradition, in which the qualitative difference between mere sensation and perceptual experience comes with innate ideas. Buffon, Condillac, and Diderot each want to register the qualitative difference between merely sensing and having an experience of an external world, and for them this qualitative difference comes with sensibility, which thereby does much of the work that innate ideas did in the pre-Lockean account.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. pp. 381-2.

“By the mid-century, in the work of writers such as Diderot, sensibility/sensitivity/sensation is a unified phenomenon having physiological, moral, and aesthetic dimensions, and it lies at the basis of our relation to the physical world: it is what natural understanding has to be premissed on. Not only that, but it has come to encompass those dimensions of natural processes that mechanism had written out of the picture, dimensions captured for example in chemistry–in the affinities that seemed to guide the relations between chemical substances, and the mixing of different bodies so intimately as to be fused and inseparable by mechanical means–and in physiology, as in the phenomenon of irritability whereby, when touched, muscles contract with a force much greater than the original cause. Nature seemed to harbour a power and responsiveness that was capturable in terms of some broad notion of sensibility/sensitivity. If natural philosophy was to provide a general cognitive model, it had to adapt its explanatory resources to these phenomena, and to become part of the programme of sensibility.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 390.

“From the mid-seventeenth century onwards, literary prose works began to appear which were ill-adapted to capturing the kinds of values that drove the classical models, but were nevertheless able to engage much the same range of issues, albeit from a completely different source, as it were. The classical ideas of passion and emotion which Descartes had explored in his Passions de l’ame of 1649, for example, were replaced by those of tendresse and sentiment. These latter were not grounded in medical concepts, as Descartes’ were, and they had a value not in relation to a natural order but in relation to an inner mental and emotional life: what we might term a personal psychology. Affective states generated in this way give us an entry into the psychology of the character rather than offering a way of placing the behaviour of the character in a natural order.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 391.

“Stahl’s [physiologist of early eighteenth century whom Leibniz opposed; see Smith J. 2011] core criticism of mechanist models was that they do not allow one to conceive of vital phenomena as specific autonomous phenomena, and he distinguished ‘mechanical’ bodies from living systems, which had their own laws, goals, uses, and effects…. Yet it is striking how much still depended on questions in matter theory, since a good deal hinged on whether matter was ‘active’ or not, and how quickly developments in physiology impacted upon matter theory. Stahl had invoked a conscious will to account for vital phenomena, but mid-century physiologists were as unsympathetic to such ‘animist’ accounts as they were to mechanist ones. The problem lay in finding some third alternative, which was conceived to lie in the middle ground between animism and mechanism. Both these construed matter as inert: the disagreement lay on whether this inert matter needed to be supplemented to account for physiological activity. Seeking an alternative to animism and mechanism automatically meant that the question of the active nature of matter had to be raised, because those two exhausted the possibilities of inert matter.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. pp. 395-6.

“… his [Haller’s] principal response to these charges [he was accused of materialism and impiety] was to argue that the powers that organs have which are manifested in irritability derive directly from God, and require no intermediary soul. They manifest something that can be characterized as a life force, by contrast both with a view of matter as inert, and that of being acted upon from outside. The local, intrinsic regulation of the operations of organs brings with it a rethinking of the nature of matter. But it also brings with it a rethinking of the idea of an organism. Centralized, extrinsic regulation of organs, of the kind advocated by Whytt, provided a source of unification for the organism whose organs these are. Local, intrinsic regulation of the kind advocated by Haller prompts the question of what the unity of the organism consists in….

“The solution to this problem was set out by Theophile de Bordeu, who developed an account whereby each organ leads a life of its own, and where the lives of organs contribute to, indeed constitute, the collective life of the organism. In general terms, one might say that it is because the parts are living that the whole is living, and it is because the living parts are connected in the way they are that the whole is the way it is. Buffon held an even stronger view, arguing that all matter is active in itself, and that ‘the life of the whole seems to be just the result of the life of all the actions, of all the separate little lives, if I may be permitted to express myself in these terms, of each of those active molecules whose life is primitive and apparently indestructible.’” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. pp. 399-400.

“There cannot be a stronger contrast with d’Alembert’s promotion of reason in understanding than Hume’s account of the relation between reason and sensibility. ‘Reason is, and ought only to be the slave of the passions, and can never pretend to any other office than to serve and obey them’, Hume tells us in his Treatise of Human Nature, published in 1739…. … in the Introduction he sets out…:

“‘For it seems to me evident, that the essence of the mind being equally unknown to us with that of external bodies, it must be equally impossible to form any notion of its powers and qualities otherwise than from careful and exact experiments, and the observation of those particular effects, which result from its different circumstances and situations. And tho’ we must endeavour to render all our principles as universal as possible, by tracing up our experiments to the upmost, and explaining all effects from the simplest and fewest causes, ‘tis still certain we cannot go beyond experience: and any hypothesis, that pretends to discover the ultimate original qualities of human nature, ought at first to be rejected as presumptuous and chimerical.’” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 438.

“On the Lockean/Newtonian account, there are forms of enquiry in which one can seek underlying causes, but there are realms of enquiry in which this is the wrong way to proceed, not only because it gets nowhere but, more importantly, because it cuts off productive avenues of research which a phenomenal approach reveals. This is a view that Newton and Locke held about natural philosophy. Hume, whose concern is with the ‘moral sciences’ rather than natural philosophy as such, generalizes the question to include any form of cognitive enquiry, including metaphysics, as indeed Locke had done.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 440.

“That there is a more general point at stake here [for Hume] is evident from the remark in the Treatise that: ‘the understanding, when it acts alone, and according to its most general principles, entirely subverts itself, and leaves not the lowest degree of evidence in any proposition, either in philosophy or in common life.’ Trying to live in accord with reason alone is misguided:

“‘Philosophy on the contrary, if just, can present us only with the mild and moderate sentiments and if false and extravagant, its opinions are merely the objects of a cold and general speculation, and seldom go so far as to interrupt the course of our natural propensities. The Cynics are an extraordinary instance of philosophers, who from reasonings purely philosophical ran into as great extravagancies of conduct as any Monk or Dervise that ever was in the world. Generally speaking, the errors in religion are dangerous: those in philosophy only ridiculous.’

“Yet the solution to this does not lie in renouncing abstract, systematic reasoning, for to do so would be to ‘cut off entirely all science and philosophy’ and would ‘subvert entirely the human understanding’. Hume is able to offer no solution to this dilemma. ‘For my part’, he tells us, ‘I know not what ought to be done in the present case.’

“There are a number of ways of thinking about the problem raised here. One is to try to explore the question of the relation between reason and sensibility in an abstract way which forces some kind of commensurability between the two, an approach that would inevitably involve translating the questions into terms of some overarching discipline. This is what Kant will do, turning the problem into one in epistemology, but this would certainly not have satisfied Hume. Another approach is to treat the dilemma as a genuine dilemma, not something that can be overcome, but as telling us something about the human condition. In concentrating on doxastic doubt, Hume’s deployment of scepticism is not part of an epistemological project, but one designed to reveal how to live, just as it was for the Pyrrhonists. It is important for this project that we understand how the idea of causation in nature has its origins in human nature. For Hume, as for many of his contemporaries, the means that we employ to divine what the dilemma posed by reason and sensibility tells us are historical. And since coming to terms with this dilemma is a crucial part of coming to understand human nature for Hume, our understanding of human nature necessarily has a historical dimension. From the last decades of the seventeenth century, history became to the moral or human sciences what observation and experiment were to natural history. History had traditionally acted as source of guidance in moral and political questions, but not in the cases of what we might characterize as psychological or anthropological questions (with rare exceptions in the travel literature). Its scope now widens radically, and it begins to act as a form of investigation that runs parallel to philosophical analysis, sometimes complementing it, at other times at odds with it.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. pp. 443-4.

“But Hume raises the fundamental question, inherent in the eighteenth-century sensibility tradition, whether understanding of the world and our place in it is exhausted by reason, and he answers that it is not.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 445.

“Hume rejects both the (originally Thomist) idea that metaphysics provides a neutral language, or a neutral set of resources, by which to adjudicate the competing claims of cognitive disciplines such as natural philosophy and theology; and he rejects the (originally Scotist) idea that metaphysics provides a fundamental form of discourse in which the competing claims of cognitive disciplines such as natural philosophy and theology can be grounded….

“It is precisely this search for closure that is questioned in Hume. The stress on the important role of sensibility in our thinking generally, and the attempt to think through what a form of comprehension that was not the product of a single system would be like, are combined, so that they become transformed into a questioning of the idea that all understanding takes a propositional form. Although the questions of sensibility and non-systematic understanding can be traced back to Locke, and were a feature of the French culture in which he composed the Treatise, Hume’s work was either completely ignored, or, later effectively neutralized, in that the reaction to it was to treat Hume as a sceptic, as someone who (a la Berkeley) ingeniously questioned something we all know to be true, such as the existence of causes, thereby representing a ‘dead end’ in the history of philosophy, as Bertrand Russell was to put it. But this is to miss the profoundity of Hume’s solution, which is not a sceptical one. At the most general level, what Hume is questioning is the attempt to found any cognitive enterprise–natural philosophy, morals, politics, and religion–on the basis of an autonomous reason or rationality. He is not denying that natural philosophy paradigmatically embodies reason. Rather, he is arguing that it is an egregious and dangerous error to imagine that, were something to embody reason paradigmatically, that would thereby entitle it to act as a model for all human understanding. He is offering an account of ‘human understanding’ whereby it is a judicious balancing of propositional and non-propositional considerations, of considerations of reason and sensibility.” Gaukroger, Stephen. 2010. The Collapse of Mechanism and the Rise of Sensibility: Science and the Shaping of Modernity 1680-1760. Oxford UP. p. 451.

“The perspective I shall defend has no unambiguous name. It is a late arrival in the history of philosophy, and even today it keeps being confused with other points of view of a quite different sort. I shall refer to it as the internalist perspective, because it is characteristic of this view to hold that what objects does the world consist of? is a question that it only makes sense to ask within a theory or description. Many ‘internalist’ philosophers, though not all, hold further that there is more than one ‘true’ theory or description of the world. ‘Truth’, in an internalist view, is some sort of (idealized) rational acceptability – some sort of ideal coherence of our beliefs with each other and with our experiences as those experiences are themselves represented in our belief system – and not correspondence with mind-independent or discourse-independent ‘states of affairs’. There is no God’s Eye point of view that we can know or usefully imagine; there are only the various points of view of actual persons reflecting various interests and purposes that their descriptions and theories subserve. (‘Coherence theory of truth’; ‘Non-realism’; ‘Verificationism’; ‘Pluralism’; ‘Pragmatism’; are all terms that have been applied to the internalist perspective; but every one of these terms has connotations that are unacceptable because of their other historic applications.’” Putnam, Hilary. 1981. Reason, Truth and History. Cambridge UP. pp. 49-50.

“When she dances, a young child already moves her body with a sensitivity to what is expected of her…. What she actualizes is nothing less than the embodiment of choreographic ideas of which she is not the author. This is a distinctively human form of intelligence at work.

“The child’s dancing is the location of what I want to call an entanglement between her native impulse to move and an artistic representation of what movement is supposed to be. We come to embody choreographic ideas when we dance. We do so naturally, and we cannot avoid doing so…. This circular, generative recursion gives us resources, and in fact is likely to compel us, to be different going forward. The representation changes what is represented. The act of dancing and the art of dancing become entangled.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. p. 11.

“What is characteristic of aesthetic experience is that by looking, describing, thinking, and interrogating artwork, we make ourselves new. Works of art–whether pictures or writings or dances or songs–rework the raw materials of our default organization. The engagement with an artwork is an engagement with oneself that tends to alter us, to reorganize us.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. p. 11.

“To learn to see is to learn to take an interest in things, and the world is full of different families of things to take an interest in. This may be what Maurice Merleau-Ponty had in mind when he wrote, ‘Nothing is more difficult than knowing precisely what we see.’

“Aesthetics is not the task of evaluating an object. It is the task of achieving the object.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. p. 12.

“Aesthetic experience refers instead to the temporally extended practice of engaging with oneself and one’s environment, with the goal of moving from not seeing to seeing, or from seeing to seeing differently…. We make aesthetic experience. It doesn’t simply happen in us.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. p. 12.

“While the aesthetic is a general feature of our lives in the world, it is also true that art has a special tie to the aesthetic. Art targets the aesthetic; it works with it and makes it a problem. By this I mean: artworks stage occasions for that distinctive passage from not seeing to seeing that is the very hallmark of the aesthetic.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. p. 12.

“We are ourselves like artworks, being whose nature refuses to be known but unfolds in the activity of working to know and see. Which is just to say that we are an aesthetic problem.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. p. 12.

“Psychology has done an amazing job collecting facts and data, but it has never quite established foundational principles. And as a result, consciousness, subjectivity, and value remain open questions, even mysterious, even now, after so long….

“The problem, rather, is that we have not yet come to grips with the fact that we ourselves are not a subject fit for science.” Noë, Alva. 2023. “Dancer from the Dance.” Selection taken from book The Entanglement from Princeton UP. In: Harper’s Magazine, July. pp. 13-14.

“There are other biological laws of nature whose consequences are similar to those of natural selection. The species-area law governs how many species live on a particular island or habitat as a function of its size. This law allows us to predict where and when species will go extinct, but also where and when they will evolve anew. The law of corridors governs which species will move in the future as climate changes, and how. The law of escape describes the ways in which species thrive when they escape their pests and parasites. Escape accounts for some of the successes of humans relative to other species and for how we have been able to achieve such extraordinary abundance relative to other species. The law frames some of the challenges that we will face in the coming years when our possibilities of escape (from pests, parasites, and the like) are fewer. The law of the niche governs where species, including humans, can live and where we are likely to be able to successfully live in the future as climate changes.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. pp. 8-9.

“The first law of diversity is manifest in the brains of birds and mammals. In recent years, ecologists have revealed that animals with brains capable of using inventive intelligence to carry out novel tasks are favored by variable environments. These animals include crows, ravens, parrots, and some primates. Such animals use their intelligence to buffer the diverse conditions they encounter, a phenomenon described as the law of cognitive buffering. When environments that were once consistent and stable become variable, these species with inventive intelligence become more common. The world becomes a crow’s world.

“A second law of diversity, the diversity-stability law, states that ecosystems that include more species are more stable through time.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. pp. 10-11.

“Biologists chart their details and their needs. But there is a problem with this approach: our own lack of awareness.

“The species we study to understand the world are nearly all unusual species. They are species that are representative neither of the realities of the living world nor of the portion of the living world most likely to affect our own well-being. Our problem is simple. We tend to assume the living world to be both like us and relatively well understood. Both of these assumptions are wrong, the result of law-like biases in the way we make sense of the world.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. pp. 17-18.

“They [Locey & Lennon] focused just on bacteria and estimated that there might be a trillion kinds of bacteria on Earth.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 27; reference: Locey, Kenneth J. & Jay T. Lennon. 2016. “Scaling Laws Predict Global Microbial Diversity.” Proceedings of the National Academy of Sciences. 113(21):5970-5975.

“… the number of kinds of bacteriophages outnumbers the number of kinds of bacteria ten to one. If there are a trillion species of bacteria, then it is possible there are also a trillion kinds of bacteriophages or even ten trillion kinds of bacteriophages.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 28.

“Over the preceding thirty years, the total biomass of insects in the natural habitats they [Hallimann et al] were studying had declined by 70 to 80 percent, unnoticed.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 35; reference: Hallimann, Caspar A. et a. 2017. “More Than 75 Percent Decline over 27 Years in Total Flying Insect Biomass in Protected Areas.” PLOS ONE. 12(10):e0185809.

“In many ways, a consideration of island biogeography leads to the conclusion that we have so squeezed, parted, and re-formed the wet dough of Earth that we have inadvertently extinguished wild species on which we depend or might depend and, at the same time, have favored the origin of species likely to cause us problems. And because extinction proceeds manyfold more quickly than the origin of new species, the numbers aren’t even. We were offered a deal by nature: if we gave up thousands of species of birds, plants, mammals, butterflies, and bees, in exchange we could have a handful of new kinds of mosquitoes and rats. It is a bad deal, but one that so far we have accepted.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 60.

“Today, in many countries the health and well-being of people and the yield of crops still depend on escape of two kinds. The first is the result of species of parasites and pests whose realized niches remain smaller than their fundamental niches. The second is experienced by human populations and crops that live and grow in conditions outside the fundamental niches of their parasites and pests. Both of these kinds of escape are now threatened by global change, the first by the ways we have connected the world through our transportation networks, the second by climate change.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 88.

“The industrial, technological approach to agriculture is well suited to helping solve some of the challenges of the future–for example, how to eke a few more calories per acre out of farms or how to produce more drought-tolerant crops. But it is not well suited to deal with variability, especially variability outside the scope of its control.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 150.

“If we manage to avoid global societal collapse during the next centuries, it will be because we figured out how to value the rest of life and the insights that arise from an understanding of that life. It will be because we realized we are dependent on the rest of life.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 171.

“… scientists have also figured out, it seems, why some C-section babies come to have normal gut microbes and others don’t. Some C-section babies, by chance, ingest fecal microbes from elsewhere in their environment. From dogs. From the soil. From wherever those microbes might be found. In doing so, they acquire the microbes they need. But this chance pickup of necessary microbes has a statute of limitations, at least in humans. As babies get older, it is progressively more difficult for them to acquire new gut microbes….” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 184.

“Vaginally born babies pick up many species of skin, vaginal, and fecal microbes from their mothers….

“C-section babies tend to acquire their first gut, skin, and other microbiomes from the hospital room and the things in the hospital room.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 185.

“The management of transgenic crops and the treatment of cancer are different. Yet they share a fundamental component. In both cases, preventing the spread of resistant organisms depends on finding ways to favor susceptible organisms [those that are not resistant to biocides]. Recently, the leader of our think tank, Peter Joergensen, has argued that our enemies’ susceptibility to our biocides is a kind of common good. It is, Peter suggests, a common good that is as important to humanity as, for example, clean drinking water. The more we manage pests, parasites, and even cancer cells so as to promote this susceptibility, the more control we will have against such species. Just how we manage for susceptibility differs from case to case, and yet keeping susceptible individuals around is something that benefits us all.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. pp. 228-9.

“… they [Rettenmeyer et al.] estimated that the colonies of a single species of army ant, the aforementioned Eciton burchellii, host more than three hundred other species of animals (to say nothing of other life-forms, such as bacteria or viruses). Carl and Marian described the army ant species Eciton burchellii as the animal species on which the most other species depend. They called it the ‘largest animal association centered on one species.’ And it appears to be, at least if one doesn’t include humans….

“Most primate species are host to tens of species of parasites; collectively, humans are host to thousands. Our bodies also host beneficial gut bacteria, skin bacteria, vaginal bacteria, and oral bacteria that live nowhere else. These bacteria species, in turn, host unique viruses, bacteriophages, that rely on life that relies on us.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. pp. 253-4, 255; reference: Rettenmeyer, Carl W, M.E. Rettenmeyer, J. Joseph & S.M. Berghoff. 2011. “The Largest Animal Association Centered on One Species: The Army Ant Eciton burchellii and Its More Than 2300 Associates.” Insectes Sociaux. 58(3):281-292.

“… there is some level of uncertainty beyond which a big brain is no longer helpful. Perhaps that is just what will ultimately befall us, an Earth on which we have engendered conditions that are just too unpredictable year to year for us to solve through our inventive intelligence. Sometimes conditions can be so challenging that the species that survive are not the smart ones but, instead, the lucky ones and the fecund ones. In the contest between the clever crow and the fecund pigeon, sometimes the pigeon wins.” Dunn, Rob. 2021. A Natural History of the Future: What the Laws of Biology Tell Us about the Destiny of the Human Species. NY: Basic Books. p. 266.

“Not until the nineteenth century did the Russian Empire encounter an enemy that it could not defeat. The name of the enemy was nationalism….

“The Russian Empire was confronted with the national question by the first Polish uprising in 1830-31. The Poles, whose multiethnic state of Poland-Lithuania had been partitioned by Russia, Prussia, and Habsburg Austria in the second half of the eighteenth century, raised the flag of modern nationalism against all the partitioning empires in the early nineteenth century….

“The empire struck back by forging a model of Russian nationalism closely allied with its empire. In 1832 in the aftermath of the first Polish uprising, the newly appointed deputy minister of education, Count Sergei Uvarov, proposed a tripartite formula to Emperor Nicholas I that could serve as the keystone of a new Russian identity to be forged by the educational system. It consisted of three concepts to which a loyal subject of the tsar would have to subscribe: Orthodoxy, Autocracy, and Nationality. In the past, Russian subjects had been obliged to be loyal to God, the Sovereign, and the Fatherland.” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. pp. 9-10.

“Vladimir Lenin’s main contribution to the history of Russo-Ukrainian relations was not the formation of a modern Ukrainian state. It was, rather, the endowment of Russia, or the Russian Federation–the name under which it entered the Soviet Union–with a territory and institutions of its own, distinct for the first time in centuries from the territory and institutions of the empire that the Bolsheviks were seeking to preserve. If anything, Lenin laid the foundations for the formation of modern Russia, not Ukraine.” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. p. 17.

“On December 1, 1991, Ukrainians delivered the final blow to the Soviet Union by voting overwhelmingly for independence. The Baltics were effectively gone by that time, as was Moldova and a good part of the Caucasus. But the Belarusians and Central Asians, who counted on a continuing supply of subsidized gas and oil from Russia, were in no hurry to leave…. But the Russian leadership decided to end the existence of the USSR because it did not want to bear the economic burden of the Union without Ukraine’s substantial human and economic resources.” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. pp. 26-7.

“In Ukraine, unlike in Russia, communists and nationalists were divided and at each other’s throats, the nationalists being pro-Western and pro-reform, the communists anti-reform and pro-Russian.” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. p. 47.

“A few months into the Clinton presidency, the renowned political scientist and international relations expert John Mearsheimer published an article in Foreign Affairs arguing that Ukraine should be encouraged to keep its nuclear weapons, not pressured to give them up. In Mearsheimer’s view that was the most effective way to prevent a Russo-Ukrainian war, which he characterized as a ‘disaster’ that could lead to the reconquest of Ukraine and ‘injure prospects for peace throughout Europe.’ He argued: ‘Ukrainian nuclear weapons are the only reliable deterrent to Russian aggression.’” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. pp. 71-2.

“In the Soviet tradition, Solzhenitsyn, who was half Ukrainian, referred to the Ukrainians as a separate nation, but, according to imperial tradition, he considered them one and the same people as the Russians.” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. p. 105.

“The Poles played a special role as the nation responsible for the breakup of the united Russian people in all imperial Russian narratives, and Putin’s version did not depart from that long-established tradition….

“Putin’s contribution to his predecessors’ historical schemas was the notion of Ukraine as an anti-Russia or, as he described it, ‘a barrier between Europe and Russia, a springboard against Russia.’ It was allegedly a concoction of evil Western forces. ‘Inevitably, there came a time when the concept of ‘Ukraine is not Russia’ was no longer an option,’ wrote Putin. ‘There was a need for an ‘anti-Russia’ concept, which we will never accept. The owners of this project took as a basis the old groundwork of the Polish-Austrian ideologists to create an ‘anti-Moscow Russia.’’” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. pp. 137-8.

“Russia’s aggression against Ukraine produced a nineteenth-century war fought with twentieth-century tactics and twenty-first century weaponry.” Plokhy, Serhii. 2023. The Russo-Ukrainian War: The Return of History. W.W. Norton. p. 295.

“Our life, what we imagine to be the most intimate and incommunicable part of ourselves, does not come from us, and there is nothing exclusive or personal about it: it was transmitted to us by others, it has animated other bodies, chunks of matter different from the one in which we are currently harboured. For nine months, the fact that the life that animates and awakens us has no one name or owner was an obvious physical, material fact. We were the same body, the same humours, the same atoms as our mother. And we are that life, shared with the body of another, carried on and taken elsewhere.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 3.

“… species are not substances or real entities. They are ‘life games’ (in the same sense as ‘language games’): unstable and necessarily ephemeral configurations of a life that likes to transit and circulate from one form to another.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 5.

“To think the relationship between this multiplicity of forms in terms of metamorphosis rather than in terms of evolution, progress, or their opposites, is not just to free oneself of all teleology. It means also, and above all, that each of these forms has the same weight, the same importance, the same value: metamorphosis is the principle of equivalence between all natures, and the process that allows this equivalence to arise. Every form, every nature, comes from the other and is equivalent to it. They all exist on the same plane. They each have a share of what the others have, but in different ways. Variation is horizontal.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 9.

“Let us call metamorphosis this twofold self-evident truth: every living thing is in itself a plurality of forms – simultaneously present and successive – but none of these forms truly exists autonomously and separately, because they are always defined in immediate continuity with an infinite number of others that come before and after. Metamorphosis is both the force that allows every living thing to be staged simultaneously and successively across several forms, and the breath of life that connects those forms with one another, allowing them to pass one into the other.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 9-10.

“The forgetting [of life before birth or in the mother] is not accidental, it is the condition of possibility for beginning to see oneself differently. It is the cognitive counterpart of the act of becoming other than one’s mother, of continuing her life and her breath apart from her womb and her consciousness.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 14.

“Birth is a corridor: a transformative channel that leads life from one form to another, from one species to another, from one kingdom to another.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 19.

“Birth is a double process, both parallel and simultaneous, shared by self and world. For it is not only the living being that is born: the world is also born, and born differently with the appearance of each new individual.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 22.

“Our life is never purely singular, unique, indivisible. That is why there is not, and never could be, a form of life as such, a transcendental unity between a life and its form: birth is precisely the negation of any such transcendental synthesis. We always come from another form, we are its deformation, its variation, its anamorphosis.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 27.

“That is why motherhood is not an experience limited to one gender. It has no essential link with the feminine: it is birth that makes the mother, and not the other way around. Motherhood is neither a destiny nor an essence nor a gender determination: it is the result of what birth does to certain bodies…. It is because living beings are capable of giving birth – because they can become mothers – that we can manipulate the world, transform it, make the world participate in this metamorphic momentum that we call life.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 29.

“The metamorphosis never stops. It is not just a birthmark, it is a destiny. It is not a past event now unavailable to us, it is every living body’s mode of life.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 38.

“… metamorphosis is the condition that obliges us to nurture the other within ourselves, without ever being able either to be entirely ourselves or to merge or fuse completely with the other. This is what it means to be born: to be impure, to not be ourselves, to have within us something that comes from elsewhere, something foreign that impels us over and over again to become strangers to ourselves. We carry within us our parents, our grandparents, their parents, prehuman apes, fish, bacteria, all the way down to the smallest atoms of carbon, hydrogen, oxygen, nitrogen, etc. We will never be homogeneous, transparent, or perfectly recognizable.

“Metamorphosis is not simply the succession of two differences, it is the impossibility of replacing the other, the paradoxical coexistence of the most distant possibilities in one and the same life.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 39.

“We have made fetishes of movement and transformation. And yet we do everything possible to make movement impossible. We aspire to move, to change our position in society, to move to a new home, to pass from one state to another. But all of these changes are illusory: we merely move the same life into a new setting – a pleasant trompe-l’oeil that diverts attention from the cobwebs that remain intact on the old furniture of our souls. Globalization promised a mobility unprecedented in the history of humanity, but it has proved to be a global-scale variation on the same old wild-goose chase. There is feverish movement everywhere, but everyone remains as they were. The rich stay rich, and on arrival the poor are still poor, with no more opportunities than they had when they set off. Westerners remain Westerners wherever they are, Africans continue to be excluded and disciplined in the West.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 46.

“We usually think about transformation and change according to two models: conversion and revolution. But metamorphosis is neither of these….

“Nothing could be further from metamorphosis that a conversion.

“Conversion is seductive, in that it exhibits and testifies to the omnipotence of the subject. The convert will be obliged to tell their friends ego non sum ego: ‘I’m not the same person you once knew’…. They will always be able to convince themselves that this change comes from them, and from them alone….

“In metamorphosis, the power that passes through us and transforms us is not a conscious and personal act of will. It comes from elsewhere, it is older than the body it shapes, and it operates outside any decision….

“Revolution is the form of change dearest to technology and politics, both of which seem to think of their relationship in the world exclusively in terms of its radical transformation. Technology is the very paradigm of a change that cannot and must not affect the subject…. This is why all technics is a practice of the exaltation of the technician, the subject of the practice, rather than a real process of improvement of the object to which it is applied. The same could be said of any politics that takes revolution as its horizon and principal objective. For in the dream of a world entirely constituted by a definite act of will there is very little love for matter or for the world, very little interest in change, but only a great deal of narcissism and an attempt to turn reality into a mirror of oneself. Any revolution, in this sense, is far closer to conversion than might be imagined: in both, the subject contemplates their own power.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 47-49.

“This [a conception of technology as an extension of the subject] is the exact opposite of what happens in metamorphosis. A cocoon is not an instrument for the projection of the self outside the limits of the anatomical body. On the contrary, it involves the construction of a threshold where all borders and identities – of self and world – are temporarily suspended. It is the chiasmus that makes the world into a laboratory of the genesis of the self, and makes the self into the most precious matter in the world, that which continually transforms it.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 49.

“It is thought that the overwhelming majority (90%) of all animal biodiversity is accounted for by their anatomical dandyism, with an estimated six to ten million species in existence today. But their somatic imagination is not limited to the invention of new species identities. They also have the ability to take on such different bodies in the course of a single individual life that they were long imagined to be magical beings capable of passing from one species to another.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 50.

“The first insects had no wings and did not undergo any transformation….

“It’s skin that is to blame [for insect metamorphosis]…. … imagine that you depended upon it [skin that is fixed like steel armour] to protect you, to give you shape and structure. Then shedding your skin would literally be shape-shifting: with a body like this, all growth is metamorphosis.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 51.

“… the insect is the life of forms, rather than a form of life.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 54.

“… Linnaeus… distinguishes three forms in addition to that of the egg: the larva, the pupa (nymph or chrysalis), and the imago. The three stages already imply a kind of teleology: it is only in the final stage that the true aspect of the insect will be revealed. Modern entomology distinguishes between three cases, speaking of ametabolism when the change appears to be exclusively one of size, as in the Archaeognatha and Zygentoma, and of hemimetabolism or incomplete metamorphosis when, as in the Orthoptera, Isoptera, and Hemiptera, the larvae look a great deal like the adults even though they are of different size, have no wings or genitals, and have certain characteristics that are not seen in the adult form. On the other hand, scientists speak of holometabolism or complete metamorphosis when, as in the case of the Coleoptera or Lepidoptera (butterflies) among others, the larvae are somatically very different from the adult and an intermediate stage (that of pupation) is present.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 55-6.

“Every life qua metamorphic force is an atlas in the process of unfolding itself: it does not inhabit a territory, in its very flesh it is the map of the territory. Space is no longer a container for life, instead life itself unfolds many forms and many worlds from out of a single body that in itself embodies a differing, diachronic cartography of the cosmos. Every metamorphosis responds to the obligation of life to make of itself a place, an inhabited space, a territory to be explored and deployed: anatomy and geography coincide.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 57.

“… Williamson argues that the morphological difference between larvae and adults, in insects as in many marine invertebrates, owes to the fact that ‘the basic forms of larvae and embryos were transferred from other taxa and were later additions to the life-histories of existing adult animals.’” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 58; reference: Williamson, Donald I. 2003. The Origins of Larvae. Springer.

“Every ecological relationship is a metamorphic relationship: the attempt to reconstruct an egg from its milieu.

“Conversely, all metamorphosis, qua process of periodic re-emergence of the egg structure after birth, is just evidence that the form of all living things is the form of the whole world. and that every living thing is a metamorphosis of the world. The inside flows out into absolute exteriority. For insects, the cocoon is not simply a boundary lying between the individual and its outside – the world, parents, children, the species – but the limit and the space of mediation between the individual and itself, the internal limit of the forms that make up the individual. The cocoon, or postnatal egg, thus marks the threshold where all life makes itself a world and an environment unto itself. Through metamorphosis a body makes of itself a space to be inhabited by forms that are always strangers. The relationship to oneself becomes the perfect equivalent of the relationship between individuals of a species and the relationship between species in the history of life on the planet. Life itself is an egg continually diversifying the form of the Earth.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 64-5.

“Alexander Braun, one of Ernst Haeckel’s teachers, was the first to propose the idea that ‘Youth and age are not mere periods of time, into which life may be divided so at to allow us to say, – Youth, ceases here and Age begins’, they are organic and spiritual forces that coexist at all times in the life of every individual….

“Youth, therefore, is not an age of life: it is a force of rejuvenation opposite but equal in intensity to the force of aging, and which manifests itself throughout the life of the individual….

“Metamorphosis is therefore only the cycle of the various periodic rejuvenations of the living: we are condemned to metamorphose only because we can never separate ourselves from our youth, from the power of rejuvenation that continues to shape our bodies.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 66, 67.

“Every technical object is an egg that steals youth from the world and implants it into our lives. We build technical objects in order to produce a shared childhood. And what is rejuvenative in them is always life, not the form that carries it into our bodies. Rejuvenation is always impersonal.

“The cocoon as technical postnatal egg thus overturns the modern idea of technics as Organsprojection [technics as an extension of humans’ limbs and bodies as first conceived by Ernst Kapp in 1877 book]….

“In the idea of technics embodied by the cocoon, on the contrary, the manipulation of the world becomes something that allows us to cast off of our own nature, to change it from within rather than to project it outward. Technics – the cocoon – is the relation that every living being maintains with itself and which leads it to radically modify its body and its identity. Any relationship with oneself is therefore technical in nature, its aim being to modify one’s own form. Every relationship with oneself produces an egg, a postnatal cocoon, which makes the world into a space for rebirth and self-shaping.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 72, 73.

“Technics – the art of building cocoons – makes of the self at once the subject, the object, and the means of the act of transformation. It is not a force that opposes life or extends it outward, it is nothing but the most intimate expression of life, its original dynamism.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 73.

“The flower is just the most visible evidence that, in the plant, every part is equivalent to every other part. In this respect the animal body cannot hope to imitate the plant body. Whereas in the latter any part can derive from any other, in the former ‘[t]he parts differ so much that it is impossible to recreate one part from another, or to say that one part is another part in amended form.’” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 75-6.

“Plumwood [Val, the philosopher who was attacked and almost eaten by a crocodile and who was more morally outraged at the impossibility of the crocodile’s eating her than she was afraid] believes that the ecological crisis we are undergoing can only be overcome if we can manage to accept ‘equality and reciprocity in the food web’: ‘All living creatures’, she writes, ‘are food, and much more than food’, and ‘thinking of ourselves as of use as food for others is the most basic way’ to think of life as a ‘circulation, as a gift from a community of ancestors’ – and death ‘as recycling, a flowing on into an ecological and ancestral community of origins.’” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 97; quotes from: Plumwood, Val. 2012. The Eye of the Crocodile. Canberra: Australian National University. p. 80.

“Whenever we claim to be animated by an exclusively and carnally personal, human life that will end with the death of our body, we are not indicating some self-evident fact (after all, in a corpse there is still life, just in other forms); we are professing our faith in the literally absolute nature of the human self.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 101.

“… language does to the mind what genes do to bodies. The word divides a mind up into portions that can be reincarnated anywhere, separately from all the other words that accompany or may have accompanied them. Every conversation, every act of thinking, is an exchange of spiritual identity, a mosaic of personalities and little selves that come from elsewhere and are in continual motion.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 107.

“… a house is only a scar left by some metamorphosis of the world that we have forgotten…. Every dwelling is a twofold invasion: we invade the space we inhabit and that space invades us.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 142.

“… cities are the real cradles of monoculture…. All political science – as a discipline of human monoculture – is therefore radically compromised and must be abandoned. A purely human knowledge is not possible, because, as we have seen, all life (whether that of the individual or the species) is an interspecies affair. The science of living beings can only be a knowledge of interspecificity. On the other hand, we seem to have forgotten that any city presupposes a second body, a second interspecies Leviathan both agricultural and zootechnical, as its presupposition and condition of possibility, even if it has been condemned to live in exile outside the body of that city.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 149-150.

“… every city lives on the bodies of the plants and animals that are necessary to give life to the men and women who live there, to provide them with shelter, tools, furniture, energy, oxygen. Every human individual is only the daily reincarnation of all the chickens, salmon, cows, wheat, barley, and corn that it has eaten, digested, and transformed.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 150.

“For each species, being in the world means living in space designed and built by others. To live is therefore always to occupy, to invade a foreign space and to negotiate what a shared space could be.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 153.

“Each species decides, in its own way, the evolutionary fate of others. What we call evolution is nothing more than a kind of generalized interspecies agriculture, a cosmic crossbreeding – which is not necessarily designed for the benefit of one or the other. The world as a whole thus becomes a kind of purely relational reality where each species is the agro-ecological territory of the other: every living being is both garden and gardener of other species. The world then is this relation of reciprocal culture…. In this sense, no ecology is possible, because every ecosystem is the result of an agricultural practice and the involvement of other species. There is no wild space, just as there are no wild animals, because everything is cultivated. The relationship between culture and nature is always reversible: any species can embody nature for us, and vice versa.

“The soil then ceases to be an autonomous reality.

“There is no soil. The soil of one is the life of others. Politics can no longer be carried out on a territorial basis, but only on the basis of the interspecies relationship: so a city is only the relationship that a group of humans has with a series of other species (and with all the species that the existence of those species requires).” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 158-9.

“All living beings are capable not only of consciously changing their own and other species’ environments, of forging arbitrary interspecies relationships that are not necessarily oriented towards some utility or other, but also of altering the destiny of other species. When looked at in this way, the world becomes the every-changing result of this universal and cosmic intelligence and sensibility of the infinite forms of life. Conversely, this cosmic mind is produced by an infinite series of arbitrary and rational encounters and decisions taken by different species at different times, according to the strangest of intentions. Mind – that is to say, interspecies evolution – is the life of the metamorphosis of the world.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 161.

“Everything that constitutes us derives from the non-human and has the same nature, but the reverse is also true: everything that defines humanity, beginning with error, art, artifice, and moral arbitration, also defines the totality of living species. The consequence that a post-Darwinian biology should be able to draw from this fact is that there is a perfect equivalence between all species not only from an ontological or a cognitive point of view, but also from a moral point of view.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 167.

“In claiming to be contemporary – that is, in claiming to embody a form of time and not a form of space or matter – art became a collective practice of the divination of the future. From that moment on, through art, every society constructs something that does not yet exist within it: no longer a harmonious reflection of its own nature, but an attempt to reproduce itself differently from what it is, a way of being different and of divining a difference that does not yet exist. Art embodies a society’s desire for and project of metamorphosis.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp.168-9.

“There is no environment – nor any environing life – but only a flow, a continuum of which we are a metamorphic action.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 173.

“For centuries we have been scanning the skies for signs to help us divine the future…. That is why the science of the future or the vernacular knowledge of what is to come is still called ‘astrology’: the science of celestial bodies….

“For centuries, we have considered the earth to be the most sacred guardian of our past. It is to the Earth that we have always entrusted our dead. It is the Earth and the ruins that spill out of its womb that we have always asked to tell us what we have been. For centuries we have considered the earth as a pure effect, a mere cosmic repository of everything that happened elsewhere, the junkyard of the human and non-human universe. A mass of ruins.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 177.

“Astrology needs to be reversed for at least three reasons. Firstly, because we know today that everything that appears in the sky happened many years ago – often millions of years ago….

“But if astrology needs to be turned upside down, it is also because we know that the Earth itself is a celestial body….

“Astrology must therefore learn to be an Earth science. And to achieve this we must understand that, if we want to know the future, we must look not up but down, and turn towards this bit of sky that is our own planet. In fact, everything that appears on Earth is a future anticipated in the form of a wager.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. p. 178.

“This is what the future is, a force for the development and reproduction of life which does not belong to us, which is not the exclusive property of an individual, and is not even common and shared, but is rather a power floating on the surface of all other bodies.”

“The future is the fact that life and its force are everywhere and cannot belong to any of us, either as individuals, as a nation, or as a species.”

“The future, after all, is the disease of eternity. A singular tumour. But a benign one. The only one that makes us better.

“We don’t need to protect ourselves from this disease. We don’t need to vaccinate ourselves against the virus of time. There’s no point. Our flesh will never stop changing. We need to be sick, very sick. Unafraid of dying. We are the future. We live fast. We die often.” Coccia, Emanuele. 2020. Metamorphoses. Translated by Robin Mackay. Cambridge UK: Polity. pp. 179-180.

“However vigorous and dedicated the biological research activity of these new players, medicine still takes center stage as the main intellectual, social, and economic engine of biological research. Medicine helps to attract the money, but more fundamentally, plays the role of integrator of knowledge. The sciences and technologies drawn to biology arrive by different paths and aim at disparate goals, but medicine dispels the cultural barriers among disciplines, facilitating their fusion in the pursuit of better strategies for uncovering the ultimate causes of disease and better interventions to preserve and restore health.

“Understanding disease and curing it is such a complex challenge that it requires ‘all hands on deck’–all the technical and scientific knowledge available. Cutting-edge medical research already combines the latest advances in AI, materials science, and robotics, and will undoubtedly use quantum computers as they become available. As anyone who has been in a modern hospital can attest, most human technologies end up being adapted for use in the clinic in one way or another….” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. pp. 2-3.

“The most powerful message of this book is that in the twenty-first century life can no longer be considered just the biochemical product of an algorithm written in genes, but a complex and magnificent realization of the laws that created the universe itself. This means that as physics, engineering, computer science, and materials science merge with biology, they are actually helping to reconnect science and technology with the deep questions that humans have asked themselves from the beginning of civilization: What is life? What does it mean to be human when we can manipulate and even exploit our own biology?” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. p. 18.

“Another way of saying all this is that biology is entering the realm of physics…. Biology has now become the natural ground where both physics and engineering are happening.” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. p. 65.

“No matter how much power a drug, enzyme, or cell has to cure a disease, the crucial feature needed for therapeutic success is to deliver it to the right place. The body has many barriers to prevent this: the mucosa of the lungs, the blood-brain barrier protecting the brain, the filters of the kidneys, and the intestinal environment are all designed to prevent pathogens and poisonous molecules from killing the organism, and so they also prevent drugs and treatments from reaching the targeted areas.” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. pp. 132-3.

“The combination of nanotechnology, electronics, physics, mathematical modeling, artificial intelligence, materials science, and biology will result in every smarter drugs, delivery systems, and diagnostic strategies, with the ultimate goal of continually monitoring the body to be able to respond quickly and fix it when it first malfunctions. This is, in fact, what our own immune system does: continuous monitoring and repair.” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. p. 134.

“In Jully 2016, Kevin Kit Parker and his collaborators introduced the first tissue-engineered soft robot. Parker and his collaborators built a 1/10th-scale version of a stingray fish with a microfabricated gold skeleton and a silicone body powered by rat heart muscle cells….

“The heart cells were genetically engineered to respond to light cues, so that the undulatory movements propelling the robot through water could be controlled by light. The speed and direction of the ray was controlled by modulating light frequency and by independently stimulating the right and left fins, allowing the biohybrid machine to maneuver through an obstacle course….

“Parker regards the stingray robot as art as well as technology….” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. p. 159; reference: Park, Sung-Jin et al. 2016. “Phototactic Guidance of a Tissue-Engineered Soft-Robotic Ray.” Science. 353:158-162.

“… the reductionist vision of biology continues to spread. A very large amount of research is devoted to obtaining detailed information on the gene expression and protein and chemical content of cells, using high-throughput techniques to bring biology to the age of ‘big data’…. By correlating genes and the epigenetic labels present on them with the proteins expressed, this approach tries to codify the output of the algorithm of life, but seems incurious about the actual physical mechanism of the algorithm, and largely ignores the principle of emergence: that in life ‘the whole is more than the sum of the parts.’ This has consequences not only for our understanding of life, but also for the success of research on drugs and drug targets.” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. pp. 163-4.

“Physics frees us from the one-dimensional, reductionist molecular tyranny of the genes and allows us to feel ourselves as emerging from the deep, multi-dimensional fabric of the universe. Ultimately, biology materializes from the interplay of forces, energy, information, space, and time that has given us our world, senses, intelligence, conscience–and our immense powers to learn how to heal, regenerate, and reinvent ourselves, our cultures, and our environments using technology.” Contera, Sonia. 2019. Nano Comes to Life: How Nanotechnology is Transforming Medicine and the Future of Biology. Princeton UP. p.169.

“All stages of the medusa Turritopsis nutricula, from newly liberated to fully mature individuals, can transform back into colonial hydroids, either directly or through a resting period, thus escaping death and achieving potential immortality. This is the first metazoan known to revert to a colonial, juvenile morph after having achieved sexual maturity in a solitary stage.” Piraino, Stefano, Ferdinando Boero, Brigitte Aeschbach & Volker Schmid. 1996. “Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa).” Biol. Bull. 190:302-312. p. 302.

“Hydrozoan life cycles are among the most varied of the animal kingdom, with a vast array of different patterns. The basic hydroidomedusan life cycle proceeds from the adult medusa (a solitary stage) to the planula larva, to the polyp (the hydroid, an asexual and often colonial stage). Medusae are produced asexually by polyps.” Piraino, Stefano, Ferdinando Boero, Brigitte Aeschbach & Volker Schmid. 1996. “Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa).” Biol. Bull. 190:302-312. p. 302.

“Transdifferentiation is defined as a change of commitment and gene expression of somatic, well-differentiated, noncycling cells to other cell types directly or through the return to a condition of undifferentiated cells.” Piraino, Stefano, Ferdinando Boero, Brigitte Aeschbach & Volker Schmid. 1996. “Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa).” Biol. Bull. 190:302-312. p. 303.

“Turritopsis nutricula is a unique medusa and its transformation potential is unparalleled within the vast array of life-cycle patterns found in cnidarians. This is the first known case of a metazoan being capable of reverting completely to a clonal life stage after having achieved sexual maturity in a solitary stage.” Piraino, Stefano, Ferdinando Boero, Brigitte Aeschbach & Volker Schmid. 1996. “Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa).” Biol. Bull. 190:302-312. p. 309.

“According to our results, the transformation of mature medusae of T. nutricula into stolons and polyps is an established trait in the life cycle of this species. It is not known whether these processes occur under natural conditions, because they take place in a rather short time and are difficult to observe in the field. Laboratory observations, however, demonstrate that T. nutricula has a transformation potential that has never been recorded in any other cultured species, and it seems improbable that such potential is expressed only under laboratory conditions.” Piraino, Stefano, Ferdinando Boero, Brigitte Aeschbach & Volker Schmid. 1996. “Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa).” Biol. Bull. 190:302-312. p. 311.

“In this article we will tell a different version of the origin of larvae, distinct from the ‘same stock’ concept but consistent with Darwin’s theory of natural selection.

“Larva and adult began as different animals, each developing from its own type of egg. At a point in their evolutionary past, their ancestors interbred and produced offspring. Most hybrid offspring did not survive. Genomes so unlike each other had many difficulties in expression–the translation of genes into proteins. The few hybrids that did survive solved the dilemma by expressing their combined genomes sequentially rather than concurrently, first the larval genes and then the adult. The new combined animal survived and went on to reproduce specialized forms, usually highly advantageous in the procurement of habitat and food, then spread their genes as adults. The legacy left by the patching together of dissimilar ancestral lines is the perilous transition we call metamorphosis, the stage at which the larva transforms into the adult. The outcome is frequently not transformation but death.” Williamson, Donald I. & Sonya E. Vickers. 2007. “The Origins of Larvae.” American Scientist. 95. p. 510.

“The novelty of the larval-transfer hypothesis is not the permanent merger of two different genomes, but the fact that each oversees a separate portion of the animal’s life history. A complete ‘changing of the guard’ takes place during metamorphosis.” Williamson, Donald I. & Sonya E. Vickers. 2007. “The Origins of Larvae.” American Scientist. 95. p. 511.

“Caterpillar larvae, however, are not confined to the order Lepidoptera. They also occur in scorpionflies in the order Mecoptera and in woodwasps and sawflies in Hymenoptera. Other hymenopterans, including ants, bees and wasps, have legless grubs as larvae.

“If you were to classify the types of insect larvae, in fact, you would come up with a pattern quite independent of the classification of the adults. Although this pattern is problematic for the theorist looking for a common ancestor, it is explicable if larvae were later additions to life histories.

“Williamson’s larval-transfer hypothesis holds that the original caterpillar larvae were transferred from adults resembling present-day velvet worms of the genus Peripatus. This is the adult counterpart for all caterpillar larvae. This worm lives in the organic-rich soils of tropical America, South Africa and Australia. These worms-with-legs thus belong to the phylum Onychophora, entirely separate from insects or even earthworms. When hybridization between different insects and velvet worms took place, the surviving chimera enjoyed the best of both worlds: a larval form specialized for feeding and a flying adult adept at spreading its genes.” Williamson, Donald I. & Sonya E. Vickers. 2007. “The Origins of Larvae.” American Scientist. 95. p. 512.

“Two sea urchins, Lytechinus variegatus and Lytechinus verruculatus, are of the same genus, but the similar adults each develop from very different pluteus larvae. Such cases are difficult to explain if larvae and their corresponding adults evolved from one common ancestor. They are explainable, however, if the larvae were acquired by hybridization, and the two similar adults hybridized comparatively recently with different species.” Williamson, Donald I. & Sonya E. Vickers. 2007. “The Origins of Larvae.” American Scientist. 95. p. 514.

“Perhaps the strangest anomaly is the starfish Luidia sarsi,… As in other starfish, the fertilized egg develops into a bilateral larva with a small radial juvenile inside. The juvenile then migrates to the outside of the larva. In most starfish the larva would then settle and degenerate, leaving the juvenile to crawl away. In L. sarsi, however, the juvenile drops off the swimming larva, and both continue to live independently for months.

“These two very unlike organisms are the same individual, hatched from same fertilized egg! How can a single individual split into dissimilar animals, both having the same genome? According to the larval-transfer hypothesis, the coexisting swimming larva and crawling starfish of Luidia sarsi evolved by the fusion of genomes of two animals that hybridized to produce one animal with a larva. The two genomes, however, have retained a considerable degree of independence, and both are expressed together during development. This is an example of overlapping metamorphosis….” Williamson, Donald I. & Sonya E. Vickers. 2007. “The Origins of Larvae.” American Scientist. 95. pp. 514-5.

“Since it was mechanism that provided the model of general understanding both for those who wanted to effect a synthesis of natural philosophy and Christian theology, as well as for those who thought that mechanism could progressively usurp at least many of the claims of Christianity, its demise was momentous. Mechanism was the only comprehensive modern system of natural philosophy [the Aristotelianism that had replaced Platonism within theology in the thirteenth century to deal with theological problems – see V 1] and Christian theology, as well as for those who thought that mechanism could progressively usurp at least many of the claims of Christianity, its demise was momentous. Mechanism was the only comprehensive modern system of natural philosophy, and as a result its collapse had significant consequences for how one established a connection between an account of the natural world and an account of our place in it…. The main thrust of mechanist thinking was to establish a mutually reinforcing relationship between natural philosophy and Christian theology, and Descartes and Boyle both proceeded in this way for example, despite profound differences in how they carried out the project….

“This is precisely what was no longer possible. If, as Locke and his followers insisted, the unificatory project to which mechanism subscribed was based on a fundamental misunderstanding of the nature of physical enquiry, then our account of the world would come not in the form of a general theory, as Aristotelianism and Cartesianism had done, but rather in the form of relatively self-contained areas of inquiry-such as chemistry, electricity, measurement of the shape of the earth, and developmental biology–which had no intrinsic or obvious connections with one another.” Gaukroger, Stephen. 2016. The Natural and the Human: Science and the Shaping of Modernity, 1739-1841. Oxford UP. p. 5.

“Natural philosophy was transformed into something that contributed to a task which had previously been the sole responsibility of Christian doctrine, namely understanding our place in nature. For this, it was crucial that natural philosophy have some overall coherence; that it be a unified enterprise, somewhat as Christian theology was.

“Here we come face to face with the core problem. By the middle of the eighteenth century, if scientific practice was to have any connection with broader issues, the path to securing this could no longer be to proceed in the way that mechanism had up to the early decades of the eighteenth century. Something very different would be needed. And if it were not provided, there was a strong chance that Western science would increasingly turn out to look like the earlier cultures with strong scientific programmes which underwent a few decades of success before interest in science gradually began to decline, as the original aims of specific programmes came to be realized. Remember also that we are not dealing here with something that had any significant practical impact before the middle decades of the nineteenth century, so legitimacy and relevance could not be established in general, practical terms.” Gaukroger, Stephen. 2016. The Natural and the Human: Science and the Shaping of Modernity, 1739-1841. Oxford UP. pp. 6-7.

“What I have set out to show is that the legitimacy of science was established anew in a new arena, and that this brought about a reversal of legitimatory priorities. In the first place, it was not the natural sciences–which had been regarded as the core of scientific activity not just for mechanists but for all natural philosophers up to the middle decades of the eighteenth century, specially the areas of mechanics and astronomy–but the newly emerging human or moral sciences that now came to the fore, providing the ground on which new scientific conceptions were forged, in the process displacing traditional religious, humanist, and other approaches. It is in the moral sciences–defined by Condorcet as ‘all those sciences that have as the subject of their researches either the human mind in itself, or the relations of men one to another’–that questions of legitimacy are pressed. Second, the move to the moral sciences changes the way in which the understanding of the natural realm and the understanding of our relation to this realm are connected.” Gaukroger, Stephen. 2016. The Natural and the Human: Science and the Shaping of Modernity, 1739-1841. Oxford UP. pp. 7-8.

“Kant, in an influential argument about the limits of theoretical reason, argued that religion came not under theoretical reason but under practical reason. This seemed to a whole generation to resolve the problems of reason versus revelation, but what it yielded was at best a rationale for morality, and while it was considered to offer some minimal understanding of the divine, this did not extend to any of the basic tenets of Christian dogma. The question of how these were to be explored fell by default to historical forms of enquiry….” Gaukroger, Stephen. 2016. The Natural and the Human: Science and the Shaping of Modernity, 1739-1841. Oxford UP. p. 308.

“Materialism and reduction to the natural sciences play a very small and inessential role in the forms of naturalization that shaped the transformation of the study of human psychology and conduct into empirical disciplines in the second half of the eighteenth century. Indeed, the most powerful naturalizing resource, in the sense of the one that led most effectively to the replacement of basic traditional beliefs about the world and our place in it, was history. The power of history lay in its ability to do something that was wholly outside the resources of reductive forms of naturalization, namely to engage non-propositional forms of understanding.” Gaukroger, Stephen. 2016. The Natural and the Human: Science and the Shaping of Modernity, 1739-1841. Oxford UP. p. 351.

“… it is a privilege to be the recipient of a sulk; it means the other person respects and trusts us enough to think we should understand their unspoken hurt. It is one of the odder gifts of love.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 63.

“What makes people good communicators is, in essence, an ability not to be fazed by the more problematic or offbeat aspects of their own characters. They can contemplate their anger, their sexuality, and their unpopular, awkward, or unfashionable opinions without losing confidence or collapsing into self-disgust. They can speak clearly because they have managed to develop a priceless sense of their own acceptability. They like themselves well enough to believe that they are worthy of, and can win, the goodwill of others if only they have the wherewithal to present themselves with the right degree of patience and imagination.

“As children, these good communicators must have been blessed with caregivers who knew how to love their charges without demanding that every last thing about them be agreeable and perfect.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 73.

“The business of repatriating emotions emerges as one of the most delicate and necessary tasks of love. To accept the risks of transference is to prioritize sympathy and understanding over irritation and judgment. Two people can come to see that sudden bursts of anxiety or hostility may not always be directly caused by them, and so should not always be met with fury or wounded pride. Bristling and condemnation can give way to compassion.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 84.

“There are other ways to look at love. In their philosophy, the ancient Greeks offered a usefully unfashionable perspective on the relationship between love and teaching. In their eyes, love was first and foremost a feeling of admiration for the better sides of another human being. Love was the excitement of coming face-to-face with virtuous characteristics.

“It followed that the deepening of love would always involve the desire to teach and in turn to be taught ways to become more virtuous: how to be less angry or less unforgiving, more curious or braver. Sincere lovers could never be content to accept one another just as they were; this would constitute a lazy and cowardly betrayal of the whole purpose of relationships. There would always be something to improve on in ourselves and educate others about.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. pp. 101-2.

“We are used to loving others in return for what they can do for us, for their capacity to entertain, charm, or soothe us. Yet babies can do precisely nothing…. They teach us to give without expecting anything in return, simply because they need help badly–and we are in a position to provide it. We are inducted into a love based not on an admiration for strength but on a compassion for weakness, a vulnerability common to every member of the species and one which has been and will eventually again be our own. Because it is always tempting to overemphasize autonomy and independence, these helpless creatures are here to remind us that no one is, in the end, ‘self-made’: we are all heavily in someone’s debt. We realize that life depends, quite literally, on our capacity for love.

“We learn, too, that being another’s servant is not humiliating–quite the opposite, for it sets us free from the wearying responsibility of continuously catering to our own twisted, insatiable natures.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 110.

“It is a wonderful thing to live in a world where so many people are nice to children. It would be even better if we lived in one where we were a little nicer to the childlike sides of one another.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 122

“We are never through with the requirement for acceptance. This isn’t a curse limited to the inadequate and the weak. Insecurity may even be a peculiar sign of well-being. It means we haven’t allowed ourselves to take other people for granted, that we remain realistic enough to see that things could genuinely turn out badly–and that we are invested enough to care.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. pp. 136-7.

“It’s a well-known thesis: the people we are attracted to as adults bear a marked resemblance to the people we most loved as children….

“Yet there is one thing we want to do with our grown-up lovers that was previously very much off-limits with our reassuring early caregivers; we seek to have sex with the very individuals who in key ways remind us of types with whom we were once strongly expected not to have sex. It follows that successful intercourse depends on shutting down some of the overly vivid associations between our romantic partners and their underlying parental archetypes.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. pp. 137-8.

“Sexual desire is driven by a wish to establish closeness–and is hence contingent on a preexisting sense of distance, which it is a perpetually distinctive pleasure and relief to try to bridge.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 139.

“The motif of a beloved taking second place to a random stranger in a masturbatory fantasy has no logical part in Romantic ideology. But in practice it is precisely the dispassionate separation of love and sex that may be needed to correct and relieve the burden of intimacy. Using a stranger bypasses resentments, emotional vulnerability, and any obligation to worry about another’s needs. We can be just as peculiar and selfish as we like, without fear of judgment or consequence. All emotion is kept wonderfully at bay: there is not the slightest wish to be understood, and therefore no risk, either, of being misinterpreted and, consequently, of growing bitter or frustrated. We can, at last, have desire without needing to bring the rest of our exhaustingly encumbered lives into the bed with us.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 141.

“From one perspective, it can seem pathetic to have to concoct fantasies rather than to try to build a life in which daydreams can reliably become realities. But fantasies are often the best thing we can make of our multiple and contradictory wishes: they allow us to inhabit one reality without destroying the other. Fantasizing spares those we care about from the full irresponsibility and scary strangeness of our urges. It is, in its own way, an achievement, an emblem of civilization–and an act of kindness.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. pp. 142-3.

“The modern expectation is that there will be equality in all things in the couple–which means, at heart, an equality of suffering. But calibrating grief to ensure an equal dosage is no easy task: misery is experienced subjectively, and there is always a temptation for each party to form a sincere yet competitive conviction that, in truth, his or her life really is more cursed–in ways that the partner seems uninclined to acknowledge or atone for. It takes a superhuman wisdom to avoid the consoling conclusion that one has the harder life.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. pp. 146-7.

“The difficulties of modern parents can in part be blamed on the way prestige is distributed. couples are not only besieged by practical demands at every hour, they are also inclined to think of these demands as humiliating, banal, and meaningless, and are therefore likely to be averse to offering pity or praise to one another, or themselves, just for enduring them. The word prestige sounds wholly inappropriate when applied to the school run and the laundry because we have been perniciously trained to think of this quality as naturally belonging elsewhere, in high politics or scientific research, the movies or fashion. But, stripped to its essence, prestige merely refers to whatever is most noble and important in life.

“We seem unwilling to allow for the possibility that the glory of our species may lie not only in the launching of satellites, the founding of companies, and the manufacturing of miraculously thin semiconductors but also in an ability–even if it is widely distributed among billions–to spoon yogurt into small mouths, find missing socks, clean toilets, deal with tantrums, and wipe congealed things off tables.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 147.

“Isn’t the rejection of adulterous possibilities tantamount to an infidelity towards the richness of life itself? To turn the equation on its head: Would it be rational to trust anyone who wasn’t, under certain circumstances, really pretty interested in being unfaithful?” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 165.

“Adventure and security are irreconcilable…. A loving marriage and children kill erotic spontaneity, and an affair kills a marriage. A person cannot be at once a libertine and a married Romantic, however compelling both paradigms might be.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 181.

“Marrying anyone, even the most suitable of beings, comes down to a case of identifying which variety of suffering we would most like to sacrifice ourselves for.

“In an ideal world, marriage vows would be entirely rewritten. At the altar, a couple would speak thus: ‘We accept not to panic when, some years from now, what we are doing today will seem like the worst decision of our lives. Yet we promise not to look around, either, for we accept that there cannot be better options out there. Everyone is always impossible. We are a demented species.

“After the solemn repetition of the last sentence by the congregation, the couple would continue: ‘We will endeavor to be faithful. At the same time, we are certain that never being allowed to sleep with anyone else is one of the tragedies of existence. We apologize that our jealousies have made this peculiar but sound and non-negotiable restriction very necessary. We promise to make each other the sole repository of our regrets rather than distribute them through a life of sexual Don Juanism. We have surveyed the different options for unhappiness, and it is to each other we have chosen to bind ourselves.’

“Spouses who had been cheated upon would no longer be at liberty furiously to complain that they had expected their partner to be content with them alone. Instead they could more poignantly and justly cry, ‘I was relying on you to be loyal to the specific variety of compromise and unhappiness which our hard-won marriage represents.’” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 182.

“We are so impressed with honesty that we forget the virtues of politeness; a desire not always to confront people we care about with the full, hurtful aspects of our nature.

“Repression, a degree of restraint, and a little dedication to self-editing belong to love just as surely as a capacity for explicit confession. The person who can’t tolerate secrets, who in the name of ‘being honest’ shares information so wounding to the other that it can never be forgotten–this person is no friend of love.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 183.

“Rather than some notional idea of perfect complementarity, it is the capacity to tolerate dissimilarity that is the true marker of the ‘right’ person. Compatibility is an achievement of love; it shouldn’t be its pre-condition.” De Botton, Alain. 2016. The Course of Love. NY: Simon & Schuster. p. 217.

“This book is a confession…. I, too, am responsible for Russia’s war against Ukraine…. Regrettably, Russian culture is also to blame for making all these horrors possible.” Zygar, Mikhail. 2023. War and Punishment: Putin, Zelensky, and the Path to Russia’s Invasion of Ukraine. NY: Scribner. p. 1.

“The oligarchic systems of Russia and Ukraine are very similar. That said, the one built by Kuchma turns out to be more stable: every Ukrainian oligarch is basically a monopolist in their industry, which stops them warring with each other; each has their own allotment, which makes them more interested in cooperation than confrontation. And together they exert a vast influence on politics: they buy politicians and regional officials, and set their own rules of the game, while the president acts like a jury foreman, preventing them from quarreling. Russia in the 1990s knows no such stability: the oligarchs fight endlessly, the president is dysfunctional, and his family cannot maintain the balance and must rely heavily on one of the business groups.” Zygar, Mikhail. 2023. War and Punishment: Putin, Zelensky, and the Path to Russia’s Invasion of Ukraine. NY: Scribner. pp. 191-2.

“But something else definitely has happened. Russia as an empire had been consigned to the past, as a direct and irreversible consequence of the war….

“Imperial history is our disease; it’s inherently addictive. And the withdrawal symptoms will hurt. But this is inevitable. We have to return to reality and realize what we’ve done.

“We have to learn this lesson. To stop believing in our own uniqueness. To stop being proud of our vast territory. To stop thinking we’re special. To stop imagining ourselves as the center of the world, its conscience, its source of spirituality. It’s all bunk.” Zygar, Mikhail. 2023. War and Punishment: Putin, Zelensky, and the Path to Russia’s Invasion of Ukraine. NY: Scribner. pp. 370, 371.

“Grief is praise, because it is the natural way love honors what it misses.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 31.

“For modern people needing to grieve but having no culture in which to really do it, this older community of the wide beautiful fish-filled ocean [or lake] is the water of all grief and will be as close to a tribe that listens as they’re probably going to get.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 48.

“The person or persons feeling such things [anger at someone who wronged them and desire for revenge] were quite right in feeling them if they truly felt them. And the older men and women would never deny their feelings or brand them as something that should not be both heard and corroborated. But feelings were considered a kind of wind, and there was no need to freeze the wind, but better to thaw the clouds of hate into a rain of tears that fed the thirsty ground of the human soul. If feelings of revenge were occulted and not listened to, they certainly would freeze and reappear toxically and violently later. Change they must.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 81.

“Wars are the pile up and oversaturation of losses of previous wars never allowed to ‘metabolize’ and break down through grief into its original particles to restore itself to the living. War is an enormity of sorrow looking for new blood to pay the overwhelming debt of ungrieved blood from the previous war. A new war declared on any level is what happens when all those involved cannot, will not, or are not allowed to grieve the sorrows and terrible losses of the previous generations of war. In any phase or action of a war for any motive, there has never been a way to grieve properly. So one war always demands another war to fill the hole and pay for the previous war.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 98.

“The willingness for violence-shattered soldiers [ex-soldiers] to heal others makes their malady into medicine.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 101.

“The unwillingness to grieve makes people search for someone upon which to project blame for the feeling of the loss they bear. This turns all losses into wars of revenge…. Wars against the natural world are carried out in the name of business profit in the name of more money, money that is nothing more than the story of the world’s grief with no one to hear it.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. pp.112-113.

“We know then that grief, like a welcome rainstorm on parched sand, is not an illness, but a primordial institution of the human soul. It is our innately supplied dressing for the fresh wounds of the losses we sustain in the struggle to love as a way of life.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 119.

“Beauty is anything seen, felt, or realized that charms or delights the better part of us into wanting to live on, in order to see, feel, and understand more without the scared part of us being in charge of what it wants the world to be.” Prechtel, Marin. 2015. The Smell of Rain on Dust. Berkeley: North Atlantic Books. p. 153.

“I once heard an Andean shaman describe evil as ‘anything that is not you and doesn’t belong in your space.’” Suler, Asia. 2022. Mirrors in the Earth: Reflections on Self-Healing from the Living World. Berkeley, CA: North Atlantic Books. p. 28.

“The abundance of water makes … gardening the ultimate master class in boundary holding. Gardening, boiled down to its minerals, is a process of deciding what you would like to cultivate and letting the world know that you are claiming this space for growth.” Suler, Asia. 2022. Mirrors in the Earth: Reflections on Self-Healing from the Living World. Berkeley, CA: North Atlantic Books. p. 31.

“Boundaries open the door to coming into a reciprocal relationship with nature itself. When we learn how to protect and enshrine our own selves, we naturally develop a healthy respect for the agency, autonomy, and boundaries of all beings–creating spaces where every creature’s sovereignty is recognized. When you honor your boundaries, you naturally cultivate respect for others. When you care for your own personhood, you open your eyes to seeing the world as a collection of animate individuals who deserve the same kind of enshrinement.” Suler, Asia. 2022. Mirrors in the Earth: Reflections on Self-Healing from the Living World. Berkeley, CA: North Atlantic Books. p. 40.

“Through the reverberations of trauma may be the farthest thing from beauty, the healing that can come after–the pirouette of our resiliency, the way we integrate that learning to become the people we were meant to be–is perhaps the most beautiful and transcendent force on Earth.” Suler, Asia. 2022. Mirrors in the Earth: Reflections on Self-Healing from the Living World. Berkeley, CA: North Atlantic Books. pp. 73-4.

“True belonging only happens when we present our authentic, imperfect selves to the world, our sense of belonging can never be greater than our level of self-acceptance.” Brown, Brene. 2015. Daring Greatly: How the Courage to Be Vulnerable Transforms the Way We Live, Love, Parent, and Lead. NY: Avery. pp. 145-6. Quoted in: Suler, Asia. 2022. Mirrors in the Earth: Reflections on Self-Healing from the Living World. Berkeley, CA: North Atlantic Books. p. 116.

“What I present in this book are translations of what I have been taught about modernity keeping us in an immature state; and the need for a political practice of healing, of radical tenderness, that can enable us to step up, to grow up, and to show up differently. This involves unlearning our learned ways: of thinking and imagining, of sensing and feeling; of relating to one another, the earth, and the cosmos, of facing life, fear, pain, loss, and death…. This requires that we learn how to face our shadows, how to compost our ‘shit,’ and how to weather storms together. For this to happen, we need a container where we can manifest unconditional regard for everyone’s being; while we commit to interrogating our thinking, our doing, our hopes and desires, and our ways of relating in order to breathe and to move together with maturity, sobriety, discernment, and accountability. This book is an attempt to create that container.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. xxi.

“Many critics of modernity/coloniality use the term epistemic or cognitive imperialism to refer to this imposition [of word meanings on select objects of reality], while the term epistemicide, coined by Boaventura de Sousa Santos, is used to refer to the delegitimization and elimination of ways of knowing and being that deviate from the imposed norm.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 22.

“[expanded patterns to overcome Modernity] “… the ‘4 Hs’: humility, honesty, humor, and hyper-self-reflexivity.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 26.

“This [‘depth education’ in contrast to mastery education or the acquisition of credentials] is defined as a mode of engagement designed to prompt us to dig deeper and to relate wider, disinvest in harmful desires, activate accountability and responsibility before will, and become open to being taught by the world in unexpected ways. Depth education focuses on complexities and paradoxes and it invites all of us to sit with difficulties; unpack investments; confront resistance; disarm affective land mines; relate beyond meaning, identity, and understanding; rationally explore the limits of rationality; and face humanity within and around us in all its complexity: the good, the bad, the broken, and the messed up.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 43.

“The bus methodology invites us to see a whole bus of people within us [as various inner voices, selves, or perspectives]. At its most basic level, this bus has a driver and many passengers who embody what has marked one’s lifetime, including childhood events, unprocessed traumas, significant others, etc. Some of these passengers are at the front of the bus and their voices are loud and well known, some are seated in the middle of the bus and can only be heard at the front in certain occasions, and some are at the back and may even be unknown to the driver(s). Sometimes there is conflict amongst the passengers. Sometimes there are rebellions on the bus and it can be hijacked by rogue passengers…. The basic premise of the methodology is that if we cannot hold space for the complexities within us, there is no chance for us to hold space for the complexities around us.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 48.

“The final beyond-reform proposition [the perspective that Modernity cannot be saved] is what we have termed hospicing, which recognizes the eventual inevitable end of modernity’s fundamentally unethical and unsustainable institutions, but sees the necessity of enabling a ‘good’ death through which important lessons are processed. These lessons are learned through the accomplishments and mistakes of the dying system, so that they can be applied as we witness and help midwife the birth of something different. This approach also requires that we hospice our own investments in modernity’s promises not as a reactive rejection of modernity and attempt to control the terms of its dissolution, but rather as self-implicated processes of facing up to our own harmful desires and habits of being.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 93.

“As I remember, in this ritual [as described to author by an Indigenous elder in Brazil, probably Guarani] a young person would be buried naked in the earth vertically, with only their head sticking out. They would be there for four days, without food or water. Since they could not move, they had to do their necessities in that same place. They would have a helper keeping a fire nearby and watching for dangerous animals.

“On the first day of the ritual, members of the community were supposed to collectively bury the person singing this person’s praises. On the second and third days of the ritual, members of the community were supposed to come to the head in the ground and spit and shout insults at it. The buried young person was not supposed to respond. They had to accept everything in silence–but not as a form of submission, quite the opposite. The young person was supposed to find their grounding on the living land that held them for the four days. In this way, their sense of intrinsic worth would not be grounded in human interactions–including the opinions of other members of their own community–but in the sense that we are held by the land itself. At the end of the fourth day, the young person was physically cleaned by members of the community, there was a feast, and dream stories were shared.

“I remember asking the storyteller if all those insults did not leave an imprint in the young person for life, which seemed really dangerous to me. His response was that Indigenous people could not shelter from insults–they received them constantly from the dominant society, and from Indigenous people who were sick on the inside as well. He said that if young people’s self-esteem depended upon external validation from other people’s opinions, they would be vulnerable to the imprint of violence–including the white man’s violence. If they depended on the praise of others for self-worth, they would not genuinely have trust in themselves, they would not trust the land, they would be weak and vulnerable to the white man’s diseases, and they could themselves become predators.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. pp. 208-9.

“Modernity dying, not on our terms, can also be considered a rite of passage for humanity.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 214.

“Social media has unrestrained our vanity and taught us to ‘like’ narcissism….” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 234.

“The end of modernity may not manifest primarily as economic or ecological collapse, but as a global mental health crisis where the structures of modernity within us start to crumble.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 234.

“Hospicing involves intellectual accountability and existential surrender. Assisting with midwifery [helping transition to something after Modernity] involves existential accountability and intellectual surrender. Intellectual accountability is about facing the truth behind our denials and projections sitting with our complicity in harm; shedding arrogance and accepting accountability without seeking recognition, redemption, innocence, or purity. Existential surrender is about interrupting addictions and business as usual, confronting fragilities, learning to compost personal and collective shit, and relinquishing colonial entitlements. Existential accountability is about staying present to what is real and painful, centering the living metabolism, integrating medicines, and choosing to grow up. Intellectual surrender is about discernment, learning to let go, tapping collective exiled capacities, developing metabolic literacies, dissolving individuality and separability, and enabling a bio-intelligence to guide us.” Machado de Oliveira, Vanessa. 2021. Hospicing Modernity: Facing Humanity’s Wrongs and the Implications for Social Activism. Berkeley: North Atlantic Books. p. 238.

“Indeed, nothing in human’s extensive knowledge about physical and chemical systems including rather intricate, non-equilibrium, ‘self-organizing’ processes suggests, even remotely, the feasibility of cellular physiology, as we observe it in nature. Nothing in principle excludes it; but nothing hints at it, either.” Ruiz-Mirazo, Kepa. 2022. “Autonomy Beyond the Proto-cell: Towards a ‘Dialectical Turn’ in Origins-of-life Research.” Dialectical Systems. p. 1.

“The metabolic activity that cells constantly carry out is thermodynamically uphill: it implies an enormous material and energetic cost (and that’s why cells are not merely open systems, but agents that actively extract resources from their local environments and transform them into their own means)…. So to speak, biology takes place within but, at the same time, beyond physics and chemistry: it belongs to the latter, no doubts about that; but it has ‘self-emancipated’ to a remarkable extent.” Ruiz-Mirazo, Kepa. 2022. “Autonomy Beyond the Proto-cell: Towards a ‘Dialectical Turn’ in Origins-of-life Research.” Dialectical Systems. p. 1.

“… I would propose that the potential of physics and chemistry to generate biological ‘hyper-complexity’ is realized, in practice, when matter implements constraining mechanisms leading to ‘dual-control’ systems. According to that classical idea, living cells, on top of obeying the universal laws of physics and chemistry, like any other natural system, are characterized by their capacity to generate and maintain their own boundary conditions, their local rules of behaviour. At this fundamental, constitutive level, such rules are essentially molecular and supra-molecular mechanisms that both constrain and enable the dynamics of other components and transformation processes pertaining to the system. As a result, cellular organization articulated around its metabolic activity by means of a suite of diverse self-constraining mechanisms (spatial, kinetic and energetic control mechanisms, among others), is to be regarded as the kernel of life, the main axis of all biological phenomenology, and surely the key to decipher its emergence.

“However, minimal living cells (bacteria/archaea) are way more complex than what the principles of autonomy seem to require for an elementary metabolism. ‘Genetically-instructed’ cellular metabolisms (involving the materially and energetically extravagant synthesis of a whole suite of interdependent macromolecules: DNA, RNA and proteins) appear to be very elaborate instances of ‘autonomous molecular agents’ (as coined by Kauffman [2003]). Despite the lack of empirical evidence on prebiotic (or infra-biological) autonomous systems, a number of theoretical results point clearly in this direction, including our own protocell modelling work over the years. Anyhow, such a ‘complexity gap’ is too evident to be ignored, on bare conceptual grounds, and those authors who do not consider genetic mechanisms as relevant for minimal biological organization might be overlooking something big there. While we wait for the field of origins-of-life (or synthetic biology) to solve the question about autonomous systems below the ‘minimal’ cell threshold’, two alternative positions can be adopted: (i) take this apparent gap as a historical/evolutionary accident (i.e., all living cells just happen to be at least as complex as current terresterial prokaryotes); or (ii) take it as a necessary historical/evolutionary outcome (i.e., all living cells need to be, here and anywhere else in the universe, as complex as currently terrestrial prokaryotes).” Ruiz-Mirazo, Kepa. 2022. “Autonomy Beyond the Proto-cell: Towards a ‘Dialectical Turn’ in Origins-of-life Research.” Dialectical Systems. pp. 1-2.

“So let us take as working hypotheses the following two ideas. First, that autonomy is an adequate theoretical construct to capture biological individuality, realized – in its minimal and most universal expression – as unicellular (prokaryotic) organisms. Second, that autonomy is also bound to illuminate fundamental transitions in the process of origins: in other words, that different forms of autonomy, simpler than unicellular (prokaryotic) organisms, are not only feasible in the world of physics and chemistry, but necessary to pave the way towards biology.” Ruiz-Mirazo, Kepa. 2022. “Autonomy Beyond the Proto-cell: Towards a ‘Dialectical Turn’ in Origins-of-life Research.” Dialectical Systems. p. 2.

“Noncovalent synthesis[:] Single-step self-assembly of a few components, such as small molecules or polymers, must shift to multistep synthetic strategies to mimic complex biological structures such as the extracellular matrix.” Vantomme, Ghislaine & E.W. Meijer. 2019. “The construction of supramolecular systems: Self-assembly must be transformed into multistep synthesis to create complex structures.” Science. 363(6434):1396-7. doi: 10.1126/science.aav4677. p. 1397.

“Similar to sophisticated covalent synthesis, the devil is in the details for noncovalent synthesis too. The formation of noncovalent structures is mostly performed under ambient conditions. However, to enlarge the energies experimentally reachable and fine tune the reactivity of the noncovalent bond, noncovalent synthesis has to be explored at low temperature, in dry solvent, and under inert atmospheres. So far, pathway selection is achieved by tuning kinetics at different temperatures and solvents, but why are catalysts hardly available to direct the noncovalent reaction, such as a template or chaperone? From the knowledge gained by a stepwise approach, new concepts should logically emerge, such as toposelectivity, the selective reactivity in one physical direction over all others possible. Many more of these questions ought to be answered to obtain a toolbox that enables retrosynthetic approaches rivaling those seen in covalent chemistry….

“To initiate this paradigm shift is to recognize that the sample preparation has a huge impact on the structures formed, and it requires rigorous reporting of the details in publishing, replacing the current stochastic method of exploration of available structure-energy combinations of the system. Assembly processes require very rigorous protocols, documenting procedures so that noncovalent synthetic routes are reproducible and can be repeated in multiple laboratories.” Vantomme, Ghislaine & E.W. Meijer. 2019. “The construction of supramolecular systems: Self-assembly must be transformed into multistep synthesis to create complex structures.” Science. 363(6434):1396-7. doi: 10.1126/science.aav4677. p. 1397.

“Based on previous works and decades of study, we propose a complete scenario divided in four ages: (i) the prebiotic age; (ii) the age of FUCA and the origin of life; (iii) the age of progenotes; and (iv) the age of organisms.” Prosdocimi, Francisco & Savio Torres de Farias. 2023. “Origin of life: Drawing the big picture.” Progress in Biophysics and Molecular Biology. 180-181:28-36. doi: 10.1016/j.pbiomolbio.2023.04.005. p. 28.

“Our proposal of a chemical symbiosis between nucleic acids and proteins as the most relevant event in the early origin of life acknowledge the relevance of both nucleic acids and proteins.” Prosdocimi, Francisco & Savio Torres de Farias. 2023. “Origin of life: Drawing the big picture.” Progress in Biophysics and Molecular Biology. 180-181:28-36. doi: 10.1016/j.pbiomolbio.2023.04.005. p. 30.

“We conjecture that the origin of a proto-PTC [Peptidyl Transferase Center – region of catalytic site of the ribosome; authors claim this region is related to structure of tRNAs] from random concatamers of proto-tRNAs was probably the first step that linked the nucleic acids world to the amino acidic world. Other authors also suggested that it was only with the establishment of the interaction between amino acids and nucleic acids that life became established. The proto-PTC enhanced the relationship between two previously separated biomolecular worlds. The existence of PTC allowed that nucleic acids and peptides could start to interact for the benefit of both, allowing the emergence of order in nature. The production of small, quasi-random peptides allowed that the nucleic acids and some of these recently formed peptides become more stable. It also allowed those amino acids to form longer chains of proteins, capable to fold in complex structures and interact with other molecules in the prebiotic soup, increasing the number of bonds, linkages, and interactions.” Prosdocimi, Francisco & Savio Torres de Farias. 2023. “Origin of life: Drawing the big picture.” Progress in Biophysics and Molecular Biology. 180-181:28-36. doi: 10.1016/j.pbiomolbio.2023.04.005. p. 31.

“Also, the RNA-world would never become living if the self-replicating RNA molecules and ribozymes did not bound [sic; = “bind”?] amino acids to produce encoded peptides. In this scenario, the origin of life is a case of chemical symbiosis, and it happened when nucleic acids and peptides started to interact, crosstalk and stabilize each other’s structures. When the proto-PTC emerged, a critical aspect of life started its way and FUCA was born.” Prosdocimi, Francisco & Savio Torres de Farias. 2023. “Origin of life: Drawing the big picture.” Progress in Biophysics and Molecular Biology. 180-181:28-36. doi: 10.1016/j.pbiomolbio.2023.04.005. p. 31.

“Under the current conjecture, the world of progenotes will endure along the entire transition from FUCA to LUCA. It was there that the metabolic routes have been created and evolved based on peptides that bound other molecules in the prebiotic soup. The world of progenotes was an age on which free, naked RNP [ribonucleoprotein] molecules created [propitious?] conditions to their living. Along this era, RNP molecules and their encoded peptides started to interact more directly with other metabolites present in the media. As life started as ribonucleoproteins, other molecules and metabolites in the pool came to be incorporated in life by interacting with peptides, RNAs and RNPs that constituted the progenotes.” Prosdocimi, Francisco & Savio Torres de Farias. 2023. “Origin of life: Drawing the big picture.” Progress in Biophysics and Molecular Biology. 180-181:28-36. doi: 10.1016/j.pbiomolbio.2023.04.005. p. 32.

“Another relevant concepts [sic] to have in mind when we understand that viruses most likely existed before cells are related to two important issues: (i) viruses are orders of magnitude simpler than cells (Occam’s razor); and (ii) the basic core of life and living organisms are related to processes involving ribonucleoproteins, not lipids.” Prosdocimi, Francisco & Savio Torres de Farias. 2023. “Origin of life: Drawing the big picture.” Progress in Biophysics and Molecular Biology. 180-181:28-36. doi: 10.1016/j.pbiomolbio.2023.04.005. p. 32.

“These three bioplymers, the subject of this paper, are polynucleotide (DNA and RNA), polypeptide (protein), and polysaccharide (polymerized sugars). Biopolymers have special properties that distinguish them from other polymers.
Biopolymers:
(ii) spontaneously fold and assemble into precise and highly elaborate yet fragile assemblies with meager stabilities,
(ii) spontaneously degrade by hydrolysis in the aqueous environments characteristic of biological systems.
(iii) are self-protective against hydrolysis (by folding) and partner-protective (by heterogeneous assembly).” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 598.

“It is a fundamental paradox of biochemistry that biopolymers are chemically unstable in their native environment–aqueous solution.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 601.

“Phosphorylated intermediates appear to be necessary for the mechanochemical coupling required for processive polymerization. The polmerases that make DNA, RNA, protein, and polysaccharide are nanoscale motors…. This coupling of directed molecular displacement (work) to association/dissociation of phosphate, which is in turn linked to pyrophosphate hydrolysis, has been characterized in myosin and kinesin, in the ribosome and in DNA, RNA, and cellulose polymerases. During polymerizations of DNA, RNA, protein, and polyglucose, translocations are structurally and energetically coupled to phosphate association/dissociation.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 606.

“Biopolymers satisfy all of the formalisms of mutualism. Biopolymers protect each other from hydrolysis and synthesize each other…. Molecules in Mutualism describes: (i) survival–extant biopolymers are more persistent than competing polymer types, which are now extinct; (ii) co-evolution–biopolymers created each other in an emergent and cooperative environment of chemical evolution; (iii) fitness–biopolymers are more ‘fit’ in combination than in isolation; (iv) distance–each biopolymer type has distinct proficiencies and chemical characteristics; (v) innovation–proficiencies of one type of biopolymer release constraints on partner biopolymer types; (vi) robustness–biopolymer types have been fixed for billions of years, meaning biopolymers compose seminal and ancient mutualism with profound stability; and (vii) parasitism–examples of molecular self-interest and escape from mutualism are seen in amyloids and phase-separated RNA gels.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 607.

“Biology requires biopolymers. Biopolymers allow processes of folding and assembly to be detached from the required investment of free energy. For biopolymers, prior free energy investment in synthesis is distributed over time and space, offsetting the subsequent cost of folding and assembly. Biopolymers appear to spontaneously fold and assemble, only because of prior free energy investments.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 607.

“The data surveyed here suggest that polypeptide, polynucleotide, and polysaccharide arose by co-evolution. Biopolymer universalities, including (i) synthesis by condensation and degradation by hydrolysis, (ii) folding by pre-organization and self-complementarity, (iii) homogeneous and heterogeneous assembly, and (iv) protection by folding or homogeneous assembly (selfishness) and (v) protection by heterogeneous assembly (mutualism), point to simultaneous origins in a shared environment.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 607.

“… polymer synthesis by condensation cooperated with hydrolytic degradation, mediated by folding and assembly, to drive chemical evolution. In contrast to the consensus, this model suggests that early selection operated at the level of hydrolytic degradation (mitigated by folding and assembly), rather than at the level of synthesis. After nearly 4 billion years of evolution, biopolymers continue to utilize self-complementarity to escape hydrolysis and increase persistence.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 607.

“Persistence of biopolymers in a hydrolytic environment is enhanced by folding and assembly. Self-complementarity is therefore an expression of self-interest, a method to escape from hydrolysis, a path to survival, and a property universal to biopolymers. Heterogeneous assemblies are expressions of partner-protection from hydrolysis, described here and elsewhere as molecular mutualisms.

“The observed nominal stability, rather than extreme stability, of biopolymer folds and assemblies, suggests that unfolding and disassembly confers advantage in some circumstances. The ability to unfold and disassemble provides pathways for prospecting for new folds and new partners and for recycling. Extremely stable folds and assemblies could persist for some period but ultimately form molecular dead-ends.” Runnels, Calvin M., Kathryn A. Lanier, Justin Krish Williams, Jessica C. Bowman, Anton S. Petrov, Nicholas V. Hud & Loren Dean Williams. 2018. “Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.” Journal of Molecular Evolution. 86:598:610. doi: 10.1007/s00239-018-9876-2. p. 608.

“We consider chemical evolution to be a process of continuous molecular change, with progression to new chemical spaces. In our model, early stages of chemical evolution selected monomers based on kinetic and thermodynamic landscapes governing condensation and hydrolysis. Intermediate stages selected oligomers on the basis of emergent properties such as folding, assembly, and catalysis. The end phases gave rise to biopolymers. Chemical evolution harvests energy provided by environmental cycling, including wet-dry cycling. A near-equilibrium chemical mixture that uses water as both reactant and product can chemically ratchet, when subjected to oscillating water activity.” Mueller, Ulrich F., Jamie Elsila, Dustin Trail, Saurja DasGupta, Claudia-Corina Giese, Craig R. Walton, Zachary R. Cohen, Tomislav Stolar, Ramanarayanan Krishnamurthy, Timothy W. Lyons, Karyn L. Rogers & Loren Dean Williams. 2022. “Frontiers in Prebiotic Chemistry and Early Earth Environments.” Origins of Life and Evolution of Biospheres. 52:165-181. doi: 10.1007/s11084-022-09622-x. p. 174.

“Two main ideas appear to contribute to the concept of reproduction. One is that ‘new individuals’ are added to the set of existing ones. In this demographic concept of reproduction, ‘new’ should be understood as a quantitative addition to the number of entities that already exist. The second is the idea of producing ‘individuals that are new’, compared to the existing ones. In this innovative concept of reproduction, ‘new’ should be understood as qualitatively different from the pre-existing kinds of entities…. According to the demographic concept, the focus is on replacing the individuals that inevitably perish, thus maintaining or possibly increasing the size of the population. In contrast, according to the innovative concept, the focus is on the appearance of ‘something new under the sun’.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 7, 11.

“At the genetic level sex can be defined as the set of biological processes through which new combinations of genetic material are created from different sources. These phenomena of genetic reassortment may or may not be associated with reproduction.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 14.

“In the cycle of the fern there are at least two generations (a sporophyte and a gametophyte), which constitute two distinct organizational forms, i.e. two distinct kinds of individuals, or kinds of generations of the same species, each with its own ontogeny. In the case of the fern, there is one that from a zygote develops into a macroscopic diploid leafy plant, and another that from a spore develops into a tiny haploid thallus….

In multigenerational life cycles there are reproductive phases where offspring are generated that are not of the same kind (of the same organizational form) as the parents(s), so that more than one generation is needed to return to the starting form.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 21-3.

“We define here the life cycle (or biological cycle) of an organism as the series of developmental transformations and reproductive phases that lead from a given developmental stage of a given organizational form, to the same developmental stage of the same organizational form in a following generation, through all the organizational forms of the organism. The life cycle summarizes the processes of physical transformation of an organism and the processes of propagation that allow it to have descendants. It can include one or more developmental processes and one or more reproductive phases.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 23.

“A possibility that we suggest here is to start from the definition of a life cycle, and to consider as development all those processes of transformation that are complementary to reproduction. In a life cycle we can have one or more reproduction events, carried out by as many generations, within which are intercalated an equal number of developmental sequences. From this idea, a definition of development follows, as the set of transformations of an individual from its individuation (however defined) until its disappearance (however defined)….

For instance, in a textbook of developmental biology it will be necessary to specify in detail which of the transformations an individual undergoes should be treated in the context of developmental processes (e.g. growth, differentiation, morpho-genesis, ageing and regeneration), and which should be left to other biological disciplines such as physiology and the behavioural sciences, which are generally concerned with reversible transformations occurring on a relatively short timescale.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 24, 25.

“All forms of asexual reproduction and all forms of sexual reproduction with a clonal outcome therefore represent a problem for a definition of individuality based on genetic uniqueness.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 26.

“But even the simple intraorganismal genetic heterogeneity that normally tends to be considered negligible may become relevant in very old or very large organisms (i.e. those with many cells), in which the last common ancestor of two cells in the same individual’s body may be traced many mitotic cycles back. In an old oak tree, numerous mutations may have accumulated in the meristems that give rise to new branches and new flowers every year. Because of the modular organization of these plants, each mutation in a meristem is inherited by the whole branch that develops from it, and each terminal branch can be an independent site of sexual reproduction (and perhaps, from an evolutionary perspective, selection), and thus the genetic make-up of the cells that form pollen and ovules in a branch can be significantly different from that of similar cells in another branch of the same tree.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 27.

“A chimera is instead [of genetic mosaicism where genetic rearrangement in a new individual comes from a single founder cell] a multicellular individual made of cell populations originating from more than one founder cell. Chimeric gametophytes originating from the fusion of several spores have been described for the red alga Gracilaria chilensis. Among cnidarians, conspecific coral larvae (planulae) often merge into one individual before differentiating into a polyp.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 27.

“Monkeys of the genus Callithrix generally give birth to two dizygotic (non-identical) twins. But these are not ‘normal’ twins. During pregnancy, connections between the two placentas are established so that cell exchanges occur between the two embryos. When the two little monkeys are born, each of them is a mixture of cells derived from the independent fertilizations of two distinct eggs. The case is even more remarkable when the two embryos are of different sexes. Thus, through this form of reproduction, two ‘genetic individuals’ and two ‘physiological individuals’ are obtained, but the two genetic individuals are distributed between the two physiological individuals.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 28.

“… a form of chimerism also frequently affects the adult females of our own species (together with those of other placental mammals). Following pregnancy, blood cells from the fetus may remain in circulation and multiply in the mother for decades after birth (fetal microchimerism).” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 28-9.

“A biological individual could be characterized as an undivided morpho-functional living unit, able to relate to the environment independently, including the ability to properly respond to environmental stimuli and the faculty to reproduce. Individuals lacking these characteristics are the members of highly integrated colonies, such as those of some marine invertebrates.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 29.

“In some abyssal fishes (Ceratioidei), the male, after a short independent life, attaches to a female, enters into intimate contact with her tissues and becomes an appendage of her body, fed by her through their conjoined circulatory systems, but able to produce sperm. The male loses his autonomy (sexual parasitism); while from this union a chimeric hermaphrodite is produced.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 29-30.

“Santelices goes beyond listing the problems that make it difficult to define an individual, and tries to define different ‘kinds of individual’, each characterized by the presence or absence of the aforementioned features…. Eight types of individual characterized by presence or absence of each of three attributes: genetic uniqueness, genetic uniformity, physiological autonomy….

“In other words, there are different kinds of individual.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 30, 31; reference: Santelices, B. 1999. How many kinds of individual are there?” Trends in Ecology and Evolution. 14:152-155.

“Most prokaryotes and many protists, including several species of amoebozoans, cryptophytes, chlorophyceans, apicomplexans, euglenozoans and radiolarians, do not seem to experience senescence. Also, there is no certain evidence of senescence in some plants that live for a very long time, over 4000 years, such as some conifers, some sponges and sea anemones, hydras, the queens of different species of social insects, some tube-dwelling polychaetes and certain bivalves.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 34.

“An individual or cell that does not age, or ceases to age at some point in its existence, is said to be biologically immortal.

“But let’s try to understand more precisely what it means to be immortal. Most prokaryotes and many protists do not show any sign of senescence and are therefore rightfully listed among the immortals. However, even here, reproduction has some role in rejuvenation. Consider an amoeba, which reproduces by binary fission. The parent individual ceases to exist when, by dividing, it generates the two daughter cells. This disappearance, which could be considered a mere by-product of our arbitrary definitions of individual and generation, is in fact of great importance. The single amoeba could not live indefinitely without dividing, and therefore as an individual it is not immortal, not even potentially. During the life of an organism, especially if this is long, irreparable damage inevitably accumulates at the molecular level (not only in DNA) for purely accidental reasons. This unceasing degradation is inexorably ruled by the second law of thermodynamics, which would lead to the organism’s death anyway. Only reproduction, by diluting the damaged molecules in the descendants, and by means of purifying selection acting on those descendants, is able to maintain the health of the clone. In a sense, reproduction has a rejuvenating effect even on organisms that to do not age!” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 35-6.

“Eventually, when the telomeric sequences have been consumed, the cell is no longer able to divide. In somatic cells, the maximum number of divisions (30-50) is known as the Hayflick limit. Shortening of telomeres due to DNA replication also affects germline cells, but here a particular enzyme (telomerase) is also expressed, which is capable of elongating the telomeric sequence. This allows germline cells to evade this form of senescence and to replicate virtually without limits.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 36.

“…for most living things, those affected by senescence, it is not enough for reproduction to generate new individuals, in addition to those already present, or to replace those that have died. Reproduction must also ensure that newborns are actually ‘young’, i.e. that they have, so to speak, ‘turned back the clock of senescence’, so that the population actually ‘rejuvenates’ through reproduction. Generating young individuals from old individuals is an imperative for the continuity of life.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 37.

“Sexual reproduction has this ability to rejuvenate. Through the cytogenetic processes that lead to the formation of gametes in multicellular organisms, or give a haploid unicellular individual competence to fuse with another, the senescence timer is effectively reset to zero. The life expectancy of a fertilized egg (zygote) is definitely higher than that of the two parents from which the two gametes were produced.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 37.

“Few would maintain that the changes in the genetic make-up of a single individual that occur without the contribution of exogenous DNA (e.g. a gene mutation) should count as the production of a new individual. To question the identity of the individual after such a transformation is equivalent to denying the possibility that an individual can remain itself through a change in its qualities, and ultimately means denying the temporal extension of an individual and its historical continuity. However, there are different opinions regarding sexual processes, i.e. those changes in the genetic make-up of an individual that occur because of the recombination of DNA from different sources.

“The most widely shared view on this question, and the one adopted here, is that, on their own, sexual processes do not count as reproduction, which is equivalent to saying that there is a category of sexual processes separate from the category of sexual reproduction. The conjugation of bacteria and the conjugation of ciliates are examples of sex without reproduction.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 42.

“According to some authors, genetic identity is the fundamental criterion for defining a biological individual. In this view, any form of clonal propagation, which produces multiple copies of an individual’s genotype without modifying it (at least to any great extent), is not seen as reproduction, but rather as the growth of one individual.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 43.

“Many plants, many invertebrates and many fungi, as well as most unicellular organisms, are able to propagate without introducing genetic novelty, by generating new individuals from portions of the parent’s body or, in the alternative interpretation, by growing new, more or less strongly connected, body modules.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 43.

“A genet is a set of genetically identical entities (which can be considered individuals or modules of an individual) derived by clonal multiplication from a single genetically unique individual. All the apple trees of the “red Delicious’ variety, which are derived by cuttings from a single tree that lived in Iowa in the late 1800s, are part of a single genet…. In contrast, a ramet is an anatomically and physiologically bounded biological entity, independent of its genetic constitution. As such, it may well be a member of a genet.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 44.

“An emblematic case of vegetative reproduction is provided by a ‘vegetal entity’ known as Pando (or the Trembling Giant). What looks like a forest of quaking aspen (Populus tremuloides) covering about 45 hectares in Utah, is nothing but a clone of a single (genetic) male individual that would constitute, according to some a single living organism, which weighs about 6600 tonnes and includes ca. 47,000 trunks that continually decay and are regenerated by a single gigantic root system. This organism would be about 80,000 years old and would thus be the heaviest and oldest known living organism.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 44.

“Although it may be difficult to produce a rigorous definition of life-cycle complexity, intuitively we might suggest that this is related to the number and scope of the changes the organism undergoes during its cycle. These may be changes in the organism’s form, such as between the pluteus larva and the adult sea urchin, or changes in the environment, such as between the pelagic larva and the benthic adult of many aquatic molluscs, or changes in the reproductive mode, when multiple reproductive phases occur in a multigenerational cycle, as in many cnidarians. Furthermore, in some cycles, several reproductive alternatives or developmental options may be available at certain life stages, so that a following stage can be reached through different paths.

“In descriptions and classifications of life cycles it is common to distinguish between simple cycles and cycles with ‘alternation of generations.’” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 47.

“In fact, there are many organisms for which the zygote represents a phase of resistance, called the zygospore, that allows the organism to get through an adverse season or to overcome a period of insufficient resources; or it may represent a phase of passive dispersal.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 50-1.

“A metagenetic cycle is a multigenerational cycle in which exclusively asexual generations alternate with sexual generations, represented by distinct organizational forms…. If the demographic criterion does not clearly separate metagenesis from metamorphosis in cnidarians, we could perhaps adopt a more restrictive criterion, considering that in asexual reproduction by budding the parent survives after the detachment of its descendants, while nothing survives metamorphosis except for the metamorphosed organism.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 57, 61-2.

“Polyembryony, the generation of more than one embryo from a single fertilization event, is usually considered a form of sexual reproduction with a partially clonal outcome, since it generates multiple identical copies of the same genotype, even if this is different from that of the parents. However, polyembryony could instead be considered a form of asexual reproduction at a very early (embryonic) stage of development.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. pp. 62-3.

“Some multigenerational cycles are characterized by one or more phases of aggregation among the individuals that are generated. These are often labelled as cycles with alternation of solitary and colonial generations. Examples are found among sponges, hydrozoans, anthozoans, bryozoans, tunicates and green algae.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 67.

“Among the life cycles of different organisms we find solitary and gregarious phases, sedentary and dispersal phases, trophic and non-trophic phases, benthic and pelagic phases, endogeic and epigeic phases, and more.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 71.

“The shortest-lived mayfly seems to be the female of Dolania americana, which completes its adult life within five minutes.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 77.

“Finally, reproductive maturity may precede the achievement of adult morphology. Ahead-of-time reproduction in a juvenile stage is called paedogenesis. In extreme cases of paedogenesis, an individual can even begin to reproduce when it is still in the body of its mother. In some aphids, within a parthenogenetic female one can find her developing daughters, and within these their own developing daughters (granddaughters of the former). Like a Russian doll, these ‘nested’ generations are called telescoped generations.” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 78.

“Parthenogenesis is the form of reproduction in which the new individual develops from an unfertilized egg. In many cases the offspring are all females genetically identical to the mother, and therefore some authors consider parthenogenesis as a form of asexual reproduction…. …here we consider it as a case (or rather, as we shall see, as a set of different cases) of sexual reproduction, because parthenogenesis uses, often in a peculiar way, developmental mechanisms of gametogenesis typical of sexual reproduction, irrespective of its clonal or non-clonal outcome. To use Boyden’s clear words, ‘there is no such thing as an “asexual egg”, regardless of whether it was produced by meiosis or mitosis.’” Fusco, Giuseppe & Alessandro Minelli. 2019. The Biology of Reproduction. Cambridge UP. p. 174; reference: Boyden, A. 1950. “Is parthenogenesis sexual or asexual reproduction?” Nature. 166:820.

“Here I present a list of properties that have been suggested as definitive of biological individuals….

“1. Reproduction
“2. Life cycle
“3. Genetics
“4. Sex
“5. Bottleneck life cycle
“6. Germ-soma separation
“7. Policing mechanisms
“8. Spatial boundaries/contiguity
“9. Histocompatibility
“10. Fitness maximization
“11. Cooperation and conflict
“12. Codispersal
“13. Adaptations….

“A more serious omission from the list is functional integration. This is a very popular criterion that defines the organism roughly as ‘any bioloigcal entity whose parts have evolved to function in a harmonious and coordinated fashion’….

“The final notable omission is autonomy.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. pp. 315-6.

“The trouble [with individuals being defined by functional integration] is that pretty much everything is organized, in some sense. The efficacy of these candidates in settling actual individual problems–i.e., distinguishing clearly between parts, individuals, and groups–depends very much on the precise way in which organization is spelled out, and whether a measure of it can be generated. Many versions are going to be overly permissive because there are many respects and degrees to which functional integration is evident in systems we clearly don’t want to describe as biological individuals.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 316.

“Where integration binds the parts of an individual together, and so distinguishes groups from individuals, autonomy separates the individual from other entities, and so distinguishes parts from individuals.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 316.

“[commenting on whether a life cycle could define the individual] There is a sense in which reproduction already implies life cycles, insofar as it implies new lives. However, a new life does not have to imply a new beginning, starting from scratch. A new life could just as well start from where the parent left off, rather than repeating some process all over again.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 317.

“These candidates [views that hold that sex could define the individual] equate the individual with the entire mitotic product of a sexually fertilized zygote. In this view, all reproduction involves the combining of genes from two parents into a single genotype. All forms of so-called asexual reproduction–vegetative propagation by cuttings or runners, parthenogenesis, apomixis, fragmentation, and fission–are actually just the expansion or division of a single biological individual.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 317.

“The bottleneck view [commenting on whether bottleneck life cycle could define the individual] identifies the entire mitotic product of the bottleneck stage in the life cycle as the individual. Reproduction is any event during which the phenotype shrinks down to the size of a single cell (or a few cells) before ballooning up again to the size of the adult. This view encompasses the sexual view because sex always involves a single-celled stage, but it is more permissive as it also counts certain asexual forms of propagation as genuine reproduction.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. pp. 317-8.

“According to Michod’s account, when a collection of parts is completely germ-soma separated, all parts have strictly zero fitness, for neither germ nor soma cells are individually able to carry out all the functions necessary for evolutionary success.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 318.

“Candidates of this type [that holds that policing mechanisms could define the individual] define the biological individual as something that necessarily possesses ‘policing mechanisms,’ ‘anti-subversion devices’, or ‘conflict modifiers’.

“Such mechanisms function to solve the problem of the commons–the fact that cooperation among a group of interactors can be undermined because they are tempted to ‘cheat’ or ‘free ride’–reap the benefits of cooperation of others without contributing to costs.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 318.

“These candidates [that holds that spatial boundaries/ contiguity could define the individual] emphasize that a biological individual should be physiologically discrete, spatially bounded, and/or spatially localized.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 318.

“”I think the case of the Portuguese man o’war [… looks just like a jellyfish, but it has a completely different developmental process so that it is usually considered a group or colony rather than an individual. It is composed of different kinds of parts that are homologous to different life stages in a single jellyfish and each has its own nervous system, p. 321] is particularly interesting. Although it is an individual according to an intuitive view, in books and papers about the problem of individuality it is usually referred to as a colony of many zooids.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 322.

“In summary, organisms are indispensable objects in biology. We know that counting particular lumps of living matter, and not others, allows us to describe and make predictions about evolutionary processes. Yet we lack a theory telling us what lumps to count.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 323.

“Biologists rely heavily on the concept of the organism, but they import different concepts into their models and discussions without reaching a consensus about which concept should be used, and usually without even being aware that they are talking about different things. There is an urgent need for the concept to be cleaned up.” Clarke, Ellen. 2011. “The Problem of Biological Individuality.” Biological Theory. 5(4):312-325. p. 323.

“Among them [artificial evolutionary systems], dynamic combinatorial chemistry (DCC) has proven to be a particularly fruitful approach: instead of designing a molecule to target a specific problem, the dynamic combinatorial chemist designs a system in which the most successful molecule is automatically selected and amplified from a pool of potential targets.” Cougnon, Fabien B. & Jeremy K.M. Sanders. 2011. “Evolution of Dynamic Combinatorial Chemistry.” Accounts of Chemical Research. doi: 10.1021/ar200240m. p. 1.

“In dynamic combinatorial chemistry simple molecular units (building blocks) are held together by noncovalent or reversible covalent bonds, generating a complex mixture of products which continuously interconvert: the composition of the mixture at equilibrium is thermodynamically controlled and is referred to as a dynamic combinatorial library.” Cougnon, Fabien B. & Jeremy K.M. Sanders. 2011. “Evolution of Dynamic Combinatorial Chemistry.” Accounts of Chemical Research. doi: 10.1021/ar200240m. p. 2.

“Moreover, dualism is incompatible with an evolutionary worldview, which sees the human mind as gradually emerging from much simpler animal, unicellular and inorganic forms of organization.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 83.

“In earlier work, I have proposed a radical resolution to this conundrum, by interpreting both objects and subjects as special cases of the more general category of agents, i.e. phenomena that act on other phenomena. The remainder of this text will spell out some of the implications of this ontology for understanding biological organization and its evolution, by interpreting not only organisms, but their physical components as well as the ecosystems they collectively form, as interrelated agencies.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 83.

“… the ontology of relational agency assumes that there are elementary processes, which I will call actions or reactions, that form the basic constituents of reality.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 87.

“Possibly the simplest way to represent an elementary process may be called a condition-action rule. It notes that given some condition X, an action will take place that produces the new condition Y. This can be interpreted as a transformation from the situation X to the new situation Y, or as a causation linking the cause X to its effect Y. It can be expressed more briefly as ‘if X, then Y’, or in symbols:
X –> Y….

“Agencies (A) can now be defined in this framework as necessary conditions for the occurrence of a reaction, which however are not themselves affected by the reaction:
A + X –> A + Y” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. pp. 87-8.

“Some conditions, such as the presence of oxygen, do trigger reactions from the agent, such as breathing. I will call such activating conditions challenges, because they incite or challenge the agent to act, i.e. to change something about the situation. For a goal-directed agent, a challenge may be positive or negative. It is positive when it helps the agent to get closer to its goal. It is negative, when it makes it more difficult for the agent to reach its goal.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 91.

“A positive challenge may be called an affordance, because it provides the agent with an opportunity to achieve some benefit, i.e. move closer to its goal. A negative challenge may be called a disturbance, i.e. something that pushes the agent away from its goal-directed course of action. A challenge can also be neutral, in the sense that the action it elicits is neither one of approach nor one of avoidance, but e.g. of exploration. In that case, I may call it a diversion: it incites a deviation from the present course of action that brings the agent neither closer to, nor farther away from, its goal.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 91.

“These [other agencies in the environment] similarly react to challenges by actions that produce new conditions. These in turn may challenge one or more agent to act. Thus, we may say that challenges propagate: the reaction to a challenge by one agent will typically create a challenge for one or more other agents, potentially setting in motion a cascade of actions triggering further actions.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 91.

“Some of these relationships [between agents] will be synergetic, in the sense that two or more agencies or reactions together can produce more of the conditions or resources they all need to continue functioning than each of them on its own. Others will be characterized by conflict or friction, in the sense that the activity of the one will impede the continued activity of the other(s). An agency surrounded by synergetic agencies will maintain more easily than one surrounded by agencies that have a relation of friction with it.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 92.

“Such a closed ecosystem [such as an ‘ecosphere’ where all components (species) match in terms of production and waste removal assuming an energy source (e.g. light) and heat output] illustrates a very important concept in reaction networks: a (chemical) organization. This concept … thus founding an approach known as Chemical Organization Theory. In this theory, an organization is defined as a network of reactions and resources (also called ‘molecules’ or ‘species’) that is closed and self-maintaining. Closed here means that no resources are produced by the reactions that are not already part of the network. Self-maintaining means that all resources that are consumed by some reactions are produced at least as much by other reactions, so that their total amount does not go to zero. In other words, the resources in a chemical organization are fully recycled and thus remain perpetually available.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 94.

“From the perspective of relational agency, evolution is always co-evolution: there is no a priori distinction between the system that is evolving and the environment to which the system has to adapt. Indeed, an environment consists itself of agencies that are trying to adapt to the environment created by all the others. Thus, adaptation in the one will in general challenge the others to adapt as well, potentially triggering a cascade of propagating challenges and concomitant adaptations. These processes of adaptation are in general not passive, but active: an agency intervenes in its environment by consuming inputs and producing outputs, thus changing the conditions for itself and others. These actions are not just mechanical responses to external forces, but directed at the internal goal of self-maintenance. The reason is that agencies whose actions were not effective in safeguarding the continuation of their organization have simply been eliminated by natural selection. Therefore, the remaining agencies are goal-directed or teleonomic: their repertoire of condition-action rules is such that a wide variety of initial conditions is made to converge to the same attractor regime of self-maintenance.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 98.

“When the system of relationships becomes so strong that an agency no longer can afford to survive without it, the self-maintaining network starts to behave like an individual agency rather than a group of collaborating agencies. In this way, agencies become integrated into a super-agency.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 99.

“Yet, there is an alternative ontology, of which the earliest incarnation is known as animism, but which I have here called relational agency. It sees the basic constituents of reality as elementary processes that define a network of interdependent agencies.” Heylighen, Francis. 2023. “Relational Agency.” pp. 79-104. From: Evolution ‘On Purpose’: Teleonomy in Living Systems. Corning, Peter, Ed. MIT Press. p. 100.

“Following Boltzman’s re-casting of the second law as nothing but a law of probability reduced to efficient cause and a ‘law of disorder’, the mechanical world view got a temporary reprieve from the macroscopic end-directedness recognized by Carnot, Clausius and Thomson. Correspondingly, the vision of the ‘two rivers’ [physics leading down to disorder and biology leading up to order] became even more deeply entrenched.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 5.

“… this [assumption of organisms’ striving for survival within Darwinian theory] puts the active striving of living things to fill out the economy of nature outside the explanatory framework of Darwinian theory. Rather than explain it, natural selection depends on it to operate. The origin and nature of living things must simply be assumed ad hoc outside the theory. ‘Evolution’ for Darwinian theory thus begins with life and all its active properties as given rather than explained.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 5.

“The Earth evolves as a population of one. Both the origin of life and planetary evolution are special cases of the ‘problem of the population of one’; examples of the deeper problem of spontaneous ordering itself.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 6.

“Because fitness is relativized to members of breeding populations, the fitness of different kinds of things are incommensurable with each other and cannot be compared, e.g. the fitness of a zebra cannot be compared with that of a mouse or an amoeba.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 7.

“… the now classic Benard cell (BC) experiment from our laboratory some decades ago. A viscous liquid is held between a uniform heat source below (source) and the cooler air above (sink). The difference between the temperatures constitutes a potential with a thermodynamic force F the magnitude determined by the steepness of the gradient between them. When F is below a critical threshold the system is in the linear disordered ‘Boltzmann regime’, and the flow of heat from source to sink is from the disordered collisions of molecules and the macroscopic state appears homogeneous. But as soon as F is increased above the threshold macro is selected from micro and hundreds of millions of molecules begin moving together as a new highly ordered macrostate comes into being. According to Boltzmann’s reduction of the second law such transitions are infinitely improbable, but this claim, as is easy to see here, is entirely falsified by this simple experiment where order arises not infinitely improbably but with a probability of one, that is opportunistically every time and as soon as it gets the chance (every time F is above the critical threshold). There are a lot of generic takeaways from this simple experiment, but the bottom line here is that it entirely falsifies Boltzmann’s reduction. The second law cannot be reduced to a law of disorder, or a stochastic collision function. The world is not a gas in a box.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 7.

“The BC is a member of the class of ‘autocatakinetic’ (ACK) systems [‘auto-‘self’ + cata ‘down’ + kinetic ‘of the motion of material bodies and the forces and energy associated therewith’], a more precisely defined term than ‘self-organizing system’ or ‘dissipative structure’ historically often used for the same kind of system…. ACKs are flow structures, their identities constituted through flow, and defined as

“ a system that maintains its ‘self’ as an entity constituted by and empirically traceable to a set of nonlinear (circularly causal) relations (constitutive relations) through the dissipation or breakdown of environmental potentials (resources) in the continuous coordinated motion of its components.

“From the definition, it is simple to see that all living systems from cells to ecosystems at whatever scale (including the planet itself) are ACK systems as are abiotic systems such as dust devils, tornadoes and experimental systems like the BC. What this definition explicitly does not include are machines, artefacts or systems that run exclusively on rules (e.g. algorithms) or rule execution.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. pp. 7, 8.

“The ‘selfishness’ of ACK systems, the ontological basis for using the term ‘self’ is causally manifested and located in the circular relations that constitute them. They are deviation-amplifying systems, or thermodynamically speaking, self-amplifying sinks that feedback internally developed forces to amplify their own input pulling resources (potential) into their own production or progressive ordering.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 8.

“Von Bertalanffy, under the rubric of ‘open systems’, and Schroedinger comparing living things to flames, helped to soften the physics versus biology problem by pointing out that as long as living systems produced enough entropy to compensate for their own internal entropy reduction (the order that defines them or potential they pull into themselves) so as to satisfy the balance equation of the second law [change of entropy is always greater than zero] then the second law as classically stated would not be violated. Later Prigogine made the same point under the term ‘dissipative structure’. The balance equation can then be separated into two terms. The first term is a measure of the change in entropy due to the ‘negentropy’, using Schroedinger’s term, or the potential (energy gradients) on which such systems ‘feed’ and import into the system, and the second term is the entropy produced and dissipated into the environment by the system’s ordering, and departure from equilibrium
ΔSe + ΔSi > 0.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. pp. 8-9.

“… spontaneous ordering (the production of ACK states), as a micro (disordered) to macro (ordered) transformation, is a process of selection. By definition, it is the selection of some much smaller number of accessible microstates M2 (the new ordered macro state) from some initially much larger set M1. This can be equivalently understood as the spontaneous production of constraints on the previously disordered or less ordered microstates dramatically constraining their degrees of freedom in the production of the ordered flow. In short, selection is entailed by autocatakinetics (spontaneous ordering), viz. if the latter has happened/ is happening then a process of selection had/is taken(ing) place. But, clearly, the fact that this selection is not between replicating entities (biological or ‘natural’ selection), while at the same time observed in simple physical systems forces the insight that there must be an overriding physical selection principle to account for it.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 9.

“… the significant point here is not that ordered flows are permitted to exist as long as they produce enough entropy to compensate for their internal entropy reduction. It is that with selection of macro from micro (spontaneous ordering) to occur the rate of entropy production must always go up. In fact, in more illuminating terms, the more order produced the greater the rate of entropy production is going to be.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 10.

“The answer … that solves the entire question of physical selection … is the law of maximum entropy production (LMEP) or the fourth law of thermodynamics:

“ (the world) a system will select the path or assembly of paths out of available paths that minimizes the potential or maximizes the entropy at the fastest possible rate given the constraints.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 10.

“The fourth law says nothing directly about spontaneous ordering per se, but coupled with the balance equation of the second law the derivation of the universal ordering principle is easy to see, namely:

“ IF The 4th Law or LMEP (the world selects paths …. fastest rate…)

“ AND IF ordered flow produces entropy at a faster rate than disordered flow (the balance equation of the 2nd Law)

“ THEN the world can be expected to select order from disorder whenever it gets the chance.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. pp. 10, 11.

“This, the intentionality of living things, is life’s central distinguishing feature. Living systems are epistemic (cognitive) systems that constitute their ACK over times and distances that are arbitrary with respect to local potentials using instead their ‘on board’ potential and information (in the semantic or meaningful sense) to seek out and access non-local potentials and access otherwise inaccessible dimensions of space-time. The dramatic increase to otherwise inaccessible dissipative dimensions afforded by the origin and progressive ordering of life and its cognitive functioning answers the ‘why’ question in the specific case. Rather than being incommensurable with the physical world as Cartesian metaphysics has it, cognition, or intentionality, and perception, the growing epistemic dimension of the world, or mind in nature, is seen instead as a direct manifestation of it.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 12.

“Cartesianism and heirs give us some version of the Cartesian circle with ‘mind’, having no possible relational connection to an outside world, simply perceiving itself. Information is something created or constructed in ‘minds’ not something otherwise existing in the world. Such a view, the idea that perception is essentially a creative process of mental operations or computations inside ‘minds’ or brains is still the dominant view today. CTM (the computational theory of mind) is a widely held form of this. ‘Perceiving as predicting’, a current leading trend in computational neuroscience, takes perception to be the probabilistic computation of models created in the brain. Adherents of this view, who as already noted assert that living things violate the second law, proclaim a ‘deep unity between perception and imagination.’” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 12; subquote: Clark, A. 2015. “Perceiving as predicting.” In: Perception and Its Modalities (eds. D. Stokes, M. Matthen, S. Biggs). pp. 23-43. Oxford UP.

“Behind the signature ability of living things to behave arbitrarily with respect to local potentials is the ability to maintain an arbitrary function in the component production process, and this is accomplished with a requisite set of rate-independent constraints (RICs). In particular, a set of internal constraints that are discrete, sequential and rate-independent relative to the rest of the ACK cycle. The order of the sequences, like the words on this page (a higher-order instantiation of this), or the sequence of base pairs in a DNA string, for example, is thermodynamically arbitrary relative to the rate at which they are ‘written’ and ‘read’ (viz., the amount of ATP used to replicate a string of DNA of the same length, is the same regardless of the particular sequence). Looking inside of an ACK system, if it has these features, that is component replication with a set of RICs, then the system is a living/ cognizing system.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 13.

“The modern scientific world view was built on Cartesian metaphysics and the incommensurability between cognition (mind) and physics (matter), and later life and physics (the autonomy of biology). Boltzmann’s view of the second law of thermodynamics as a ‘law of disorder’ cemented the idea of ‘two opposing rivers’, the river of physics ‘flowing down’ to disorder and the river of life and mind ‘flowing up’ into contemporary science, and is a widely accepted cornerstone today.” Swenson, Rod. 2023. “A grand unified theory for the unification of physics, life, information and cognition (mind).” Philosophical Transactions of the Royal Society: A. 381:20220277. doi: 10.1098/rsta.2022.0277. p. 13.

“Now we come to an important consequence of the strength of that field [the 150 mV voltage across the membranes of heart cells]. It can cause proteins to change shape. In the case of ion channel proteins, the shape change can be the difference between the channel being open and being closed.

“When they are open, the channels themselves cause changes in the voltage, since they carry charged particles into or out of the cell. So the proteins and the cell membrane form an automatic feedback loop. A change in protein shape can cause a change in field, which in turn causes the channel to open or close. Some channels open when the cell electrical potential becomes positive, others close.

“What was shown 60 years ago is that this feedback loop is sufficient to produce electrical rhythm. No single protein, nor the gene forming its template, can do that alone….

“What subsequent research has shown is that many more than four proteins are involved. So many that, even when one of the key proteins is knocked out or blocked, the rhythm continues.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. pp. 6-7, 8.

“This separation of mind and body and the gene-centric view have something in common, which is that they both look for an organiser of something that is in fact self-organising: the organism.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 12.

“Erwin Schroedinger’s seminal book, What is Life?, published in 1944, contains two fundamental errors that continue to influence thinking about genetics. The first is that what is passed on to subsequent generations is so vast that it must all be stored at the molecular level. It is indeed vast, which is one of the reasons it is not all stored at the molecular level. The second is that the genetic material faithfully self-replicates like a crystal.

“Physicists already knew about the molecular structure of crystals and how such arrangements could replicate automatically by incorporating further similar molecules to form an ever-larger lattice. There are two problems with Schroedinger’s idea. First, if the information is stored in a molecular crystal, it wouldn’t contain molecular sequences that could be interpreted by the organism unless it was an unusual crystal. Second, the form would be only just enough to enable that crystal structure to grow rather than replicate.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 14.

“Schroedinger’s explanation of replication, however, is where the real problem begins. A standard crystal replicates simply by forming a template for further molecules of the same type to add themselves endlessly to the growing crystal. The genetic material does not do this. Schroedinger would not have known this, but he sowed a seed that influences the development of the Modern Synthesis in three critical ways:

“* The genetic material self-replicates. I does not. It depends on the cell.
“* The genetic material replicates faithfully. It does not, and the extent to which it does depends on the cell.
“* Faithful replication is the purpose of life. It is not. Responding to change is.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 15.

“The gene-centred dogma derives from at least five erroneous assumptions: the concept of the gene as a precise self-replicator; the view of the organism as simply a vehicle to transfer genes with no agency; that natural selection is a passive process in which organisms have no active part; that changes in the organism cannot be transferred across generations; that DNA is a code or blueprint instructing the organism in its function and behaviour. Not of these contentions is true.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 29.

“Natural selection by contrast [to the artificial selection of animal breeders] is thought not to involve any choice by any individual. So differential survival in natural selection is regarded as more like a passive filter. This is wrong, because the environment itself is in the largest part other active organisms. Over time it is organisms that are selecting. Evolution is an iterative ecological process. The selection process is behavioiural and physiological.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. pp. 31-2.

“When we talk about purpose, we mean two different but related things in functionality:

“1. What function is served, what the thing does – for example, muscle cells contract, creating movement or tension; this is a capacity to act or achieve something and may be used in achieving diverse kinds of goals. The arrangement of our fingers and thumbs enables us to manipulate objects in many ways, including typing letters on a keyboard. We will call this ‘facultative purpose’ in this book.

“2. Purpose in relation to achieving goals – for example, the use of movement or action directed to specific goals or outcomes. We will call this ‘goal-directed purpose’ in this book.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 54.

“Wherever we look, we see life harnessing and doing things in processes that solve problems. Without life, there would be no problems. The issues are the creation of life itself, and so also are the solutions. Life creates both the problems and the solutions. This is what gives agency to the processes of life. A rock tumbling down a hill may have consequences, but it has no agency. Agency is a feature of life. Living forms have goals, objectives, such as building a nest, obtaining food, moving from A to B, finding a mate, and many other objectives, including sometimes having fun. Maintaining integrity gives rise to all issues and to all problem-solving, and in this sense, intelligence is a necessary capacity of life.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. pp. 58-9.

“So how can a living organism constructed from the material of the universe have purposes? How can anything be intended? Philosophers and scientists have struggled with this problem for centuries. But it is the wrong question. Intention does not come from anywhere. It is definitively what living things (organisms) do.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 59.

“Imagine a lock for which you must find a key while it is changing. Nature is doing this all the time, as in the immune system, for example, as it continually meets new lock-and-key challenges when new viruses, bacteria and other antigens invade the body.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 61.

“In evolution we see changes in facultative purpose, which in turn influences other faculties such as goal-directed behaviour. A Euglena has chloroplasts – green power packs, making sugars using the energy of light during photosynthesis. But it also has an eye, of sorts, enabling it to find better light conditions for photosynthesis.

“Using this simple ‘eye’ at its front end, a Euglena seeks light. A small red shield or stigma, the eyespot, filters light falling on a light-sensitive spot at the base of a long, whip-like flagellum that lashes the water when the organism changes direction. So the Euglena eye is a simple but effective invention. It has purpose in function. Euglena also has purpose in its behaviour – optimising light for its chloroplasts. And here we see the interplay of facultative and goal-directed purpose or functionality in enhancing fitness.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. pp. 61-2.

“Organisms and environment are continually changing each other. The environment is itself composed of other organisms whose agency continually alters the physical and social environment of all organisms. We will call the intimate interaction between organisms ‘ecological social intelligence’.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 64.

“The gene-centric view separates the organism from its environment, and in large part, removes agency from the organism. The ‘environment’ becomes a box within which ‘gene-motivated’ organisms behave. Thus, it misleadingly partitions ‘genetic’ from ‘environmental’ causes, giving primacy to the former. Therefore, altruism is denied because ‘in reality’ organisms behave to enhance their genes in the ‘gene pool’ – and love, hate, desires and other motivations flow through and from genes. With this there can be no creativity. The organism is a prisoner of its genes. This is evidently nonsense because, if there is a prisoner, it must be the genes, locked in the organism and obeying its will. It is the organism as a self-organising entity that has motivation and uses genes in its capacity to act.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 65.

“Reproduction does not simply replicate. It brings about change.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 66.

“All organisms are intelligent, for they make directional choices. They have agency.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 67.

“Ironically, whilst deterministic machine metaphors distort our view of life, we try hard to create lifelike machines with creativity and purpose, for this is the real secret of life, not its DNA. Purpose is the driving force of life.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 99.

“Agency requires causal independence. It also requires intentionality – in other words, a sense of purpose – in order to be causally effective as a driving force.

“As the study of living organisms shows, agency also involves anticipation and surprise.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 106.

“If we human beings wish to survive as a species, we need urgently to recognise our dependence on life as an interdependent ecological system.” Noble, Raymond & Denis Noble. 2023. Understanding Living Systems. Cambridge UP. p. 131.

“Although a single influenza virus encodes fewer than 20 proteins, it is able to kill a person–indeed, to kill half a million people every year, even though human beings have tens of thousands of genes.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 7.

“… estimates suggest that there are at least 10 times more viruses than there are cells on Earth. Given that there are at least 1030 bacterial and archaeal cells, the number of viruses and viral genes is mind-boggling. Even if each virus encoded only 10 genes, that comes to 1032 viral genes. In contrast, astronomers estimate there are only about 1023 stars in the universe.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 8.

“… viruses share four fundamental traits. In combination, these four traits define the viruses unambiguously by excluding cells and some other noncellular nucleic acids, such as plasmids and transposons. First, viruses are obligate intracellular parasites that have an infectious extracellular stage. Most virologists refer to this extracellular stage as a virion. Until the virion makes contact with a susceptible host cell, the virion’s macromolecules are inert, unable to catalyze any chemical reactions. Some forms of cellular life can give rise to metabolically inert spores, however, so the virion’s state of metabolic inactivity cannot alone define the viruses as different from cells. Neither does being obligate intracellular parasites alone unambiguously define the viruses, because there are many cellular obligate intracellular parasites, such as Chlamydia and Wolbachia….

“Second, all viruses encode at least one capsosmere protein. Capsomeres cover and protect the nucleic acid in a virion, and all viruses carry genetic instructions for synthesizing at least one capsomere. The existence of an extracellular stage and the encoding of capsomeres that are component parts of this extracellular stage separates viruses from the many selfish DNA molecules that provide no known benefit to their cellular hosts yet replicate inside the cell. Furthermore, cells do not encode capsomeres, except in cases where cellular DNA of viral origin encodes one. There are subviral particles such as satellite viruses, conjugative plasmids, and prions that also do not encode a capsomere, but these entitites are not, strictly speaking, viruses.

“All viruses replicate, not by growing larger and dividing as do cells, but by assembly. That is, cells infected by viruses synthesize the component parts of the virion, and then the parts, once synthesized, spontaneously assemble into new virions without further input of energy. Reproduction by assembly is therefore the third defining characteristic of viruses.

“The fourth defining characteristic of viruses is the capacity to evolve.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. pp. 8-9.

“At a minimum, virions are made up of nucleic acids protected by capsomeres. The protein coat of capsomeres that surrounds the nucleic acids is called a capsid…. … virions can be separated into two classes based on whether they have an external layer consisting of a proteinaceous lipid bilayer. Enveloped virions have a lipid bilayer, whereas naked virions do not.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 10.

“In other cases, the nucleic acid genome and the capsomeres are so intimately associated that their structure is termed a nucleocapsid.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 10.

“The newly discovered mimiviruses, for example [in contrast to much smaller ones], are 500 nm in diameter. Mimiviruses can even be infected by their own viruses, such as the Sputnik virophage.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 10.

“Advances in DNA sequencing technology and the sequencing of hundreds of animal and plant genomes have revealed that the genomes of multicellular organisms contain viral DNA and DNA that is complementary to viral RNA…. For example, the human genome has over 100,000 partial segments of human endogenous retroviral (HERV) DNA in it. Endogenous retroviral sequences are DNA complementary to the genome of a retrovirus. That DNA is now inherited through the germ line cells (sperm and egg) and most sequences are no longer able to encode infectious virions. These DNA sequences may have a function. The developmental program to build a mammalian placenta depends on a protein encoded by an endogenous retrovirus…. Infection by a retrovirus made the emergence of placental mammals possible by providing a viral protein that enables formation of the placenta. The placenta is a single example; other functional consequences of endogenous retroviral DNA may be discovered.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 14.

“… a typical virus replication cycle can be divided into six steps:

“1. Attachment….
“2. Penetration and uncoating….
“3. Synthesis of early proteins….
“4. Synthesis of new viral genomes and late proteins….
“5. Assembly….
“6. Release” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 22.

“The proteins expressed early in an infection often have one of three functions: to shut down the synthesis of host proteins, to regulate expression of viral genes, or to synthesize viral nucleic acids.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 22.

“The host range of a virus is the variety of different species that the virus can infect. The attachment stage can be largely responsible for host range….

“The tissue tropism of a virus is the different tissue or cell types that a virus infects once it is inside a susceptible animal.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 35.

“Although tissue tropism and host range are often determined by the ability of a virus to attach to, penetrate, and uncoat in a certain cell, there are examples in which host cells prevent virus replication at a later stage. An example is HIV, which can attach to and enter chimp immune cells but cannot replicate inside them. The chimp cells produce host restriction factors that block HIV replication after the penetration and uncoating stage.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 35.

“Defective viruses that deliver only a subset of viral gene are probably also common, a phenomenon that has been studied among animal viruses. Among animal viruses, the ratio of infectious virions to total virions is lower than 1:1 and can even be as low as 1:10,000…. In some cases, the virion particles are released without a complete set of genes, which may be especially common among viruses with segmented genomes (such as influenza), or particles lacking any genome at all are present.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 37.

“The first stage of attachment is reversible binding to host cell surfaces through nonspecific electrostatic interactions between the virion surface and the host cells. The plasma membranes of animal cells are heavily glycosylated on their exterior surfaces, providing a net negative charge. It is likely that numerous nonspecific electrostatic interactions between virions and these sugars help restrict the diffusion of the virions to two dimensions in the plane of the membrane, making it more probable that the virion will encounter its specific receptor, which in turn enables irreversible attachment.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 41.

“… most viruses attach to specific host proteins. These proteins serve a purpose in the cell’s normal physiology; through binding to a certain cellular receptor, a virus subverts that normal protein for its own purpose. Proteins that protrude from the surface of animal cells are typically glycosylated, so it is more strictly true to refer to most animal virus receptors as glycoproteins.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 42.

“Virions are at least 10-100 times larger than their protein component parts. Nevertheless, naked virions (lacking a membrane) can also be studied using X-ray crystallography. The crystallization of tobacco mosaic virus was one of the earliest clues that virus structure is much simplified compared to the structure of their host cells, even though viruses can overtake their larger, more complex host cells. Enveloped virions, by contrast, cannot form analyzable crystals so their structures are most commonly examined using Cryo-EM or even atomic force microscopy.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 49.

“Influenza virions are enveloped and contain eight different viral nucleoprotein complexes of single-stranded(-)sense RNA. The virion contains multiple copies of two different spike proteins: neuraminidase (NA) and hemagglutinin. Although neuraminidase is particularly important for the release stage of the virus replication cycle, hemagglutinin is used for the attachment and penetration stages of the replication cycle. Influenza A viruses, the cause of devastating human pandemics, are often named according to the type of immunologically distinctive HA and NA proteins they encode. There are seventeen immunologically distinctive HA molecules and ten different NA proteins. All HA proteins share the same function, but antibodies that react with HA protein type 1 (H1) do not react with H2 proteins, and so on. The same is true of different NA proteins. An influenza A virus might therefore be called H1N1, indicating that it has the first type of HA protein (HA type 1) and the first type of NA proteins (NA type 1). Similarly, H7N3 denotes the presence of HA 7 and N3 spikes.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. pp. 52-3.

“Fundamentally, virions have two distinct roles: to protect the virus genome during transmission and to release the virus genome into a host cell. These two roles are somewhat paradoxical, as the ability to protect the genome seems to be antithetical to that of exposing the genome for transcription and replication. The key to this paradox is that virions are metastable particles, and intermolecular interactions affect their stability. Thermodynamically, the infectious virion’s structure is not the conformation with the lowest possible free energy. However, the energy barrier (the energy of activation) between the virion structure and the rearrangement of the virion that would release the genome is high so that it rarely, if ever, occurs until the virion interacts with a host….

“How does the virion achieve its two roles? The intermolecular interactions among the structural proteins of a virion, and between them and the genome, maintain the virion in its characteristic shape. Virions exist in this metastable state until a host cell triggers them to advance from attachment to the penetration and uncoating stage.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. pp. 59-60.

“Fusion [for enveloped viruses] can be defined as the two lipid bilayers becoming a single lipid bilayer. Simple collision of lipid bilayers does not result in fusion of those bilayers or else the eukaryotic cell would be unable to maintain the distinctive characteristics of each membrane-bound organelle. Instead, membrane fusion requires catalysis. In the case of enveloped viruses, a component of one of the virus spike proteins, termed the fusion protein, has a region, termed the fusion peptide, that becomes catalytically active following irreversible attachment.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 60.

“The role of the cytoskeleton in uncoating is particularly prominent, and better understood, for those viruses that must introduce their genomes into the nucleus. On a molecular scale, a virion that is 100 nm in diameter can have a distance greater than 50,000 nm, or 500 times its own diameter, to travel from the cell periphery to reach the nucleus. To move the same relative distance, an adult person would have to run the length of five soccer fields…. … all particles as large as virions diffuse slowly within the cell, where the viscosity can be likened to that of wet sand. Thus, viruses and their component parts must use the cytoskeleton and its associated motor proteins to move to and from the cell periphery as needed.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. p. 65.

“How does a virus get into a plant cell in the first place, given the cuticle and cell wall? The first method is to avoid this problem entirely by being inherited through the generations, by infecting pollen, or by infecting seeds so that the seedlings become infected…. Another common route of entry [is] through mechanical inoculation. During mechanical inoculation, a grazing animal damages the cuticle and provides an opportunity for viruses to take advantage of the physical breach.

“The third method, the most common when considering all known plant viruses, is transmission during feeding of an arthropod. Arthropods are invertebrate animals such as aphids and mites that have mouth parts that pierce through the plant cuticle and cell wall in order to feed on the contents of the plant. They can thereby inject a plant cell cytoplasm directly with virions. Plant viruses may require damage to the actual plasma membrane for transmission. We reach this conclusion because plant viruses don’t seem to have specific plant cell receptors for attachment, and they do not appear to enter plant cells through receptor-mediated endocytosis or other processes that result in vesicle formation.” Lostroh, Phoebe. 2019. Molecular and Cellular Biology of Viruses. Boca Raton, FL: CRC Press. pp. 71-2.

“We believe this early version of metabolism [a metabolism first view without complex polymers] consisted of a series of simple chemical reactions running without the aid of complex enzymes, via the catalytic action of networks of small molecules, perhaps aided by naturally occurring minerals. If the network generated its own constituents–if it was recursive–it could serve as the core of a self-amplifying chemical system subject to selection….

“Networks of synthetic pathways that are recursive and self-catalyzing are widely known in organic chemistry, but they are notorious for generating a mass of side products, which may disrupt the reaction system or simply dilute the reactants, preventing them from accumulating within a pathway. The important feature necessary for chemical selection in such a network, which remains to be demonstrated, is feedback-driven self-pruning of side reactions, resulting in a limited suite of pathways capable of concentrating reagents as metabolism does.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 208.

“In the abiotic world of the early Earth, likely in a chemically excited environment, reservoirs of energy accumulated. In effect, electrons (along with certain key ions) were pumped up chemical hills. Like the water in our analogy [a pond on a high with high potential energy], those electrons possessed stored energy. The ‘problem’ was how to release it. In the words of Albert Szent-Gyorgi: ‘Life is nothing but an electron looking for a place to rest.’

“For example, carbon dioxide and hydrogen molecules are produced copiously in ordinary geochemical environments such as deep sea vents, creating a situation analogous to the water on the hill. The energy of this system can be lowered if the electrons in the hydrogen ‘roll down the hill’ by combining with the atoms of carbon dioxide in a chemical reaction that produces water and acetate (a molecule with two carbon atoms [C2O2]). In the abiotic world, however, this particular reaction takes place so slowly that the electrons in the hydrogen molecules find themselves effectively stranded at the top of the energy hill.

“In this example, the problem that is solved by the presence of life is getting energized electrons back down the chemical hill. This is accomplished by the establishment of a sequence of biochemical channels [analogous to a rivulet channel for the water or ionized molecules channel in air for lightning], each contributing to the whole.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 210.

“In most present-day life forms on Earth, the citric acid cycle operates to break organic molecules down into carbon dioxide and water, using oxygen to produce energy for the cell–in effect, ‘burning’ those molecules as fuel…. When the cycle operates in this way, we say that it is in the oxidative mode.

“The cycle can also operate in the opposite direction, taking in energy (in the form of high-energy electrons) and building up larger molecules from smaller ones. This is called the reductive mode of the cycle. If an organism has access to high-energy electrons like those produced by geochemical processes, in fact, it can thrive with the cycle exclusively in the reductive mode, having no use for the oxidative mode at all. One way to think about the two modes of the cycle is this: In the oxidative mode, the input is an organic molecule, and the output is chemical energy, carbon dioxide and water. In the reductive mode, the input is chemical energy, carbon dioxide and water, and the output is a more complex molecule.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 211.

“In the reductive mode, the [citric acid] cycle provides a way for high-energy electrons to flow down the chemical hill. It is similar to the acetate reaction shown earlier, which is thermodynamically feasible but very slow, but with the addition of a network of small molecules–the reductive citric acid cycle–acting to mediate and speed up the reaction. On biochemical and tehrmodynamic grounds, then, the reductive citric acid cycle would be a good candidate for the threshold of early life–the point where the pond of high-potential water is breached and the downhill pathway is etched out.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 211.

“In the metabolic maps of all modern organisms, the small molecules and reactions of the citric acid cycle are the starting point of every biosynthetic pathway–all roads lead from the citric acid cycle. However, in some organisms the reactions do not form a closed–cyclic–reaction sequence. For that reason, even among researchers convinced that these reactions are vestiges of the first metabolism, debate remains over whether the very first metabolic footpath was a cycle. However, because only cycles can act as self-amplifying channels, and because in organisms not running the closed cycle, sophisticated compensating adaptations are required, we consider a primordial reductive citric acid cycle the most likely route from geochemistry to life–the rivulet that formed at the top of the energy hill, through which the pond of energy began its thermodynamic escape.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 211

“Even in the deep core of metabolism, however, we do not see the cycle in isolation. Its lowest-energy molecule, acetate, is the starting point for other pathways that make the essential oils used in cell membranes, harvesting another third of the electron energy. Further reactions, such as those that generate methane, can capture the remaining available energy, though methane is a gas and therefore a waste product, unlike the earlier molecules in the pathway, which are constituents of biomass.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 211.

“Technically, one cannot talk about the entropy ‘of a state’ if the state depends for its context on a process of change; only the entropy of the whole process is expected to be maximized. To return to our pond on the hill, there is not a separate entropy of the pond, except as an approximation. Rather, there is an entropy of paths of change that include pond, channel, construction and relaxation. When such a formulation is analyzed for a simple system, the establishment of a channel can be seen as a phase transition, similar to the freezing of an ice cube or, to use a more precise mathematical analogy, the formation of a magnet from molten iron. (In the latter case, the phase transition occurs as the metal cools when the atomic dipole magnets line up in the same direction–paradoxically, a more ordered state). The full entropy of the process will be maximized in the system, even though the approximate entropy associated with the ‘state’ of the channel may not be, thereby eliminating the paradox….

“The hope is that when a full theory is available, we will see the formation of life as an inevitable outcome of basic thermodynamics, like the freezing of ice cubes or the formation of magnets.” Trefil, James, Harold J. Morowitz & Eric Smith. 2009. “The Origin of Life.” American Scientist. 97:206-213. p. 213.

“What is ‘chemical evolution’? It describes the chemical processes that took place on the prebiotic Earth about 4,500 to 3,500 mya.” Follmann, Hartmut & Carol Brownson. 2009. “Darwin’s warm little pond revisited: from molecules to the origin of life.” Naturwissenschaften. 96:1265-1292. doi: 10.1007/s00114-009-0602-1. p. 1266.

“… it is believed that the planet had solid rocks and an atmosphere between 4,400 and 4,100 mya. When temperatures dropped below its critical point (374̊C), water condensed and filled crater lakes and early oceans; this occurred an estimated 4,000 million years before present.” Follmann, Hartmut & Carol Brownson. 2009. “Darwin’s warm little pond revisited: from molecules to the origin of life.” Naturwissenschaften. 96:1265-1292. doi: 10.1007/s00114-009-0602-1. pp. 1267-8.

“… organic matter would have been annihilated on a global scale in one of the frequent asteroid bombardments that continued to about 3,900 mya.” Follmann, Hartmut & Carol Brownson. 2009. “Darwin’s warm little pond revisited: from molecules to the origin of life.” Naturwissenschaften. 96:1265-1292. doi: 10.1007/s00114-009-0602-1. p. 1268.

“Margulis’ vigorous promotion of the role of symbiosis in eukaryotic cell evolution sparked a spirited debate throughout the 1970s and into the 1980s between proponents of autogenous origin (‘origin from within’) and xenogenous origin (‘origin from without’) theories of organelle evolution.” Gray, Michael W. 2017. “Lynn Margulis and the endosymbiont hypothesis: 50 years later.” Molecular Biology of the Cell. 28:1285-1287. doi: 10.1091/mbc.E16-07-0509. p. 1285.

“The current consensus, however, is a single, separate, endosymbiotic origin of mitochondrion and plastid….” Gray, Michael W. 2017. “Lynn Margulis and the endosymbiont hypothesis: 50 years later.” Molecular Biology of the Cell. 28:1285-1287. doi: 10.1091/mbc.E16-07-0509. p. 1286.

“Perhaps the best-known mito-early model is the hydrogen hypothesis, in which the host, an anaerobic, hydrogen-dependent archaeon, takes up an α-proteobacterium that is able to respire but that generates molecular hydrogen as a waste product of anaerobic heterotrophic metabolism. Here selection for endosymbiosis is driven by metabolic syntrophy between the two partners: the waste product (hydrogen) of one is used as an essential metabolic resource by the other. In this scenario, the origin of the mitochondrion and the origin of the eukaryotic cell are contemporaneous, with the subsequent emergence of the defining subcellular features of the latter directly dependent on a pronounced increase in cellular energy provided by the latter.” Gray, Michael W. 2017. “Lynn Margulis and the endosymbiont hypothesis: 50 years later.” Molecular Biology of the Cell. 28:1285-1287. doi: 10.1091/mbc.E16-07-0509. p. 1286.

“… the concept of the virocell. Forterre explains that ‘the intracellular phase has been largely excluded from traditional virus definitions’ and he differentiates between the metabolically inactive, extracellular state of a virus (the virion) and the metabolically active, intracellular state (the virocell)…. According to the virocell concept, if a cell is a living entity then so too is a virus, at least when its genes are being translated into proteins within an infected host. All life can still be cellular under this view, but there are competing strategies within the cell for replication, depending on the genome that is in control of the ribosome.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 3; subquote: Forterre, P. 2016. “To be or not to be alive: how recent discoveries challenge the traditional definitions of viruses and life.” Stud. Philos. Biol. Biomed. Sci. 59:100-108. doi: 10.1016/j.shpsc.2016.02.013.

“A well-known example of how morphology can disguise true evolutionary relationships is that whales and hippopotami are each other’s closest living relatives.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 4.

“The horizontal transfer of genes from one cell to another occurs by three mechanisms: transformation, conjugation, and transduction. Transformation is the uptake of naked DNA from the environment by a cell, which can then be broken down into individual nucleotides or used in DNA repair. Conjugation occurs between cells in contact when a bridge known as a pilus is formed that allows the transfer of DNA, usually by a plasmid. Transduction happens when a virus accidentally packages host DNA into its capsid, sometimes transferring this DNA to a new host…. A fourth mechanism, vesiduction, has recently been proposed to explain the transfer of DNA by extracellular vesicles (EVs)–an event that has been observed in all three domains of life. Another important player in HGT is the transposable element, a ubiquitous and very diverse group of genes that code for enzymes involved in splicing and insertion of their own DNA. Sequences that can be horizontally transferred are generally referred to as mobile genetic elements (MGEs).” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 6.

“Just because there is an unbroken history of cellular division linking LUCA to all modern life does not mean that pre-LUCA genes do not reside on post-LUCA genomes. This brings us back to the distinction between the evolutionary history of genomes versus the evolutionary history of individual genes–two competing ideas in the light of HGT.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 8.

“Can the ToL [tree of life] survive the genomic revolution? The species ToL is only a very crude approximation of the complexity of biological evolution at a molecular level. The ToL is also a dynamic model that has evolved conceptually to include a forest of gene trees, statistical central trends, and a network encapsulating both vertical and horizontal gene transfer.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 8.

“Three general frameworks have been used to explain the origin of viruses…. In the virus-first hypothesis, the origin of viruses predated the origin of cells. These viruses would have arisen before cellular parasitism, perhaps existing as free-living replicators. How did they evolve to get inside cells and usurp their cellular machinery? Where did their capsids come from? The reduction hypothesis sees viruses evolving from cellular ancestors. In this scenario, viruses evolve after FUCA and before LUCA. The most popular scenario is one in which some lineages of cells have already evolved to parasitize other lineages, their genomes then shrinking over evolutionary time to a minimalist parasitic lifestyle. This is how bacterial endosymbionts evolved their reduced genomes, such as many species of the genus Mycoplasma. We can envisage a parasitic genome losing genes to become more dependent on the host cell, but how would it then evolve to package itself inside a protein shell before bursting the cell open to spread out and infect new cells? The escape hypothesis posits the evolution of cellular genes that break away from the coordinated efforts of the genome to adopt a parasitic existence. This hypothesis is associated with the multiple and independent origin of viruses in all three domains of life–Bacteria, Archaea, and Eukarya–although there is evidence to suggest that monophyletic virus groups are not confined to a single domain. While this adaptive strategy can be linked to theoretical models on the emergence of parasitism, the presence of genes that are unique to viruses suggests that not all viral genes originate from cellular homologs. In fact, there is evidence to suggest that many novel genes originate in viruses and that gene flow between viruses and their hosts is dominated by host acquisition of viral genes. These three hypotheses on viral origins do not cover the full breadth of possibilities.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. pp. 8-9.

“Giant viruses containing thousands of genes were first discovered in 2003. They are the largest members of the phylum Nucleocytoviricota that multiply within molecular virus factories in the host cytoplasm and they primarily infect species of ameba. Their gene repertoire includes informational genes formerly thought to be exclusive to cells, a finding that led to a rethinking of the very notion of viruses….

“Nucleocytoviricota were proposed as a fourth domain of life in 2010…. While Nucleocytoviricota do not form a separate domain, recent evidence suggests they played an important role in the evolution of modern eukaryotes. They have been implicated in the origin of the eukaryotic nucleus, while phylogenetic analysis of informational proteins suggests that transfer took place between ancestral giant viruses and eukaryotes, possibly in both directions.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. pp. 9, 10.

“Likely, viruses did not evolve just once. Viral supergroups and extra domains present simplistic scenarios where viruses remain largely separated from the evolution of their cellular hosts. But viruses can be viewed more as a strategy and less as a single lineage that originated in a single time and place… Forterre writes that ‘the origin of viruses then becomes the question of the origin of virions as a specific mechanism of gene dissemination in the RNA/protein world.’ There is no reason to assume that a strategy as successful as virion production arose just once.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 10; subquote: Forterre, P. 2011. “Manipulation of cellular syntheses and the nature of viruses: the virocell concept.” C. R. Chim. 14:392-399. doi: 10.1016/j.crci.2010.06.007.

“Numerous capsid-like structures are present in cells. A good example of these is bacterial microcompartments (BMCs). BMCs form shells that compartmentalize certain biochemical reactions in the cytoplasm. They are composed of two shell proteins, BMC-H and BMC-P, that form an icosahedral assembly bearing a striking morphological resemblance to viral capsids. The similarity ends there, however, as neither protein shares structural similarity with viral capsid proteins.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 11.

“A virus with plasmid origins, coupled with the co-option of existing viral capsids from a different type of replicator is a fascinating scenario. A plasmid ancestor begs an obvious question: if there is a place for viruses on the ToL, why not plasmids too? We can logically ask the same question about other selfish replicators such as DNA transposases, which, after all, show distant homology to viral sequences.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 12.

“Forterre states that ‘the tree of life is infected by viruses from the root to the leaves’. This metaphor captures the numerous, independent origins of viruses from early RNA parasites pre-dating LUCA to more recent viral lineages such as the ssDNA [single stranded] viruses that evolved from plasmids combined with RNA capsid proteins. It is obvious that there is no single branch into which viruses can be placed. It is likely that many viruses are a hybrid of genes from divergent lineages, existing both before and after the emergence of LUCA.” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 12; subquote: Forterre, P., M. Krupovic & D. Prangishvili. 2014. “Cellular domains and viral lineages.” Trends Microbiol. 22:554-558. doi: 10.1016/j.tim.2014.07.004.

“Our understanding of life is limited but growing. We need dynamic and evolving models that can answer our questions about the nature of biology. In this review, we argue that viruses should be included in future models of biological evolution–models that have historically been represented by the ToL. These models will need to be digital and multi-dimensional in nature. They will also be very difficult to create. One option is to be cynical and heed the words of Steven Benner on lifeforms: ‘We do what we generally do when a reality is too complex to meet our constructive needs: we ignore it and continue with a simpler, if arguably false, view.’” Harris, Hugh M.B. & Colin Hill. 2021. “A Place for Viruses on the tree of Life.” Frontiers in Microbiology. 11:1-16. doi: 10.3389/fmicb.2020.604048. p. 14; subquote: Benner, Steven. 2010. “Defining life.” Astrobiology. 10:1021-1030.

“Rather than the passive role in generating hereditary change that Modern Synthesis assigns to the evolving organism, we have to recognize that all organisms possess powerful biochemical and cellular tools for reshaping their heredity. Using these tools, living beings play a decidedly active role in the evolutionary process. Furthermore, genomic change does not arise uniquely in the siloed species genomes of classical theory. Many important evolutionary changes result from interactions between different kinds of cells, species, and infectious agents (both microbial and viral).” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xix.

“Today we know of several different processes by which genomes acquire new protein and protein domain coding sequences. Examples include horizontal transfer across virtually all taxonomic boundaries from an unrelated organism or virus, reverse transcription of a processed or recombinant RNA into so-called retrogenes, or conversion of noncoding repetitive mobile DNA sequences into protein-coding sequences.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. pp. xx-xxi.

“Organisms actively restructure their genomes in the course of evolution using a set of biochemical and cellular NGE [natural genetic engineering] tools to rewrite their DNA. This means in informatic terms that the genome is a RW (read-write) data storage system, not an ROM (read-only memory) system that changes only by copying errors.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xxii.

“The neo-Darwinists were determined to expunge any hint of organismal volition or function in genome change. Natural Selection requires no biological input other than the ability to reproduce more successfully than competitor organisms. To give Natural Selection deterministic power over the evolutionary process, it was necessary to assume that genetic changes were random, of small phenotypic effect, and generated significant adaptive differences by accumulating over long periods of time due to selective advantages they conferred. Although Darwin himself, in his 1874 6th edition of Origin of Species, recognized how this narrow view of change excluded real-world processes of hereditary variation that occurred ‘independently of Natural Selection’ (Chapter XV, p. 395), his 20th Century followers insisted on gradualist evolution. Thus, neo-Darwinian evolutionary theory blinded itself to the importance of ecologically responsive saltatory modes of hereditary variation, even when they were documented in the DNA sequence data. Today, by contrast, we are in a position to appreciate the complex interplay in all organisms of genome transmission, repair and modification systems, cell regulatory circuits, and organismal sensory networks that control the several processes of hereditary variation at work in somatic, germline and microbial cells.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xxii.

“A major shortcoming of the Modern Synthesis is that it was based on a ‘gene-centric’ view, which assumed that the genome is basically a collection of genes that are both the protein-coding units of heredity and the major sites of heritable variation. This view failed to take the evolutionary importance of chromosome structure into account. It also blinded evolutionary biologists to the importance of McClintock’s mid-20th-century discovery of mobile ‘controlling elements’. The ideas of genetic transposition and control of gene expression by these noncoding mobile elements were heretical notions that did not fit within the narrow confines of the Modern Synthesis concepts of genome function and variation.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xxiii; reference: McClintock, Barbara. 1987. Discovery and Characterization of Transposable Elements: The Collected Papers of Barbara McClintock. NY: Garland.

“Today we know that the human genome contains at least 30 times as much repetitive noncoding DNA as protein-coding DNA. A 2013 plot of organismal complexity against protein-coding and noncoding DNA showed that coding DNA peaked at approximately 3 x 107 base-pairs (bp), while the noncoding DNA increased linearly with growing complexity up to ~2-3 x 1010 bp. In other words, noncoding DNA tracks organismal complexity better than the protein-coding genes.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xxiii.

“Our current understanding of mobile and repetitive DNA element functionality falls into two categories relevant to evolutionary change.

“(1) The first functional category follows McClintock and also Britten and Davidson in recognizing that this noncoding fraction of the genome can format transcriptional and epigenetic regulatory networks by placing the same sequence at different locations in the genome. Among the evolutionary innovations wired by these mobile repeats are C4 photosynthesis in plants and viviparous reproduction in mammals, which is essential to our own reproduction.

“(2) The second functional category comes from direct observations showing that repetitive DNA elements contribute to a sizeable fraction of genomic sequences transcribed into noncoding RNAs (ncRNAs) that are key to cellular differentiation, genome transcription, and epigenetic regulation (small interfering [si]RNAs). Long noncoding RNAs (lncRNAs), in particular, coordinate all kinds of phenotypes, such as fruit ripening in tomatoes, sex determination in Drosophilia, and pluripotency in human stem cells. We are still in the phase of discovery regarding the innumerable functions ncRNAs, especially lncRNAs, play in genome regulation and maintenance, cell biology, and multicellular development.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. pp. xxiii-xxiv; references: McClintock (as in quote above); Britten, R.J. & E.H. Davidson. 1971. “Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty.” Q. Rev. Biol. 46(2):111-138.

“… evolution science has effectively turned itself upside down conceptually. What I mean by conceptual inversion is that the 20th century Modern Synthesis considered the evolving organism to be the passive beneficiary of random mutations and natural selection, whereas the 21st century view recognizes that evolving organisms play active and very diverse roles as agents of their own genomic, phenotypic, and adaptive changes.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xxiv.

“Although the mammalian adaptive immune system is exceptional in the complexity and specificity of its multiple actions on the antibody-coding loci in our genomes, it is far from unique in using DNA manipulations to modify cell-cell interactions. Even the simplest of prokaryotic cells, not to mention more complex eukaryotic parasites like the ones that cause sleeping sickness and malaria, rearrange the DNA encoding their surface proteins to alter them so they can escape antibody-guided destruction. The general name for such genome manipulations is antigenic variation. In other words, our immune system is in a constant NGE arms race with the microbes that try to take over our bodies for their own ends.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. xxvi.

“Two recent excursions into novel scientific territory, in particular, have fortified my conviction that an evolved ability to rewrite the genome is a fundamental vital property of all living organisms…. …cellular cognition… cognitive activities are clearly documented for mycoplasmas, the most elemental living cells with the smallest naturally evolved cellular genomes. Along with learning about Mycoplasma cognitive behaviors, I also learned that these microbes devote a significant portion of their limited genomes to NGE functions: repetitive DNA; several kinds of mobile DNA elements; site-specific, transpositional and homologous recombination activities; CRISPRs; and a very active sex life resulting in an enormous capacity to transfer DNA between cells. Evidently, even the simplest organisms have found it essential to mobilize and rearrange their genomes…

“… cancer genomics…. …human (and other mammalian) cells have two kinds of biochemical systems for repairing broken DNA molecules. The one that is used in normal tissues is called canonical nonhomologous end-joining (cNHEJ), and it makes very few changes in the DNA. But the backup system that is active in cells that already are or may become cancerous is called alternative end-joining (altEJ), and it uses a highly mutagenic DNA polymerase θ (Pol theta or Pol θ) as it connects the broken ends. Pol θ is a remarkable protein. It creates all kinds of new DNA sequences by jumping from one chromosome region to another as it lays down new DNA strands complementary to its different templates, generating chimeric sequences that may encode fusion proteins with different genomic sources for each part of the molecule, something often seen in cancer. And sometimes Pol θ even synthesizes completely novel DNA strands with no template at all. If altEJ existed just as a backup to the normal cNHEJ break repair system, there is no reason for it to perform all these prodigious DNA gymnastics. The reason for Pol θ’s creativity may well be that some failures causing chromosome breakage signal to the cell that drastic genome change is necessary. In other words, DNA Pol θ’s inherent mutator functions have evolved not just for DNA repair but also to carry out repair that quite literally makes a difference and leads, as it does in cancer, to significant genome change.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. pp. xxviii-xxix.

“For me, NGE is shorthand to summarize all the biochemical mechanisms cells have to cut, splice, copy, polymerize, and otherwise manipulate the structure of internal DNA molecules, transport DNA from one cell to another, or acquire DNA from the environment. Totally novel sequences can result from de novo untemplated polymerization or reverse transcription of processed RNA molecules. NGE describes a toolbox of cell processes capable of generating a virtually endless set of DNA sequence structures in a way that can be compared to erector sets, Legos, carpentry, architecture, or computer programming.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 11.

“In summary, NGE encompasses a set of empirically demonstrated cell functions for generating novel DNA structures. These functions operate repeatedly during normal organism life cycles and also in generating evolutionary novelties, as abundantly documented in the genome sequence record. Some NGE functions help us to understand the mechanistic details of rapid evolutionary changes. Rapid changes include the evolution of novel proteins by reorganization of existing functional domains to generate new combinations of biochemical activities and the distribution of regulatory signals to multiple sites in the genome.

“Like all biochemistry, NGE functions are subject to cell regulation (turning on and off in response to sensory inputs), and NGE operations are targetable to particular locations in the genome by well-defined molecular interactions. A surprisingly large number of external stresses and life history events activate NGE genome change operators. Many of these, such as interspecific mating, are just the kinds of unusual biological interactions that we would expect after major ecological disruption.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. pp. 11-12.

“Transposons are segments of DNA that have the capacity to move (or transpose) from one location in a genome to another. In order to make an antibiotic resistance sequence itself part of a transposon, it is sufficient to surround it by two copies of an existing transposon. This sometimes occurs normally as part of the transposition process….

“Once an antibiotic resistance determinant has the capacity to transpose, it is easy to see that it can insert into a plasmid and become transmissible to other cells. This is clearly the source of many resistance plasmids.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 27.

“Transposable elements are chromosome segments that can change position, or transpose, in DNA…. In fact, dispersed mobile genetic elements account for between 40% and 65% of our own DNA. They exceed protein-coding sequences by more than 25:1.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 29.

“Today, we know that inhibiting cell division is a checkpoint control that prevents formation of daughter cells until genome damage has been repaired.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 37.

“The second discovery [after the realization that exons in DNA could be combined to make novel proteins] was that proteins are not organized simply as strings of individual amino acids. Certain protein subregions, called domains and composed of dozens to hundreds of amino acids, were found to be present repeatedly. Sometimes the domains were repeated in the same protein, and generally, they were found to be present in many different proteins. This modular organization as series of domains was a radically new way to think about protein structure. It fit beautifully with the idea of proteins encoded by different combinations of exons. By laboratory genetic engineering, it was possible to add domains together in new combinations. The results showed that the domains retained their functions when combined in new ways. Thus, they were truly independent modules capable of rearrangement.

“Genome sequence data have abundantly confirmed that domain recombination has been a major source of functional novelty in evolution….

“If we think about how domain accretion and shuffling must happen naturally, we realize that they have to involve cutting and splicing extended DNA sequences encoding the multiple amino acids in each domain. In other words, protein evolution requires natural genetic engineering. Fortunately, we know that different extended sequences can be spliced together by several different mechanisms in living cells. Some of these mechanisms operate purely at the DNA level, while others involve RNA that is reverse transcribed to DNA and inserted in the genome.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 41.

“Our own genomes contain over 40% of their DNA as dispersed repeats. Recombination between repeats at different locations leads to chromosome rearrangements. Because the locations of the repeats determine where the rearrangements occur, this is another nonrandom feature of recombinational exchange.

“Different organisms take advantage … of nonrandomness to target recombinational exchange for functional goals. Cells transfer different DNA sequence information from one genomic location to another when the differences are surrounded by homologous repeats. The cells use specific cleavage at a repeat to initiate recombinational exchange. The generic term for a sequence flanked by homologous repeats is cassette. Cassete exchange serves a number of different adaptive purposes, illustrating how inherent nonrandomness in natural genetic engineering can be used and reused.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 48.

“Mobile genetic elements come in many forms. Some operate purely as DNA. Others make an RNA copy and reverse transcribe it back into DNA as it inserts at a new location. Elements that move, or transpose, to multiple new locations are called transposons or rerotransposons (if they use an RNA intermediate). Other mobile elements only insert in particular locations by a process called site-specific recombination….

“What all mobile elements share are proteins that aid them to cut and splice DNA chains so that they can construct novel sequences, much as human genetic do in their test tubes. These proteins have various names, such as recombinase, transposase, and integrase. It is the specificity of the cutting reactions involving these proteins that determines where a mobile element moves in the genome.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. pp. 49-50.

“In the immune system, purposeful and having a predestined outcome are far from the same thing. Your immune system follows a regular process, but the end result is not fixed in advance.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 58.

“Three remarkable things about somatic hypermutation and CSR [class switch recombination] [of things that the immune system does] are explicitly excluded from prevailing philosophy of genetic change. First, they are adaptive and purposeful genome changes. Second, they are functionally targeted. Third, for CSR, targeting involves intercellular signals that depend on how other cells in the immune system perceive a particular infection.

“If immune cells can do all the above, is there any scientific reason we would assume that other cells cannot do the same?” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 61.

“How do genomes encoding complex networks evolve to provide novel functions in any reasonable period of time? According to the conventional view of evolution as a random succession of independent, localized, slight changes–each providing its own selective advantage–the evolutionary process appears hopelessly slow and subject to taking too many steps backwards before it takes one forward. The ideal solution would be rapid ways of copying and modifying the DNA encoding the network components on a wholesale basis. Although such processes were ruled out a priori by the founders of conventional evolutionary theory, they are just what molecular biologists studying DNA change and genome sequences have discovered: duplication and natural genetic engineering processes for amplifying and distributing DNA encoding network components throughout the genome. In other words, NGE is a way to build molecular circuits, Lego-like, rapidly….

“The first step is often, but not always, duplication of the entire genome. This is one of the evolutionary benefits of sexual reproduction because rare couplings, either within a species or between different species, produce individuals that have undergone whole-genome doubling (WGD). WGD has been documented in yeasts, other fungi, protists, and even vertebrates. WGD is extremely common in plants and is now recognized as a major factor in Darwin’s abominable mystery, the rapid diversification of see plants.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 64.

“Many eminent scientists had opined that the noncoding DNA, much of it repeated at many different locations, is nothing more than junk DNA. ENCODE [a project – Encyclopedia of DNA Elements] revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 66.

“The modern concept of the genome has no basic units. It has literally become ‘systems all the way down.’ There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other ‘DNA elements’ (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair, and evolution.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 74.

“It is common today for molecular, cell, and developmental biologists to speak of cells ‘knowing’ and ‘choosing’ what to do under various conditions. While most scientists using these terms would insist they are just handy metaphors, I argue here that we should take these instinctive words more literally. Cell cognition may well prove itself a fruitful scientific concept.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 75.

“If the different biochemical and biomechanical processes fall out of sync [in a cell division cycle], or if there is either a mistake or damage, sensory molecules detect the problem. They activate a checkpoint to hold up the entire cycle until everything has been set right for renewed progress.

“Cells set distinct checkpoint systems for growth and division. The easiest to appreciate is the spindle checkpoint. This makes sure that each daughter cell gets one and only one copy of each duplicated chromosome. The reliability of cell division depends on this sensory process. Left to random chromosome distribution, less than one in a billion divisions of our own cells would be successful.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. pp. 76, 77.

“When eukaryotic cells suffer injury (particularly well studied in the case of DNA damage), there are at least 2 different outcomes:

“(1) A checkpoint, repair of the damage, and then resumption of the cell cycle
“(2) Cell suicide following an organized cascade of events, labelled apoptosis. The dying cell disintegrates in an orderly way.

“The cell chooses between repair and survival, on the one hand, and apoptosis, on the other, based on its environment. The key environmental features for human cells are nutrition and the presence of intercellular signalling molecules called cytokines.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 77.

“How do these insights apply to economics? Checkpoint systems notably break down in cancer cells. Cancer may usefully be viewed as an analogy to an economic system in crisis. The analogy may be particularly appropriate to the US economy, in which financial market turnover expanded from 1.5 times the gross domestic product in 1960 to over 50 times the GDP in 2000. It is not unreasonable to argue that the housing bubble and 2007-2008 collapse were chiefly the results of uncontrolled proliferation by aberrant forms of normally useful constituents in the body economic: mortgages and financial derivatives. The crisis might never have happened if proper checkpoints (i.e., government oversight and regulation) had been fully operational.” Shapiro, James A. 2022. Evolution: A View from the 21st Century: Fortified. Chicago: Cognition Press. p. 79.

“If continuous improvements accumulate toward progressive forms (e.g., through the generation of complex organs as Darwin expected), the bearers of these improvements must finally be the fittest organisms, which is not the case in nature. Bacteria as well as protists had enough fitness to survive for a longer time than even vertebrates. The accumulation of complex organs and functions from single cells to vertebrates (which is usually referred to as progress, also by Darwin) delivers anything but enhanced survival capacity.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 10.

“The view that progress might be a simple accumulation of fitness is not necessarily an element of modern Darwinian thinking, but the relationship between fitness and progress has remained unresolved since the days of Darwin. Gould points out this relationship: ‘I have long been entirely underwhelmed by the standard arguments for general advantages of increasing complexity in the Darwinian game…. I can envisage just as many situations where more elaborate forms might be a hindrance – more parts to fail, less flexibility because all parts must interact with precision.’ Remember that Darwin expected functional improvements through the building of organs that were more complex, and today complexity is often equated with progressiveness.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 11; reference: Gould, S. 1996. Full House: The Spread of Excellence from Plato to Darwin. NY: Three Rivers Press. p. 199.

“Autonomous systems are organizationally closed in the sense that their organization is characterized by their internal network processes, which recursively depend on each other and thus constitute the system as a unit. These processes generate a far-from-equilibrium situation as long as the system is living. Equilibrium with the processes in the environment arises when the system is dead.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 21.

“Luisi emphasizes that there is an interesting contradiction between biological autonomy and dependence on the external medium and that all living organisms must operate within this contradiction.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 21; reference: Luisi, P. 2003. “Autopoesis: a review and a reappraisal.” Die Naturwissenschaften. 90:49-59.

“The basis for autonomy is the special interdependence between the whole and its parts within the organism, which include a differentiation in subsystems and organs.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 22.

“… plants exhibit a predominantly open relation to their environment, whereas animals have a more closed form of organization. In animals, the exchange surfaces for metabolism are turned to the inside. Special internal organs and internal cavities appear, while exchange surfaces on the outside are reduced. Thus, animal life steps to a certain extent out from the direct environmental relation. The enclosure from the environment requires – on the other hand – a sensorimotor interzone, which restores the contact with the environment, however, on a new level. This condition shows separate organs for sensory and motor activity and their central nervous connections. The principle of a closed-body organization enables the independent movement of the animal….

“Thus, not a rigid, but rather a flexible relation between organism and environment emerges.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 23.

“…robustness encompasses a relative, not an absolute, property because no system can maintain stability for all its functions when encountering any kind of perturbation.

“Robustness is concerned with maintaining the possibility of a system to function rather than maintaining an actual state of a system. Thus, Kitano differentiates it from stability and homeostasis, which predominantly describe a function that keeps a condition relatively constant. A system is robust as long as it maintains functionality, even if it transits to a new steady state or if instability actually helps the system cope with perturbations. Such transitions between states are often observed in organisms when facing stress conditions. One such condition can be extreme dehydration, to which some organisms can react with a dormant state, becoming active again on rehydration. These examples of extreme robustness under harsh stress conditions show that organisms can attain an impressive degree of robustness by switching from one steady state to another rather than trying to maintain a give state.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 24; reference: Kitano, H. 2007. “Towards a theory of biological robustness.” Mol. Syst. Biol. 3:137.

“Robustness can be seen as a prerequisite for autonomy….

“However, it is also justifiable to regard robustness as a part of autonomy itself. Robustness, also in different actual states of a system, maintains basically that the system is kept in a far-from-equilibrium state. Even dormant forms are different from their immediate surroundings in a self-organized manner, including when the metabolism is completely reduced.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 24.

“Weiss sees a living system as an entity that imposes restricting (i.e., regulating) functions on its component parts so the functionality of the whole system is ensured. The system itself contains constituting properties and thus possesses information that does not stem from the parts themselves. The system must be regarded as a spatiofunctional entity that integrates the functions of its parts. It has an ontological weight of its own.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 28; reference: Weiss, P.A. 1977. “The system of nature and the nature of systems: empirical holism and practical reductionism harmonized.” In: Schaefer, K.E., H. Hensel & R. Brady. Towards a man-centered medical science: A new image of man in medicine, vol. 1. Futura Publishing Co.

“Living systems are autonomous in the sense that they maintain themselves in form and function within time and achieve a self-determined flexibility.

“These living systems:

“I. Generate, maintain, and regulate an inner network of interdependent, energy-consuming processes, which in turn generate and maintain the system;
“II. Establish a boundary and actively regulate their interaction and exchange with the environment;
“III. Specify their own rules of behavior and react to external stimuli in a self-determined way, according to their internal disposition and condition;
“IV. Establish an interdependence between the system and its parts within the organism, which includes a differentiation in subsystems;
“V. Establish a time autonomy; and
“VI. Maintain a phenotypic stability (robustness) in the face of diverse perturbations arising from environmental changes, internal variability, and genetic variations.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 32.

“The term autonomy cannot be taken in an absolute manner but always describes relative autonomy.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 37.

“Generally, an extrinsic relation and an intrinsic relation of autonomy can be distinguished. The extrinsic relation describes the system-environment relation. The intrinsic relation describes the self-referential, internal organization within the system (e.g., homeostatic stabilization of processes, intraorganismal signaling, connectivity within neuronal systems). This is basically identical with what has been called interactive autonomy (how autonomously a system behaves in interaction with its environment) and constitutive autonomy (within the context of the biological system itself).” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 37.

“Several biological elements can contribute in different degrees to changes of autonomy….

“One such element is spatial separation from the environment, such as with cell membranes, cell walls, integuments of metazoans with cuticles, shells, hairs, or feathers….

“Homeostatic functions are means to establish and enhance internal functional stability. This overlaps to a large extent with changes in robustness. Another element is the displacement of morphological structures or functions from an external position into an internal position within the organism, here summarized as internalization….

“A gain in size during many transitions leads to a reduction of the surface-to-volume ratio. This means that in larger animals there is less direct contact to the immediate environment relative to the existing body mass….

“These elements are prerequisites for establishing a certain amount of physiological flexibility within a given environment, that is, a capability of organisms to generate flexible functional answers to conditions and changes in their environment. Finally, this principle can be widened to include all forms of behavioral flexibility, emancipating organisms from mere short-term reactions to environmental factors. Together, these elements are able to generate certain degrees of physiological and behavioral freedom.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. pp. 38, 39.

“A set of resources can be involved to change autonomous capacities:
“I. Changes in spatial separations from the environment;
“II. Changes in homeostatic capacities and robustness;
“III. Internalization of structures or functions;
“IV. Increase in body size; and
“V. Changes in the flexibility within the environment, including behavioral flexibility.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 39.

“Comparable to single cells, neurons of metazoans have receptors on their surface. Here, however, incoming signals are transmitted into action potentials, not into the direct change of movement. The action potentials influence other neurons, through which only indirectly is a reaction (e.g., of contractile organs) initiated. Therewith, an additional level of integration is present: First, the sensible neuron integrates incoming stimuli and activates action potentials or not. If an excitation occurs, the signals are processed in one or several postconnected neurons, and depending on the result, a reaction is initiated or not. Both principles show basic elements of independence regarding the physical environment and a certain amount of self-determination. Even single cells do not behave like billiard balls, which when hit only move according to the physical principles of cause-effect relations, but rather they calculate the incoming signals. The advantages of a nutrient, for example, may be weighed against a concentration of toxins. However, with the generation of nervous systems, the capacity for this indirect and self-determined reaction is largely expanded. An increasing uncoupling or detachment of signals and reactions is introduced, so that the signals are processed in neuron intermediate steps before a reaction follows.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. pp. 131-2.

“The larger the number of interneurons between input and output correlates with widened behavioral flexibility and is the basis of an increased learning potential.

“The concentration of neurons within central nervous systems provided the potential for many neurons to be located near each other, so that the possibilities for generating connections and networks were increased.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 133.

“The neural system for locomotion control in vertebrates consists of two main components: the CPGs [central pattern generators; clusters of neurons firing together] in the spinal cord and the superimposed systems in the centers of the brain stem and the forebrain. The CPGs generate autogenously the rhythmic patterns of muscle activity that are characteristic for locomotion. Each segment of the spinal cord contains two pairs of CPGs, one for each side. The left and the right CPGs of a segment can interact through reciprocal inhibitory connections.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 135.

“… for the present discussion, it is only important that the principle of evolutionary uncoupling of the system of CPGs exists [to allow the fine tuning of detailed movement]. Dubbeldam assumes that such an uncoupling is not restricted to locomotion. Further rhythmical movements, such as jaw movements during feeding or vocalization is some species and breathing, are also under the control of CPGs and need to be uncoupled so finely tuned movements can be performed.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 137; reference: Dubbeldam, J.L. 2001. “Evolution of playlike behaviour and the uncoupling of neural locomotor mechanisms.” Netherlands J. Zool. 51:335-345.

“The basal ganglia are essentially responsible for the activation of only those muscles (of more than 600 in mammals) needed for highly differentiated intentional movements. The large number of movements possible for a limb has been called the ‘degrees-of-freedom problem in motor planning.’ The neural loops within the basal ganglia contribute essentially to selecting movements of appropriate muscles to perform a movement initiated by cortical areas….

“In mammals, all tlhese centers of movement control are increasingly subordinated to the influence of the neocortex. Each consciously and intentionally initiated movement has its origin here. For this reason, the motoneurons are arranged in the neocortex according to the body parts they innervate. Basal ganglia and the cerebellum are connected with the neocortex by extensive nerve tracts and build separate feedback loops for control and estimation of the outcome of the planned actions from the neocortex….

“Also in mammals, most standard movements can be carried out without the influence of the cortex, but they would be slower and automaton-like. However, voluntary movements and goal-directed movements, which need sensory guidance, are not possible without cortical control. This exemplifies that, with the enlargement of the cortex, especially the more flexible, goal-directed, and – in the meaning supported here – more autonomous movements become possible.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 142.

“In mammals, the pyramidal tract is gradually added to the descending pathways. It constitutes a direct connection from the cortex to the motoneurons, bypassing the motoric centers of the brain stem and the forebrain…. In monotremes and marsupials, relatively primitive mammals, the tract is still small. Within the placental mammals, it is generally more developed, but it gains importance especially in primates. The evolution of the pyramidal tract is related to increased precision in the use of fingers, especially in apes, but also in raccoons and in many rodents, such as squirrels and hamsters….

“This precision is mediated by the pyramidal tract and requires cooperation with an elaborated somatosensory system for the fine-tuning of movements to the immediate consequences of the actions.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 143.

“Origin and generation of endothermy in mammals and birds are a challenge for evolutionary biology, as it is still not clear which forces initiated and selected this ‘wasteful strategy of energy use’. In terms of adaptation and efficiency considerations, it even becomes a paradox that such an energetically expensive lifestyle became so successful.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 149.

“The extensive modifications that are needed to reach endothermic physiology took place independently in the avian and mammalian lineages.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 149.

“Each of these scenarios [among about five for evolutionary understanding of the path to endothermy] has various problems and shortcomings.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 151.

“In mammals and birds [with endothermy], the availability of movements is largely expanded with significantly longer periods of intense activity, including prolonged nocturnal activity. Large-range and long-duration movements, including migrations, become possible for the individual in many species.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 156.

“By far the majority of lizards and snakes are restricted to microhabitats with burrows, bushes, or rocks, where they can hide. After phases of high anaerobic energy production, they can be vulnerable for a long time, until the oxygen debt is repaid. Thus, the hiding place is essential for survival.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 156.

“In nature, lizards have annual energy budgets that are only about a 40th of those of birds and mammals of equivalent size, and reptiles can often survive long periods without energy input.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 156.

“… it is proposed here to regard flexibility as an essential component of the intelligence of animals. Flexibility of behavior allows the individual to find its own solution for problems and tasks or even to act independently from external necessities, as is the case during play…. On the contrary, inherent or early imprinted forms of behavior are mainly fixed and relatively inflexible, especially if they are well adjusted to environmental circumstances.

“Intelligence, however, may include more than flexibility. Abilities such as memory, intentionality, representation, and many more can be viewed as essential to intelligence. These abilities are so complex and diverse that it is still difficult to describe them adequately.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 169.

“Increased flexibility of behavior was generated during evolution by way of the principle of uncoupling. Beginning with the generation of simple nervous systems, sensory stimuli were uncoupled from reactions, which subsequently could be increasingly modulated.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 169.

“Fuchs differentiates a horizontal from a vertical circular interrelationship. Horizontal interrelationships are seen, for example, within the metabolism. Vertical interrelationships are the relations between the different system levels such as cells, organs, organisms, and so on. Fuchs describes both of them together as integral causality, thus extending well beyond simple linear causality.” Rosslenbroich, Bernd. 2014. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer. p. 250; reference: Fuchs, T. 2009. Das Gehirn – ein Beziehungsorgan. Eine Phaenomenologisch-oekologische Konzeption. Stuttgart: Kohlhammer.

“Riskin unravels a long-standing conflict betwen those who wanted to outsource agency to a divine engineer and those who reduced agency to mechaniscs of components parts of the perceivable organism. In both cases the organism itself is not the active entity but is driven by principles in the background.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 16; reference: Riskin, Jessica. 2016. The Restless Clock: A History of the Centuries-Long Argument over What Makes Living Things Tick. U of Chicago Press.

“It is, however, remarkable that the field [genetics], which is expected to provide a firm chemical and physical basis for understanding life, early on introduced the notion of information to understand the function of DNA and thus already relinquished a purely materialistic explanation. This has not been realized by the majority of scientists.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 38.

“The term reduction describes a mode of operation in scientific studies. From a certain complex entity like a whole organism, a cell, or an ecosystem, only a selected part is regarded and studied in detail to get more information about this part…. Reduction is a mode of analysis, and the dissection of a biological entity permits a better understanding of the separated part….

“The term reductionism, however, denotes the expectation that higher-level phenomena can be completely understood in terms of the properties of their constituent parts and that any further studies of higher-level entities are useless. Thus, reduction is a method of science, whereas reductionism is an ontological claim about reality.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 43.

“Bertalanffy regarded organicism within biology as having three major components: (1) an appreciation of wholeness through regulation; (2) the notion that each entity is a dynamic, changing assemblage of interacting parts; and (3) the idea that there are laws appropriate for each level of organization (from atoms to ecosystems), which follow from emergent properties.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 45-6; reference: Bertalanffy, L. 1952. Problems of Life: An Evaluation of Modern Biological and Scientific Thought. NY: Harper & Brothers.

“Consequently [because concept of form challenges reductionism and classical integrative systems biology], O’Malley and Dupre identify two variants of the term systems biology that are presently in use: ‘pragmatic systems biology’ and ‘systems-theoretical biology.’ The pragmatic version, which is the younger one, examines intracellular networks by characterizing each of the components in the networks individually and then modeling the interactions between them using computational tools. The expectation is that by means of this bottom-up model, one will arrive at a full understanding of the cell as a whole. Such an approach is thoroughly reductionistic given that it privileges the molecular level and then expects that the pooling of the data will calculate up to the behavior of the whole complex….

“For systems biology to succeed where previous approaches failed, it needs to embrace a truly system perspective. It must move beyond the study of individual molecules and their interactions and study systems as systems rather than as collections of parts, which is at the heart of the systems-theoretical approach.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 50-1; reference: O’Malley, M.A. & J. Dupre. 2005. “Fundamental issues in systems biology.” BioEssays. 27:1270-1276.

“My impression–and also my thesis–is that biology today develops, or should develop, toward such a synthesis concerning knowledge from analytical research on the one hand and an organismic understanding of life on the other hand.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 59.

“How are these two perspectives [processes and organization] interrelated? Which one is more important, the view of process or the view of organization? I think the key to understanding this relationship is to comprehend that both principles apply simultaneously at any given time: There is an organization, which is maintained by an active process. The process generates the organization, and the organization structures and directs the process. Neither of them is possible without the other. Processual turnover means that the very structure of every organism, its organization, unlike that of any machine, is wholly and continuously reconstituted as a result of its own active operation(s)….

“Thus, an organism is a constantly changing and processing organization. Organization enables the organism’s stable identity, and the constantly running process generates and sustains the organization. Here we encounter a principle that will appear repeatedly in the following discussion of organismic properties.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 71.

“Therefore, an essential statement of the concept developed next will be that living beings exhibit an indissoluble interdependence of process, substance, energy, and information.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 74.

“This is exactly what usually emerges in biochemistry and molecular biology: many processes turn out to be cycles. One component is dependent on the next one; there is neither a first cause nor a final effect. Rather, one process is the prerequisite for the next one, which is the prerequisite for the next one and so on. Such processes are dependent on each other (interdependent) within cycles or regulatory networks, which often is called ‘circular causality.’ Many networks, such as gene-regulatory networks, constantly grow in complexity, so that diagrams of them are becoming ever more complex the more components are identified.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 78-9.

“Different proposals have been brought forth to describe organic functions more adequately in form of reciprocal relationships. Fuchs describes the principle as ‘circular causality’ and differentiates a horizontal from a vertical form. Horizontal circular causality is found, for example, within cellular metabolism or between cells or tissues. Vertical circular causalities are relations between different system levels such as cells, organs, and organisms. Fuchs describes them both together as integral causality.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 81; reference: Fuchs, T. 2018. Ecology of the Brain: The Phenomenology and Biology of the Embodied Mind. Oxford UP.

“Here are some possible basic forms of interrelations that can be found in organismic processes:

“• Linear causation….
“• Multiple effects: One cause may generate several effects.
“• Multiple causality: In other situations, several causal influences may generate one reaction or one outcome within the organism.
“• Circular causation: Cyclic organization came to the focus of biology in the twentieth century with the discovery that large numbers of biological systems involve cycles….
“• Networks: Network approaches try to describe the complexity of interconnections between components.
“• Trigger causality: Many influences on the organism generate a complex cascade of reactions and processes so that these influences act as a trigger….
“• Constraints….
“• Regulatory (cybernetic) system: A cybernetic system incorporates a closed signaling loop, which regulates specific properties of a controlled function or process.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 85-6.

“Green et al present an overview of different network approaches. Besides the approach of Barabasi and colleagues [scale free networks with nodes of high degree of attachment and many more nodes of low degrees], the survey also takes the following models into account: a hierarchical modular network approach, which focuses on the hierarchical organization of several modules in larger networks; approaches that describe the analysis of temporal expression data of proteins, thus representing the dimension of time; approaches that are able to regard context-sensitivity of processes; and approaches that are able to regard specific dynamic states of the respective system.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 95-6; references: Green, S., M. Serban, R. Scholl, N. Jones, I. Brigandt & W. Bechtel. 2018. “Network analyses in systems biology: New strategies for dealing with biological complexity.” Synthese. 195(4): 1751-1777; Barabasi, A.L. & Z.N. Oltvai. 2004. “Network biology: Understanding the cell’s functional organization.” Nature Reviews Genetics. 5:101-113.

“Overall, the former ideas, that cellular and molecular mechanisms are complex chains of causally reacting components that together result in the generation of the phenomenon of interest, are being increasingly replaced by understanding functions by means of nonlinear circular causation, interdependencies, as well as system- and network-characteristics. In every respect, the components of an organism are much more interdependent in manifold ways than has been previously assumed.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 96.

“The complex of interacting components, together with the coherent entity itself, can be called an integrative system. Hence, key features of a biological system are active integration, regulation, interaction of components, and the autonomy of the respective system as a whole.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 96.

“The majority of today’s systems biologists belong to the pragmatic school, which studies large sets of molecular data to reconstruct systemic properties….

“In contrast, theoretical systems biologists recognize that complex physiological phenomena also take place at biological levels of organization higher than the subcellular one. For this approach it is crucial to analyze systems as proper systems, not as mer collection of parts. Systems are taken to constitute a fundamental ontological category, which integrates the components and processes involved. Therefore, this understanding will be called hee integrative biological system.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 97-8.

“Weiss points out that in contrast to the infinite number of possible interactions and combinations among the parts, in the living system only an extremely restricted selection from the opportunities for chemical processes is being realized at any one moment–a selection that can be understood solely in its bearing on the concerted harmonious performance of a task by the complex as a whole.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 101; reference: Weiss, P.A. 1969.”The living system: Determinism stratified.” In: Beyond Reductionism: New Perspectives in the Life Sciences. Ed. Koestler, A. & J.R. Smythies. pp. 3-55. London: Hutchinson.

“The ten principles of systems biology
“First principle: biological functionality is multilevel.
“Second principle: transmission of information is not one-way.
“Third principle: DNA is not the sole transmitter of inheritance.
“Fourth principle: the theory of biological relativity–there is no privileged level of causality.
“Fifth principle: gene ontology will fail without higher-level insight.
“Sixth principle: there is no genetic program.
“Seventh principle: there are no programs at any other level.
“Eight principle: there are no programs in the brain.
“Ninth principle: the self is not an object.
“Tenth principle: there are many more to be discovered–a genuine ‘theory of biology’ does not yet exist.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 104.

“The idea of biological relativity can then be stated as a natural consequence of the fact that the system is open at each scale and therefore subject to the boundary conditions determined at higher scales.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 105.

“The flagella of a V. carteri colony [a spherical collection of cells with flagella to the outside] beat in a synchronized wave that travels from the anterior to the posterior of the colony. Amazingly, these ‘metachronal waves’ appear to result entirely from hydrodynamic coupling. In other words, despite the apparent high degree of coordination among the flagella of separate cells within a colony, no actual communication between cells is necessary. Synchronization emerges from indirect interactions mediated by the liquid medium. Brumley et al. describe experiments in which somatic cells were physically separated from a colony and held at various distances from each other. Despite there being no direct physical connection between the cells, they beat synchronously when close together, with a phase shift that increased with increasing cell-to-cell distance. Other factors for synchronization seem to involve a sensibility of differential light intensities for the respective cells when the colony rotates as well as some impact of gravity. Whatever the functional details are, the coordination of flagellar beats is generated by the context.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 110-1; reference: Brumley, D.R., M. Polin, T.J. Pedley & R.E. Goldstein. 2015. “Metachronal waves in the flagellar beating of Volvox and their hydrodynamic origin.” Journal of the Royal Society: Interface. 12:20141358. doi: 10.1098/rsif.2014.1358.

“… organisms establish an energetic gradient toward their environment The maintenance of this gradient and its defense against the influences from the environment need to be actively performed. Thus, agency is a primary property of an organism.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 131.

“Agency can appear in three different, thogh related forms:

“1. nondirected agency
“2. directed agency
“3. agency with a preconceived goal.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 131.

“He [Walsh] describes that the category ‘organism’ plays only a very little role in evolutionary theory. Conventional theory today principally deals with the dynamics of supraorganismal assemblages (populations) of suborganismal entities (genes).” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 137; reference: Walsh, D. 2015. Organisms, Agency, and Evolution. Cambridge UP.

“However, Walsh does not just transfer the active role solely unto the organism but rather describes the relation of the active organism within the conditions and prerequisites of the respective environment. In this context he formulates an ‘organismic perspective by arguing that the unit of greatest theoretical significance for evolution is not the gene, or for that matter even the organism per se. It is the organism situated in a system of affordances. Affordances are emergent entities; they are properties of a system, in this case, a system comprising an organism and its conditions of life. Affordances are constituted in large measure by the ways that organisms can exploit or ameliorate these conditions.’” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 138; reference: Walsh, D. 2015. Organisms, Agency, and Evolution. Cambridge UP.

“In general, the motor proteins belong to three classes–kinesins, dyneins, and myosins–which utilize two types of polar cytoskeletal filaments to transport cargoes. Microtubules are long filaments that are typically arranged in a radial array with the plus ends near the cell periphery and the minus ends anchored near the cell center. Kinesins and dyneins move along microtubules and are responsible for most long-range movements of organelles and membranes. Actin filaments, in contrast, are shorter, and although the filaments themselves are polarized, they typically form a randomly oriented meshwork. Myosin motors that move along actin filaments mostly contribute to more localized short-range movements of cargoes. By utilizing two distinct types of transport networks, delivery of cargoes within a cell can be both efficient and precise.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 142-3.

“The membrane [e.g., of a cell] is constantly maintained in a special status of fluidity, avoiding hardening as well as dissolution. The intermediate state of fluidity is a result of the activity of the cell. If membranes tend to harden, the cell integrates more phospholipids with unsaturated fatty acids, and when they tend to dissipate the cell integrates more phospholipids with saturated fatty acids. Also, the cell is able to regulate membrane fluidity by regulating the amount of cholesterol being integrated.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 146.

“During the synthesis of the biomembrane in the endoplasmatic reticulum of the cell, new lipid molecules are first integrated only into the cytosol side of the endoplasmatic reticulum’s membrane. Then it is necessary to translocate some phospholipids to the other side, to complete both sides of the new piece of membrane. This ‘flipping’ does not occur spontaneously. Rather it is performed actively with the help of a membrane-bound phospholipid translocator (called a scramblase), which transfers lipid molecules from the cytosolic half to the lumenal half so that the membrane grows as a bilayer.

“However, this translocator is not specific for particular types of phospholipids, so that the two sides of the piece of bilayer at first are identical. But in the cellular membrane, to which the piece is transported and where it is integrated, there is a difference between the inside layer and the outside layer. Here, another enzyme is active, one that flips specific phospholipids directionally from the extracellular to the cytosolic leaflet, creating the characteristically asymmetric lipid bilayer of the plasma membrane of animal cells. This enzyme is called flippase, and it is ATP dependent, which is the universal energy carrier in the cell. In addition, there too is a phospholipid translocator in the cellular membrane, which guarantees that both layers are inhabited by the same total number of lipid molecules.

“Once again, there is an interdependence between the activity of the cell on the one hand, and the chemical properties of the molecular arrangements.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 146-7.

“Corresponding to an osmotic gradient, there is also for water a certain restricted possibility of diffusion directly through the membrane. However, the cell generates special proteins that enable and regulate water transfer through the membrane. After it had been clarified that the membrane is mainly composed of lipids, it was suspected that water movement across the membrane was in some way enhanced or facilitated by pores or channels, but the search to identify these channels was long and tedious. The identification of water channels then began in 1992. Today these channels are known as aquaporins. Currently thirteen aquaporins have been identified in mammals, distributed in most tissues, but many more have been determined in other groups of animals and in the plant kingdom….

“Aquaporins do not transport water actively; rather the exchange takes place through osmotic water flow along a concentration gradient. But again, the generation and recruitment of the appropriate aquaporin within a specific membrane is an active function of the living cell….

“Thus, even with a process that basically draws on a physical principle such as osmosis, the cellular activity is the crucial organizer of the resulting function. The cell arranges the conditions for the facilitated diffusion.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 147-8.

“… there is also an essential distinction for the biological realm between the information content (its ‘meaning’) and the information carrier. The structure of DNA, its chemical components, and the principle of how the information is encoded are well known today. But its meaning is different from that and is not understood by analyzing the carrier. However, studying transcription, translation, and the resulting proteins and their functions can generate more understanding of the meaning as well.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 150.

“Cavalier-Smith has described some inherited features of animal and plant cells as the ‘membranome,’ because lipids are not formed from DNA templates. An organism needs to inherit the membranome, and it comes complete with the fertilized egg cell. The precise composition of the cellular membrane, chemically describable by phospholipids, proteins, glycolipids, and glycopeptides, contains a robust order, which needs some organization. This is also a clear hint at a form of embodied information, however, still difficult to grasp in a precise way.

“At present it is unusual to talk about such a form of embodied information. But already the necessity to search for information on further levels than just DNA, as it is done in epigenetics, shows that conceptual expansions are necessary.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 154, 155; reference: Cavalier-Smith, T. 2004. “The membranome and membrane heredity in development and evolution.” In: Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. ed. Horner, D.S. & R.P. Hirt. pp. 335-351. Boca Raton: CRC Press.

“The bacterium Escherichia coli, for example, not only reacts to the pH-value and to the temperature of its environment but also to fifty different substances, having just four types of receptors.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 155.

“But what exactly is happening when an agent makes a ‘choice’? Obviously, a choice implies that more than one action is possible. From a physics perspective this might suggest a system that was in metastable equilibrium, like a pencil balanced vertically on its point. It could fall in any direction, so many ‘actions’ are possible. However, such a system would be at the mercy of noise, random fluctuations that would determine in which direction it ‘fell’–hardly a candidate for autonomous choice in its own interests! The key to autonomous choice is not in equilibrium physics but in that the agent must be a far-from-equilibrium system, poised in such a way that the internal states corresponding to different actions being initiated are reliably inhibited yet able to be triggered by essentially tiny signals that bear some correlation with a relevant aspect of the environment.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 156-7.

“Penzlin rejects this analogy [that a flame is like life] because the ‘flame’ is a stationary flow system, but not an organism. It is a catabolic system, while an anabolism is lacking completely….

“Contrary to a combustion [energy flow in a cell], this does not happen within one big incident but is unfolded into many steps, which are controlled by enzymes. This guarantees that the energy that is released during the process is not just exploding, leaving nothing but heat. Rather, the major portion of the energy can be transferred in small amounts to carriers of energy such as ATP and some other compounds. This is what happens during glycolysis, in the citric cycle, and especially within the respiratory chain… Energy in such small quantities, which can be used well-directed and precisely within the organism, is beyond anything within the purely chemical and physical nonliving world.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 160-1; reference: Penzlin, H. 2014. Das Phaenomen Leben. Grundfragen der Theoretischen Biologie. Springer.

“Within the human body, each molecule of ADP/ATP switches several thousand times per day between the mitochondrium and the cytoplasm. It has been estimated that a resting human has a turnover rate of ATP of about 1.7 kg per hour. During intensive exercise this amount can increase to 30 kg per hour.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 161.

“The process generates the organization, and the organization structures and directs the process. Neither is possible without the other [in life].” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 165.

“In my view a coherent picture emerges when the following claim is made: A living organism is an organized, active process or a continuous activity, and what is being processed are substances, energy and information.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 166.

“In a slight extension of a citation from Dupre and Nicholson it would be appropriate to say: Organisms, despite their apparent fixity and solidity, are not only material things but concurrently fluid processes. They are metabolic streams of matter, energy and information that exhibit dynamic stabilities relative to particular timescales. As active processes, and unlike nonliving things or substances, organisms have to undergo constant change to continue to be the entities that they are. (The words in italics are my supplements.)” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 167; reference: Dupre, J & D.J. Nicholson. 2018. “A manifesto for a processual philosophy of biology.” pp. 3-45. Everything Flows.

“The term form is included within the word in-form-ation.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 169.

“Mueller describes how the continuous production and fixation of parts has resulted in the thirty-seven or so presently known extant body plans, and even more existed in the past. All minor clades are modifications of those major body plans, each characterized by distinct, hierarchical combinations of homologues, altogether represented in several million species.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 175; reference: Mueller, G.B. 2003. “Homology: The evolution of morphological organization.” In: Origination of Organismal Form: Beyond the Gene ni Development and Evolutionary Biology. Ed. Mueller, G.B. & S.A. Newman. pp. 51-69. MIT Press.

“Turner studied the physiology of termite chimneys, which are known for a very effective ventilation system, providing homeostasis concerning parameters like O2 and CO2, constantly being adapted to requirements of the growing colony. The question was how do the termites manage to control this homeostasis? As it turned out, termites continuously transport material from points with a higher concentration of CO2 to points with a lower concentration, which at once modifies the air current within the chimney. This amounts to a continuously adapted form fulfilling the regulatory functions in an optimal way…. For the chimney as a whole, this adds up to an ‘embodied physiology’ or an ‘embodied homeostasis,’ simultaneously resulting in the form of the chimney.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 175, 176; reference: Turner, J. Scott. 2007. The Tinkerer’s Accomplice: How Design Emerges from Life Itself. Harvard UP.

“All known variables of life, be they levels of potassium ions in a cell, stages of sleep, or the opening and closing of flowers, have either directly or indirectly been found to display rhythms. These rhythmic changes of life represent an enormous network of biological rhythms, passed on from one generation to the next. The range of periods for biological rhythms is broad, extending from cycles that are measured in milliseconds to cycles that are more than 100 years in length.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 185.

“If the circadian rhythm is regarded as a standard, biological rhythms can further be divided into ultradian rhythms with a period of less than 24 hours, and infradian rhythms with a period longer than a day. Ultradian rhythms are usually related to cell functions. Indeed, presently about 400 different ultradian rhythms have been identified. Most of these ultradian rhythms are clearly endogenous.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 186.

“Biosemiotics is the approach within today’s biology that most systematically advances Uexkuell’s point of view. The main idea of biosemiotics is that life and semiosis, or sign exchange, are coextensive. It is assumed that life has a semiotic nature, because it is based on an endless interpretation of environmental cues and transfer of life-related functional meanings vertically across generations and horizontally to neighboring organisms.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 197.

“Signs carry meaning, and life carries properties that enable meaningful interpretation of perceived signs. One implication of this view is that life has certain mindlike properties, enabling such meaningful interpretation of signs.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 198.

“‘We believe that the study of cognition is on the cusp of a seismic shift similar to the Copernican and Wegnerian revolutions. If we truly recognize, in a biologically realistic fashion, the deep evolutionary inheritance of cognitive behaviour–individually and collectively, in both unicellular and multicellular organisms–a great deal of data that currently resist understanding will be more comprehensible and their implications less obscure. Or so we aim to demonstrate. Evidence that cognitive concepts such as ‘sensing’, ‘memory’, ‘learning’, ‘communication’ and ‘decision making’ can be applied non-metaphorically to the behaviour of bacteria (for example) is extensive and growing.” Lyon, P., F. Keijzer, D. Arendt & M. Levin. 2021. “Introduction: Reframing cognition; Getting down to biological basics.” Phil Trans of the Royal Society B: Biological Sciences. 376(1820): 20190750. doi: 10.1098/rstb.2019.0750. p. 2. Quoted in: Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 202.

“Unlike dead objects, a living being senses, however rudimentarily, a difference between itself and the world. Without the opening to the world, a living being would have no relation to itself; and without the sensation of itself, it would not perceive the world. One can indeed construct inanimate systems that control their movements through causal feedback mechanisms. However, in the case of living beings, the relation to themselves and to the world is determined by an experience: there is a sense of ‘self.’” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 207.

“Ginsburg and Jablonka developed an approach for studying the evolutionary origins of consciousness, which they call the unlimited associative learning (UAL) framework. The central idea is that there is a distinctive type of learning that can serve as a marker for the evolutionary transition from nonconscious to conscious life. They define the term unlimited as follows: the possibilities for learning are sufficiently open-ended, such that there is no serious prospect of all the possible associative links that could be produced actually being formed by a real organism. A system with a capacity for UAL can, within its own lifetime, learn about the world and about itself in an open-ended way.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 209; reference: Ginsburg, S. & E. Jablonka. 2019. The Evolution of the Sensitive Soul: Learning and the Origins of Consciousness. MIT Press.

“As already described, increasing knowledge in comparative molecular biology produced a huge surprise: Where the synthetic theory expected the most variation, on the level of genes and their products, there is far-reaching conservation. This is the starting point for the discussion by Gerhart and Kirschner, who developed the theory of facilitated variation. Conservation means that even distantly related organisms use similar processes for cellular function, development, and metabolism. Each process, with many protein components working together, contributes to the phenotype. When a process is conserved, most of its protein components are conserved. Details of metabolism are the same in certain bacteria and humans, basic cell organization and functions are similar in yeast and humans, and some developmental strategies of fruit flies are strikingly similar to those of human beings.

“There are also new features that had no forerunners in more ancestral organisms, so that organisms are a mixture of conserved and nonconserved processes. However, novelty in the organisms’ physiology, anatomy, or behavior arises mostly by the use of conserved processes in new combinations, at different times and in different places and amounts, rather than by the invention of new procedures….

“The conserved processes are fundamental cellular processes. They operate on many levels within the development and functioning of the organism. Gerhart and Kirschner call them ‘the core cellular processes.’

“Central to the argument of Gerhart and Kirschner is that these conserved processes facilitate rather than constrain evolutionary change. These processes have been conserved they suggest, not only because changes would be lethal but also because they have repeatedly facilitated changes of certain kinds around them. Many of the conserved core processes have the capacity to be easily linked in new combinations….

Thus, some genetic–and possibly much epigenetic–variation is needed to integrate conserved components into new heritable functions. Genetic changes might especially have occurred in regulatory regions of genomes. Gerhart and Kirschner call the increasing possibilities of integrating conserved functions into new combinations and the involved regulatory changes to give new outputs of the conserved processes ‘facilitated variation.’” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 219-220; reference: Kirschner, M.W. & J.C. Gerhart. 2005. The Plausibility of Life: Resolving Darwin’s Dilemma. Yale UP; Gerhart J.C. & M.W. Kirschner. 1997. Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability. Malden: Blackwell.

“Evolutionary changes in development might proceed by a ‘phenotype-first’ route, with genetic change following, rather than initiating, the formation of phenotypic novelties.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 226.

“They [Kitano & Oda] suggest that, over evolutionary time, robustness against external perturbations was enhanced by adding diverse new functions to the input and output components of the organism, and that many of these new functions were gained through symbiosis. They argue for a ‘self-extending symbiosis’ as a process to further enhance robustness. Self-extending symbiosis refers to phenomenon by which evolvable robust systems continue to extend their system boundary by incorporating foreign biological forms (genes, microorganisms, etc.) to enhance their adaptive capability against environmental perturbations. Thus, robust evolvable systems have consistently extended themselves by incorporating ‘nonself’ features into tightly coupled symbiotic states….

Kitano and Oda also argue in the sense of modern systems theory that different degrees of symbiosis add additional systemic layers within an organism.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 230, 231; reference: Kitano, H. & K. Oda. 2006. “Self-extending symbiosis: A mechanism for increasing robustness through evolution.” Biological Theory. 1(1):61-66.

“What is of importance in our context here is that with many of the new concepts and considerations, the approach to understand evolution is becoming much more organismic…. Especially the following properties are involved in these new considerations.

“Integrated systems evolve
“Regardless of where the initiation of an evolutionary change comes from what changes is the whole organism….

“Interdependence
“Several of the newer considerations are based on the biological principle of interdependence and circular causation…. …causation not only flows from the lower levels of biological organization, such as DNA, ‘upward’ to cells, tissues, and organisms, but also from higher levels ‘downward,’ such as through environmental- or tissue-induced gene regulation….

“Another aspect of interdependency lies in the fact that populations of organisms are not relegated to being passive recipients of environmental selection pressures but exert influence on their surroundings through various forms of active niche construction….

“Autonomy….

“Agency….

“…if changes on the level of the phenotype are relevant for evolutionary transitions, then every activity of the organism in its way of life and its circumstances can be involved in this process…. Especially the role of behavior as a source of innovations has been discussed for a long time.

“Variation in time processes
“Especially the findings in evo-devo demonstrate that differences in species, orders, or phyla might be less based on variances of their genes but rather on differences in the spatial and temporal expression of conserved genes….

“Processes of shape.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. pp. 232, 233, 234.

“Thus DST [developmental systems theory] describes identity as a continuity of organization.

“However, the description of a process as such is not enough either, because it tends–at least formally–to neglect the order within the process, which leads to a highly specific organization.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 241.

“Even more profound is the metamorphosis of the butterfly, which goes through the stages of the caterpillar, the pupa, and the imago. Each of these stages has a special organization, with a special shape, special functionality, and particular behavior. This means that it is not a process as such. Rather, the process generates different forms of organization with extremely specific shapes.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 241.

“… the organism achieves this [how the ‘extremely improbable state of living systems far from thermodynamic equilibrium’ can be sustained] not by preventing ‘decay’ but by balancing the degrading and constructing (synthesizing) processes. Every organism, every single cell, exists in a state of permanent decay and reconstruction, in an uninterrupted process of self-renewal, even when it is not growing or is in an apparent state of rest.

“Thus, life is only understandable within the continuous polarity between synthesis and degradation, between production and reduction, between life and death. In this sense, death is an inclusive element of life itself.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 252.

“Many of the genetic and protein elements involved in regulated cell death of multicellular organisms have now been identified in diverse unicells, and an argument can be made that regulated cell death is almost as old as cellular life itself….

“Within a single taxon (especially with eukaryotic taxa), there is usually more than one molecular pathway leading to death, although there is frequently cross talk between them…. In addition to the variation in the death phenotype itself, it has also become clear that the molecular pathways overlap with other outcomes such as cell cycle arrest, dormancy, senescence, aging, spore formation, and sexual reproduction.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 258.

“Therefore, every science consists of the careful observation of the phenomena on the one hand, and the recognition of the underlying order, the regularities, on the other hand. We are never satisfied with the mere collection and listing of phenomena, we want to understand ‘what holds the world together at its core.’ Thus, in essence, the merging of perception and phenomena on the one hand, and thought, ideas, and understanding on the other hand is the essential process of scientific work.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 263.

“In inanimate objects form results from specifications of the material, and in organisms, matter is subordinated to form.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 271.

“When one studies an organism, say a particular specimen of an adult bird, some of its current characteristics are accessible, others are not.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 272.

“The mechanistic doctrine in biology always reaches its limits when it comes to context, network connections, and autonomous and self-generated processes, and even more so when it comes to properties such as subjective experience and consciousness. Yet, these are the central elements of organismic existence.

“However, this also raises the question whether a new organismic understanding of life cannot also be taken as a primary starting point for studying organisms and also for dealing with them in practice. The detour via the mechanistic analysis is perhaps no longer necessary today, so that one could primarily presuppose the specific liveliness from the outset. In this way, some one-sided standpoints, which have certainly arisen through the mechanistic doctrine, could be avoided or even be overcome.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 274.

“The image of the organism as a molecularly and genetically determined survival machine urgently needs to be revised.” Rosslenbroich, Bernd. 2023. Properties of Life: Toward a Theory of Organism Biology. Springer. p. 283.

“In this review, we propose that the integration of biological organization principles (BOPs) is the next natural step for the advancement of biofabrication, allowing the development of specifically tailored molecular and cellular structures in a manner analogous to how nature fabricates.” Hill, Jordan, Ricky Wildman & Alvaro Mata. 2022. “Exploiting the Fundamentals of Biological Organization for the Advancement of Biofabrication.” Current Opinion in Biotechnology. 74:42-54. doi: 10.1016/j.copbio.2021.10.016. p. 43.

“Our group has exploited the possibility to access non-equilibrium by enabling and controlling gradients in chemical potential and mechanical perturbations to generate guided self-assembling systems. This capacity to access non-equilibrium states enables temporal and spatial control of self-assembly as well as emergent properties such as growing and self-healing. These kinds of properties are difficult to achieve with traditional biofabrication approaches.” Hill, Jordan, Ricky Wildman & Alvaro Mata. 2022. “Exploiting the Fundamentals of Biological Organization for the Advancement of Biofabrication.” Current Opinion in Biotechnology. 74:42-54. doi: 10.1016/j.copbio.2021.10.016. p. 48.

“From the BOPs presented here, we believe that molecular SA [self-assembly] holds the most immediate promise for the advancement of biofabrication. For example, SA links are already demonstrating a unique capacity to fabricate structures capable of selectively communicating with cells and guiding their behaviour.” Hill, Jordan, Ricky Wildman & Alvaro Mata. 2022. “Exploiting the Fundamentals of Biological Organization for the Advancement of Biofabrication.” Current Opinion in Biotechnology. 74:42-54. doi: 10.1016/j.copbio.2021.10.016. p. 48.

“Anton van den Broek never held an academic university position but was an econometrician by profession and had initially trained in the law. It was van den Broek rather than any of the famous profession physicists of the day who first realized that the elements should be ordered according to increasing atomic number rather than atomic weight…..

“Meanwhile, the leading physicists of the day including Thomson, Rutherford, Barkla, and even Bohr did not concentrate quite so much on the periodic table although some of them did publish early electronic accounts of chemical periodicity. The fact remains that the amateur van den Broek was able to reach a conclusion that had eluded the expert physicists and one which they quickly accepted after he had made it public. The experimental establishment of this view by Henry Moseley is well-known, but as Moseley readily acknowledged in his articles, he undertook his research ‘with the express purpose of verifying van den Broek’s hypothesis.’” Scerri, Eric. 2017. “The Gulf between chemistry and philosophy of chemistry, then and now.” Struct Chem. 28:1599-1605. 10.1007/s11224-017-0948-5. p. 1601.

“While emphasizing the theoretical demands on living organisms, the autonomy tradition has, for the most part, not addressed how the organism caries out the activities required of an autonomous system. One way to provide such an account would be to identify the responsible mechanisms, but historically autonomy theorists have resisted invoking mechanisms since they seem to be too rigid to account for the flexibility and versatility organisms must exhibit to maintain autonomy.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 391?

“We begin with the two essential elements of a control mechanism: (1) a sensor which sets the value of a constraint in the control mechanism as a result of measuring a variable, and (2) an effector that acts on a flexible constraint in another mechanism, altering how it operates…. What distinguishes a control mechanism is that the constraints that determine the work that is performed are determined by the measurement process and that the work that is performed results in changes in the constraints operative in other mechanisms.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 392?

“Examples of sensors are molecules whose conformation is altered as a result of binding to other molecules whose presence or concentration is being measured. Examples of effectors include transcription factors, which bind to DNA sequences and activate or inhibit the transcription of individual genes or operons, and kinases, which phosphorylate proteins (including themselves in the case of autokinases) thereby altering their conformation and hence their ability to catalyze reactions.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 392?

“The basic sensory mechanism … would not provide the bacterium with information about whether the concentrations of the individual ligands [at the front end of the bacterium are MCPs – methyl-accepting chemotaxis proteins – which bind to a specific set of ligands] are increasing or decreasing. This is the information which the bacterium needs to determine whether it is approaching a nutrient or moving away from a toxin. To detect the gradient, E. coli employs two other proteins [in between MCP sensors and effectors of flagella motors], CheR and CheB, to adapt each MCP to the current concentration of the ligand to which it responds. CheR constitutively adds methyl groups to each receptor, changing the receptor’s conformation to render it more responsive over time. Recall that CheA is a histidine kinase–in addition to phosphorylating CheY [to regulate the flagella motor], it also phosphorylates CheB. Phosphorylated CheB removes methyl groups from the [MCP] receptors, countering the conformation change generated by CheR and making the MCPs less responsive. The overall effect is that the conformation of the MCPs changes in response to whether the bacterium is moving up or down the various gradients.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 393?

“One consequence of decoupling, that is, freeing the components in a control mechanism from a role in ongoing metabolism, is that control processes can gain in complexity independently of any changes in metabolic mechanisms. One way it can increase in complexity is by adding components between the sensor and effector. In the simplest case of control mechanism, control through an allosteric enzyme, the sensor and effector components of control process and tightly linked as they belong to the same molecule–the conformation change resulting from the measurement by the sensor causes changes in the catalytic site of the enzyme.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 397?

“The process intervening between sensor and effector is often characterized as signaling. Signaling pathways can be very short. Control mechanisms in which the signal involves a conformation change within one molecule are referred to as one-component signaling systems.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 397?

“In addition to adding or removing a phosphate from a residue on a protein [apparently having bacteria in mind], signaling sometimes involves the synthesis (and subsequent degradation) of a small molecule that can then diffuse through the cell, potentially carrying a signal to multiple recipients. These small molecules are often referred to as second messengers, a designation that was adopted to distinguish them from intercellular signaling molecules such as hormones and neurotransmitters employed in multicellular organisms that had been discovered earlier.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 397?

“In addition to allowing one measurement to act through multiple effectors, the inclusion of intermediates allows one effector to respond to multiple sensors measuring different variables.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 397?

“Another second messenger employed by E. coli both illustrates how such messengers can produce widespread effects and how they can be produced by multiple sensors. Guanosine tetraphosphate (ppGpp) figures in the stringent response. ppGpp is known as an alarmone since, in conditions in which the bacterium is running desperately short of resources to synthesize new constituents, it binds to any RNA polymerase it encounters, inhibiting it and thereby inhibiting synthesis of ribosomal RNA, ribosomal proteins, translation factors, and tRNA. It thereby effectively shuts down protein synthesis. ppGpp is also synthesized by two different sensors: RelA and SpoT. RelA is released from the ribosome when unbound tRNAs accumulate because they fail to find amino acids to which to bind. Once free, it functions first as a guanylate kinase that removes a pyrophosphate from ATP and adds it to GTP, yielding the pentaphosphate ppGppp, and then as a hydrolase to dephosphorylate ppGppp to ppGpp. SpoT functions similarly as a sensor detecting a shortage of multiple amino acids, lipids, phosphates, or iron to initiate the formation of ppGpp. Either sensor can thus initiate the shutdown of protein synthesis.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 397?

“A further level of complexity arises when the same signaling components are employed by multiple control mechanisms. This results in what is known as crosstalk.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 398?

“As the term is used in engineering, crosstalk is usually regarded as undesirable since it undermines the ability to segregate different activities. That can be a problem in biology as well, but in many cases it can also be advantageous–it can enable the organism to integrate its responses to the particular combination of conditions it confronts. Segregation and integration are both important features of control processes. But they also compete–the more crosstalk there is in a system, the easier it is to integrate multiple responses, but the harder it is to segregate responses so that those not appropriate in a given circumstance do not occur.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 398?

“In recent years, however, researchers have discovered a variety of ways in which the bacterial cytoplasm can be differentiated into different environments in which operations, including control operations, can be segregated. We note three.

“First, intracellular membranes and vesicles, which are thought to be derived from invagination of the plasma membrane, occur frequently in bacteria, including E. coli. Proteins, including those figuring in control, are often positioned structurally vis a vis one another in membranes. This enables them to selectively bind to those bound to the same membrane but not with those not so bound.

“The second mode of segregation is an extension of this–often a protein serves as a scaffold to which other selected proteins can bind, creating a local environment in which only specific proteins interact. One context is in cell division, which in E. coli begins with the formation of a Z-ring around the middle of the cell. The primary constituent of the ring is FtsZ; FtsZ molecules polymerize end to end to form the ring around the circumference of the cell. The FtsZ ring provides a scaffold to which specific other proteins attach. Some of these contribute to the construction of a cell wall between daughter cells, but others serve to regulate these activities. As a result of the arrangement in which they bind to FtsZ, some actions are facilitated, and other possible interactions are prevented from occurring.

“Third, researchers have recently found evidence of condensates resulting from the separation of phases within liquids (liquid-liquid phase separation). The phase separation is brought about through weak protein-nucleic acid and protein-protein interactions involving intrinsically disorganized regions of the proteins. The condensates are known as membraneless organelles. Since they do not have a membrane barrier, molecules can diffuse in and out of the condensates, but they typically do so slowly, creating differentiated environments that favor specific molecular interactions.” Bich, Leonardo & William Bechtel. 2022. “Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.” Adaptive Behavior. 30:(5):389-407. 10.1177/10597123221074429. p. 401?

“The scientific goal of systems biology is not merely to create precision models of cells and organs, but also to discover fundamental and structural principles behind biological systems that define the possible design space of life.” Kitano. Hiroaki. 2007. “Towards a theory of biological robustness.” Molecular systems biology. 3(137):1-7. 10.1038/msb4100179. p. 1.

“‘…robustness is a property that allows a system to maintain its functions against internal and external perturbations’…. To discuss robustness, one must identify system, function, and perturbations.

“It [is] important to realize that robustness is concerned with maintaining functions of a system rather than system states, which distinguishes robustness from stability or homeostasis.” Kitano. Hiroaki. 2007. “Towards a theory of biological robustness.” Molecular systems biology. 3(137):1-7. 10.1038/msb4100179. p. 1; subquote: Kitano, H. 2004. “Biological robustness.” Nat Rev Genet. 5:826-837.

“Whereas homeostasis and stability are somewhat related concepts, robustness is a more general concept according to which a system is robust as long as it maintains functionality, even if it transits through a new steady state or if instability actually helps the system to cope with perturbations.” Kitano. Hiroaki. 2007. “Towards a theory of biological robustness.” Molecular systems biology. 3(137):1-7. 10.1038/msb4100179. p. 1.

“Some species gain robustness by increasing instability in a part of its system. The HIV-1 virus is robust against numerous therapeutic interventions due to a high mutation domain, which is one of the general mechanisms for viral survivability.” Kitano. Hiroaki. 2007. “Towards a theory of biological robustness.” Molecular systems biology. 3(137):1-7. 10.1038/msb4100179. p. 2.

“Does a trade-off between robustness and fragility indicate some kind of conservation principle as claimed b Csete and Doule? Highly optimized tolerance (HOT) theory demonstrates, taking the example of a forest fire, that a system that is optimized for a specific perturbation inevitably entails extreme fragility for unexpected perturbations. Commercial jet airliners with fly-by-wire control are highly robust against most component failures and atmospheric perturbations, but become extremely fragile against highly improbably events such as total power failure as they depend entirely on electric control….

“In addition, biological trade-offs may actually not only involve robustness and fragility, but also resource demands and performance of the system. For example, having an entire backup copy of the system enhances robustness against component failure due to redundancy, but it doubles the resources required and may therefore degrade the performance of the system.” Kitano. Hiroaki. 2007. “Towards a theory of biological robustness.” Molecular systems biology. 3(137):1-7. 10.1038/msb4100179. p. 2; reference: Csete M.E. & J.C. Doyle. 2002. “Reverse engineering of biological complexity.” Science. 295:1664-1669.

“But the very search for motifs [chemical motifs a la Alon] also provides a novel heuristic strategy for detecting regulatory units–the computational screening of vast networks–thus extending mechanistic research.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1756.

“One limitation of this kind of network analysis [Alon’s motifs] is that it represents regulatory interactions as pairwise relations between discrete and static objects (nodes in the network) and assumes that these are uniformly distributed throughout the cell.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1756 (note 2).

“Most mathematical analyses of graphs in the mid-20th century focused on either randomly connected networks, which are characterized by a short MSPL [mean shortest path length] and a low average clustering coefficient [degree to which a given node’s neighbors are connected among each other], or lattice structures, which have a long MSPL and high average clustering. Watts and Strogatz attracted much attention when they theoretically introduced the class of small-world networks that exhibit both short MSPL and high average clustering.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1757.

“… it turns out that, as a matter of statistical probability, nearly every network with a large enough number of nodes and connections will be a small-world network…. Historically, graph theorists assumed that the degree of distribution p(k) would be normal (e.g., Gaussian), but Barabasi and Albert found that in many real world networks, node degree is distributed according to a power law of the form p(k)=ck-a (where the parameter a is often between 2 and 3). This exponentially decliing distribution means that there is great variation in the number of connections for individual nodes. Most nodes have a very low degree (e.g., only 1 or 2 edges to other nodes) but a small number of nodes–called hubs–have many connections. Since the tail of a power-law distribution extends over many orders of magnitude and the node degree across the system cannot be characterized using a unique scale, these networks have been called scale-free networks.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1757?; reference: Barabasi, A.-L & R. Albert. 1999. “Emergence of scaling in random networks.” Science. 286:509-512.

“The characterization of hierarchical modular networks was introduced… to resolve a tension they [Ravasz et al.] had identified between two network measures that were concomitantly exhibited by a wide class of biological networks…. … they both (1) have high average clustering–standardly associated with the presence of fairly isolated modules–and (2) are scale-free, having some hub nodes with many connections across the network….

“The combination of modules and nodes with high degree seems contradictory–modules are relatively isolated, whereas nodes with high degree interconnect the whole system. Ravasz and colleagues proposed to resolve this tension by constructing a model of a network that would exhibit both properties. They began with a module of four completely interconnected nodes …. They then created three replicas, connecting the peripheral nodes of each replica to the central node of the original module. This procedure was then iterated. The network that resulted after several iterations exhibits high average clustering, due to it being built by replicating highly-clustered units, and is scale-free, as a consequence of connecting the peripheral units in a replica only to a common unit in the original….

“This creates a hierarchy in which the nodes generated at each replication step are connected not only to their own central node but also the central node of the entire structure. Ravasz et al. refer to this network structure as a hierarchical modular network and propose that networks organized in this way might account for the combination of high clustering and scale-freeness in the metabolic networks of the 43 species they examined.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1759?; reference: Ravasz, E., A.L. Somera, D.A. Mongru, Z.N. Oltvai & A.L. Barabasi. 2002. “Hierarchical organization of modularity in metabolic networks.” Science. 297:1551-1555.

“They [Ravasz et al on hierarchical modular networks from previous quote] propose a new way of thinking about biological mechanisms, according to which they can both be specialized and closely integrated into a larger network–where the latter goes beyond the assumption of traditional mechanistic research that systems can be treated as decomposable.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1761?

“Most graph-theoretic studies of biological networks offer a static view of the systems under investigation–edges between nodes represent activity that occurs at some time, but the timing of activities at nodes is not differentiated.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1761?

“Protein-protein interactions (PPIs) occur when two or more proteins are shown to be able to bind, which is taken to indicate that they might interact in living cells.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1762?

“The importance of context and reversible dynamics of cejl states is further supported by experimental interventions showing that normal cells can turn cancerous when placed next to neoplastic tissues and that cancer cells can be normalized if transplanted from tumors to a location next to normal stroma.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1768?

“This approach [Dynamical Systems Theory (DST)] represents the dynamic state of a system in a state space in which each point represents a possible state of the whole system (e.g., expression rates of genes or concentrations of various proteins). Activity of the system is represented as a trajectory through state space. By mapping the trajectories that biological systems do or can follow, investigators can identify attractors to which the system will evolve and where it will remain unless perturbed.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1768?

“Proponents [that cancer should be described in terms of attractor states] argue that viewing cancer in terms of dynamic attractor states may resolve some of the problems facing the traditional view that cancer is caused by somatic mutations or specific molecular pathway-interfering causes. The view of cancers as attractors aligns with the ‘cancer stem cell hypothesis’ that highlights similarities between carcinogenesis and developmental processes, such as clonal expansion, fast proliferation, sustained angiogenesis, and tissue invasion. To make sense of how cells with the same genome can differentiate into qualitatively distinct cell types, some researchers investigate the conditions that enable both transformations and stable dynamic states of gene regulatory networks. An important question in this context is why living systems often display stable discrete (or discontinuous) phenotypes, rather than continuous ones that would follow if genetic changes directly caused phenotypic changes.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1769?

“Thinking in terms of cancer attractors leads to a shift of focus from how mutations interfere with specific activities in cells to how they reshape the landscape, alter the possible trajectories, and allow access to new cancer attractors. This representational strategy using landscapes also provides the analytical insight of how the same mutation can be associated with both carcinogenesis and tumor suppression, depending on the current state of the network as a whole.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1771?

“Although the DST approach emphasizes that the existence of robust macroscopic dynamics renders many molecular details explanatorily irrelevant for studies of many general features of living systems, the empirical applicability of the models is dependent on extensive gene expression data to bridge the gap between abstract state representations and empirical observables.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1771?

“Among the different network research approaches we have discussed, the Dynamical Systems Theory framework is the one that most decisively differs from traditional mechanistic strategies. Not only does it call for the experimental investigation of larger networks as opposed to individual pathways (a perspective all network approaches share), but in terms of the conceptual analysis of systems, it questions the utility of the heuristic strategy to approach a system as nearly -decomposable.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1772?

“To a first approximation, we argued that localist analyses directly enhance mechanistic approaches through identification of the ways that mechanisms are organized. Some globalist approaches, on the other hand, either connect indirectly or induce a departure from the previously articulated strategies for mechanism discovery.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1772?

“From a traditional mechanistic perspective, a module or part of a mechanism is defined by its concrete internal structure (which underlies its functioning), whereas module identification within large-scale networks initially does not characterize the specific internal organization of modules (as the representation of a motif would), but instead identifies a module in terms of its relatively low number of connections to other modules of the overall network. This strategy enables the identification of modules without any knowledge about the functions of different system parts or the specific causal nature of their connections.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1773?

“Unlike graph theory, dynamical approaches to networks are explicitly geared at characterizing the temporal character of biological phenomena.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1774?

“Representing biological processes as attractors in state space rather than connections between specific molecular entities in a mechanism diagram reveals significant differences in the conceptual approach. A specific attractor state can be reached by many different mechanistic pathways. Therefore, the proposed therapeutic intervention need not target any specific mechanism but the dynamics of the network as a whole. The predictive potential of these newer approaches is still dependent on grounding the dynamic analysis in details of actual biological systems (such as patterns of gene expression or molecular concentrations in cells). Yet, conceiving of cancer in terms of attractor states has important implications for the view of what cancer is, as it presents a therapeutic alternative to the focus on specific somatic mutations or specific molecular pathway-interfering causes.” Green, Sara, Maria Serban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese. 195:1751-1777. 10.1007/s11229-016-1307-6. p. 1774?

“Many philosophers and scientists are convinced that there can be no strong emergence in chemistry, and that this view is supported by evidence from physics and chemistry. In this paper, I will argue that they are mistaken in believing the second part of that sentence to be true. I am not going to argue against reductionism: my aim is the weaker epistemic one of convincing the reader that the scientific evidence for the existence of strong emergence in chemistry is at least as good as the evidence for reductionist positions that rule it out. I want the reductionists to stop thinking not only that their position is forced on us by the evidence, but also that it is in any way more plausible or better supported by the evidence than the strong emergentist’s.” Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 147.

“Now the possession of novel causal powers does not require the violation of more fundamental laws. Strong emergence requires not that these laws be broken, but only that they fail to determine what happens. This will be the case where, for instance, fundamental laws fail to favour one of a number of different possibilities, with the missing determination provided by the strongly emergent property.” Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 147.

“Even if one takes the strongest essentialist reading, according which [sic] to be water is to be H2O, then on the only scientifically plausible reading of what it is to be H2O, reductionism does not follow…. Pure liquid water contains other things apart from H2O molecules: a small but significant proportion of H2O molecules (at room temperature, about 1 in 107) dissociate (or self-ionise) forming H3O+ and OH- ions…. Furthermore, H2O molecules are polar and form hydrogen-bonded chains which are similar in structure to ice. One might regard the ionic dissociation products and chains as impurities, but the presence of these charged species is central to understanding water’s electrical conductivity. Since chemists regard the electrical conductivity they measure as a property of pure water, it seems gratuitous for we philosophers to interpret it instead as a property of an aqueous solution of water’s ionic dissociation products. Looked at this way, liquid water can at best be considered to be composed of some diverse and constantly changing population of species at the molecular scale, including H2O molecules, H3O+ and OH- ions, and various oligomolecular species. Can we defend the claim that water is H2O? Yes, by considering water in all its forms to be the substance brought into being by interactions among H2O molecules….

“In a less exciting sense, wateriness is therefore an emergent property because nothing below a particular size (that of an H2O molecule) can be water on its own account, and some smaller fragments acquire the property by association. But that doesn’t tell us whether being water is a strongly emergent property, i.e., whether or not being water confers additional causal powers…. Steam, liquid water and (the various forms of) ice do have bulk properties, each bearing distinct sets of properties produced by the distinct kinds of interactions between their parts. Wherever there is significant interaction between the H2O molecules, there is scope for that interaction to bring new powers into being. This is particularly obvious if that interaction includes self-ionisation and the formation of oligomers: the excess charge of solvated protons can be transported across a body of liquid water without the transport of any matter to carry it, via what is called the Grotthuss mechanism. This, in fact is why water conducts electricity so well, unlike other, similar hydrides. The power to conduct electricity is not possessed by any sum of (neutral) H2O molecules. The mechanism by which that power is exercised requires some part of the molecular population to be charged. It therefore depends on a feature of a diverse population of molecular species.” Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. pp. 150, 151.

“The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation.” Dirac, P. 1929. “The Quantum Mechanics of Many-Electron Systems.” Proceedings of the Royal Society of London. A123:714-733. p. 714. quoted in: Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 152.

“The problem raised by Dirac is that for any chemical system bigger than a hydrogen atom, the Schroedinger equation, the central equation of this theory of everything, is insoluble analytically. This means that approximations must be introduced: known falsehoods that will affect the calculations in well-understood ways. For molecules, this means the Born-Oppenheimer or ‘small oscillation’ approximation. It is worthwhile separating this into two separate moves. First, nuclear and electronic motions are considered as separate (even though electrons and nuclei are known to interact), yielding an overall wavefunction that is a product of nuclear and electronic wavefunctions. In the second step, the nuclei are then assumed to be at rest, on account of their much higher masses, and therefore slower motion. The problem of calculating the wavefunction for the electrons can now be addressed on its own, and the molecule’s energy calculated from that. In the last twenty years or so this problem has increasingly been addressed through density functional theory (DFT), in which the aim is to calculate the electron density, rather than the molecular orbitals of yore. The electronic energy can be calculated for a few nuclear configurations near the (empirically given) equilibrium configuration, and the fact that it is the equilibrium configuration is thus explained [sic], after a fashion: it is the local minimum in a particular region of the potential-energy surface. The problem is that it is explained in a way that seems to undermine the status of non-relativistic quantum mechanics as a theory of everything for molecules, and therefore for chemistry.” Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 153.

“For good physical reasons, the only force appearing in molecular Schroedinger equations is the electrostatic or Coulomb force: other forces are negligible at the relevant scales. But the Coulomb force has spherical symmetry. How, from this slim basis, do we get the great variety of different symmetry properties (chiral (asymmetrical), cylindrical, hexagonal and many more) exhibited by real molecules? In practice the lower symmetries are introduced as part of the Born-Oppenheimer approximation. Surely ‘approximation’ is a misnomer for a procedure that changes the symmetry properties of the problem, introducing the specific symmetry properties we need to understand the behaviour of each kind of molecule on a case-by-case basis.” Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 154.

“I now turn to the strong emergentist interpretation of this situation, which I offer not because I am committed to it, but to establish the plausibility of an alternative to ontological reductionism, and its strong interpretation of what it is to be a ‘theory of everything.’ The strong emergentist sees the role of quantum mechanics as much closer to that of thermodynamics: its universal laws deepen our understanding of the behaviour of the systems to which we apply it, but it cannot explain everything. Thermodynamics must always be applied in tandem with other information about the system. Likewise, the Schroedinger equation provides an important framework for studying molecules, because it encompasses all the possibilities, but for that very reason it is implausible to see it as fully specifying the dynamical behaviour of every kind of molecule, given only the charges and masses of the constituent particles. It is too abstract on its own, and too far removed from the particular structures we study in chemistry. It allows too many other, un-chemical possibilities, and we have no general account of the different classes of solutions it does allow, or of the relationships between them. So, instead we simply assume that the known structures exist, and explore the energetic landscape around them to provide an understanding of their dynamical behaviour.” Hendry, Robin F. 2017. “Prospects for Strong Emergence in Chemistry.” pp. 146-163. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 154.

“Furthermore, we say that properties are emergent (in the strong sense of the word) if they provide the system with new causal powers, and, then, if the behaviors they produce at the systemic level cannot be predicted from lower-level properties.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 182.

“Emergent properties can be defined as properties that are possessed by a dynamical system as a whole but not by its constituent parts.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 182.

“The concept of self-organization implies the existence of a dynamical interdependence between the molecular interactions at the microscopic level and the emerging global structure at the macroscopic level. In other words, there is an active combination of upward and downward processes. The upward processes show that, under non-equilibrium constraints, molecular interactions tend to spontaneously synchronize their behavior, which initiates a collective, macroscopically ordered state. At the same time, the downward process shows that the newly forming macroscopic state acts upon the microscopic interactions to force further synchronizations.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 182.

“To show the effective causal role played by wholeness and systemic properties in biology, let us consider the following three examples. (1) The first example concerns the many cases of cooperative feedback inhibitions of metabolic pathways, which are now well known, such as the inhibition of asparto-kinase in bacteria by lysine. This type of observation is often explained by supposing that the biosynthetic flux is regulated by this feedback inhibition, and it would be subject to uncontrolled variations if there were no feedback loop. However, as the previously mentioned authors [Cornish-Bowden & Cardenas] pointed out, this explanation goes wrong, because fluxes can be controlled perfectly well without feedback inhibition, either cooperative or not. The need comes not from flux control, but from concentration control: without feedback inhibition in this pathway, the rate at which lysine would be synthetized would still match the rate at which it is used in protein synthesis, but there would be huge and potentially damaging variations in the concentration of lysine and the intermediates in the pathway from aspartate. This sensitivity of metabolite concentrations to perturbations has major implications for the regulatory design of metabolism in living organisms. To understand this, it is necessary to represent biosynthesis pathways in a way that allows for analysis in terms of supply and demand, namely, in a more complete way than the one that is usually provided in textbooks of biochemistry….

“(2) The second example concerns the failure of genome sequencing to provide an effective explanation of how living organisms develop and evolve…. The functional relevance of spatial and temporal genome organization at three interdependent levels must be stressed: the organization of nuclear processes; the organization of chromatin into higher-order domains; and the spatial arrangement of chromosomes and genes within the nuclear space….

“(3) The third example regards the relationship between genotype and phenotype…. … the problem is not so much that genome sequences contain no phenotypic information, but that we do not have reliable methods for undertaking all of the steps involved in deducing a phenotype from them.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. pp. 183-5; reference: Cornish-Bowden, A. & M.L. Cardenas. 2005. “Systems Biology May Work When We Learn to Understand the Parts in Terms of the Whole.” Biochemical Society Transactions. 33:516-519.

“Systems biology is about interactions rather than about constituents…. Interactions often bring about new properties, called emergent properties.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 188.

“In the sense of systems biology, a biological phenomenon or being is a system if emergent properties result from it.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 189.

“… the way in which we taste the saltiness of sodium chloride is not reducible to the properties of sodium and chlorine gas.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 190.

“As boundary conditions are somehow involved in determining initial conditions (the state of the components of the system at the time at which we start analyzing and modeling it), they can therefore be considered as a form of downward causation.” Boi, Luciano. 2017. “The Interlacing of Upward and Downward Causation in Complex Living Systems: On Interactions, Self-Organization, Emergence and Wholeness.” pp. 180-202. In: Paoletti, Michele Paolini & Francesco Orilia (eds). Philosophical and Scientific Perspectives on Downward Causation. Routledge. p. 199.

“Biologists discuss the blood coagulation cascade, the complement cascade, and cell signalling cascades, to name a few. Psychologists study developmental cascades, ecologists examine trophic cascades, and economists cite cascading failures. In physics and chemistry, we find collision cascades, oxidative cascades, cascade showers, and cascade liquefaction.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 6?

“What exactly is a cascade? I am going to suggest that cascades are causal systems that involve (i) an initial trigger, (ii) sequential amplification, and (iii) stable progression from start to finish. A key feature of these processes is that they involve amplifying steps that convert a small signal into a huge, explosive effect.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 6?

“The field [study of blood coagulation] was soon transformed by two similar but independent publications suggesting the ‘cascade’ and ‘waterfall’ models of blood coagulation. Instead of a single enzymatic system these theories postulated a ‘multiple-factor theory’ involving an eight-step sequence of enzyme activations, in which one enzyme activated another, which activated another and so on, in series. This new theory suggested that blood coagulation involved many factors, that these factors that were initiated in succession, and that the final enzyme was amplified relative to the starting material. When these amplified steps were arranged in succession, they could account for the huge explosion of final clotting product, which explained an important and previously mysterious aspect of the clotting process.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 7?; publications: Macfarlane, R.G. 1964. “An Enzyme Cascade in the Blood Clotting Mechanism, and its Function as a Biochemical Amplifier.” Nature. 202: 498-499; Davie, E.W. 2003. “A Brief Historical Review of the Waterfall/Cascade of Blood Coagulation.” Journal of Biological Chemistry. 278:50819-32.

“The three features discussed in this section start to reveal why we are so interested in cascades. We are interested in cascades because they are powerful causal systems. Their power is related to their (a) amplification and (b) stable progression. Cascades produce a huge, expansive outcome and they do so in a way that is difficult to stop…. We have a strong interest in identifying cascades and their triggers because of their explosive effects and nearly unstoppable nature.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 12?

“Mechanisms involve constitutive relations, cascades to not. Cascades are analogized to the snowball effect, mechanisms are analogized to machines, and so on.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 16?

“A first difference between these concepts is that cascades lack the constitutive, part-whole feature of mechanisms. Mechanisms have a hierarchical structure, in which their lower-level parts produce some higher-level outcome of the whole mechanism.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 16?

“Cascades can have causes and effects at the same level, higher-level causes that produce lower-level effects, and lower-level causes that produce higher-level effects….

“[note] Enzymatic cascades are an example of the first type as the cause and effect are both enzymes. An example of higher-level causes producing lower-level effects are energy cascades involved in turbulence, which involve the transfer of energy from ‘large scales of motion to the small scales’. Another example are traumatic experiences that alter gene expression, referred to as ‘downward cascades’. Finally, a cascade example with a lower-level cause that produces a higher-level effect is a hormone cascade, in which a hormone trigger produces some system-level behaviour. Another example is a pharmacological intervention that alters behaviour, sometimes called an ‘upward cascade’.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 17?

“While mechanisms are expected to contain fine-grained and mechanical details, cascades are not…. First, when cascades are explanatory their lower-level mechanistic detail is often unnecessary for the explanation.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 19?

“It should be clear how this structure [cascade causality] relates to the ‘butterfly effect’, positive and negative feedback loops, and systems that involve causal dampening, as opposed to amplification.” Ross, Lauren N. 2022. “Cascade versus Mechanism: The Diversity of Causal Structure in Science.” The British Journal for the Philosophy of Science. 10.1086/723623. p[of 30]. 25?

“Although causation – a relationship between two events, cause and effect, related by a temporal succession–is the traditional and predominant way of approaching chemical reactions, it is insufficient to study every aspect of them. In fact, the causal perspective minimizes or completely neglects much of the conceptual richness of chemical phenomena, based on a complex network of simultaneous relationships. By contrast, the concept of reciprocal action or interaction makes it possible to account for the simultaneous interdependence between several entities. As a consequence, it provides a fertile framework to conceive chemical reactions. The main difficulty that the interactive approach faces is to describe simultaneity by means of language, since its very nature involves succession. As Borges clearly says: ‘What my eyes saw was simultaneous, what I shall write is successive, because language is successive.” Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. pp. 375-6; subquote: Borges, Jorge. “The Alelph.”

“In quantum mechanics the principle of causality refers to the possibilities of the realization of events (properties). In other words, in quantum mechanics it is not individually realized events that are causally related, but only the possibilities of the realization of these events. This is the essence of the quantum-mechanical meaning of causality.” Subquote of: Tarasov, L.V. 1980. Basic Concepts of Quantum Mechanics. (English Translation). Mir Publishers, Moscow. pp. 158-166. From: Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. p. 377.

“Let us consider the transition of an electron in an atom from level E1to level E2 by absorbing a photon of energy ℏω = E2 – E1 We recall that the contradiction in transition was connected with the question whether the absorption of the photon precedes the transition of the electron or vice versa. It is easy to see that this question simply loses its meaning now. In fact, if we have a bound electron with energies E1 and E2 before and after interaction with radiation, respectively, then during the interaction we have one quantum-mechanical system including both the electron and the radiation. This system exists for a definite time (while the interaction with the radiation takes place) and, according to [Heisenberg’s uncertainty relation], cannot have any definite energy. Hence it is meaningless to find out precisely what takes place in such a system. Strictly speaking, during the interaction of the electron with the photon there is no electron and no photon, but a single entity which must be treated as such, without going into details. This example shows that in quantum mechanics a physical process cannot be infinitely detailed in time. That question ‘what follows what”? cannot always be posed in the case of microphenomena.” Subquote of: Tarasov, L.V. 1980. Basic Concepts of Quantum Mechanics. (English Translation). Mir Publishers, Moscow. p. 50. From: Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. p. 377.

“… following Hacking’s terminology, the ultimate goal of chemistry is not to describe but to intervene in nature. Therefore, it seems reasonable to conceptualize the practice of chemistry by means of a theory that conceives causation in terms of intervention. But the perspective needs not be the same when the question is not about the practice of chemistry, but about the chemical world, independently of human intervention. In this case, is causation still the category that better explains how the chemical world works?” Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. p. 378; reference: Hacking, I. 1983. Representing and Intervening: Introductory Topics in the Philosophy of Natural Science. Cambridge UP.

“Different authors have tried to define the concept of interaction or reciprocal action in terms of causation, for example, as a bidirectional causal relation where the causes become effects and vice versa. This approach faces the problem that, since events are causes and effects at the same time, it should be admitted that a single event is previous and posterior in time to another one, which is a logical absurdity.” Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. p. 378.

“According to Torretti, within the framework of Kantian philosophy, there are two temporal relationships that can be established between phenomena: succession and simultaneity. As time itself is not perceivable, these relationships cannot be characterized in temporal terms, but they must be defined by directly linking the phenomena to each other. The relation of succession is established according to the principle of causality, while the relation of simultaneity is established by the principle of interaction or reciprocal action.

“Kant formulates the principle of causality as follows: ‘All alterations occur in accordance with the law of the connection of cause and effect.’ In turn, he expresses the principle of interaction in the following terms: ‘All substances, insofar as they can be perceived in space as simultaneous, are in thoroughgoing interaction.’” Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. p. 379; references: Torretti, R. 2013. Manuel Kant. Ediciones Universidad Diego Portales. Santiago de Chile; Kant, I. 1998. Critique of Pure Reason. In: Guyer, P. & A.W. Wood (eds). Cambridge UP. pp. 304, 316.

“In this work, a model for representing chemical reactions is presented, and is called ‘interaction diagram’. This model tries to block – or, at least, to attenuate–the tendency to understand chemical reactions from the ‘cause-effect’ perspective by representing them in a simultaneous framework.” Zambon, Alfio. 2022. “Chemical reactivity: cause-effect or interaction?” Foundations of Chemistry. 24:375-387. 10.1007/s10698-022-09430-1. p. 386.

“In a nutshell, the genidentity view, which has been explored in the contexts of psychology, physics, and biology, says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Of course, this claim is not sufficient in itself; every precise application of the genidentity view requires a clarification of exactly which continuous states are being followed, and why….

“According to the genidentity view, the identity through time of an entity X is given by a well-identified series of continuous states of affairs.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 97.

“Let us call substantialism the view according to which the identity of a thing X must be understood as the identity of a substance identified beforehand, and continuism the view according to which the identity of a thing X is given by a mere continuity of states. Substantialism is defended by Leibniz, but also by many contemporary philosophers, under different forms. One version of substantialism is essentialism, which states that what makes the identity of X through time is the fact that a core constituent or characteristic of X remains constant through time. In the case of living things, genetic essentialism says that a living thing remains the same through time in virtue of the fact that it possesses the same genome throughout….

“I suggest here that the genidentity view constitutes a particularly interesting and fruitful version of continuism, and that it can shed light on the question of the diachronic identity of living things.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 98.

“Hull’s [David Hull, early philosopher of biology] starting point is that, at least since Aristotle, most philosophers have had a naive view of biological individuality. Philosophers often use fictitious examples and, when they do actually speak of a living thing, they generally mean an animal, even a higher vertebrate in most cases. In contrast, Hull insists on the importance of using biological examples that are both more realistic and more diverse. According to him, such examples are more interesting, more complex, and in the end more challenging than the fictitious examples and thought experiments favoured by metaphysicians. Taking into account the actual diversity of the living world implies, for Hull, a suspicion towards conceptions of biological individuality based on common sense and intuitive perception. Indeed, common sense individuation is too strongly biased by our relative size and perception abilities. For example, in dealing with many plants, colonial animals, fungi, microbes, and so on, common sense individuation is of no help whatsoever. Some cases have been much discussed in the biological and in the philosophical literature, such as dandelions, aspens, social insects, ascidians, siphonophores, and biofilms….

“According to Hulll, organisms and species belong to the same ontological category, as both must be understood as spatio-temporally localized entities. More radically, Hull’s thesis is that any organism or any species is a portion of space and time. Every organism has a starting point and an end, and goes through different but continuous states between these two extremes. Exactly the same is true of every species. For Hull, because living things can undergo massive and unpredictable change, retention of substance and resemblance (the idea that X looks sufficiently like itself) are useless criteria for biological diachronic identity. The only satisfying criterion is continuity of change.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. pp. 99-100; reference: Hull, David. 1978. “A Matter of Individuality.” Philosophy of Science. 45(3):335-360.

“To describe and defend this continuity-based conception of identity, Hull explicitly endorses the notion of ‘genidentity’ in several texts and grounds it in the idea of a continuous internal organization:

“‘Three traditional criteria for individuality in material bodies are retention of substance, retention of structure, and continuous existence through time (genidentity). If organisms are to count as individuals, then the first two criteria are much too restrictive. In point of fact, many organisms totally exchange their substance several times over while they retain their individuality. Others undergo massive metamorphosis as well, changing their structure markedly. If organisms are paradigm individuals, then retention of neither substance nor structure is either necessary or sufficient for continued identity in material bodies. The idea that comes closest to capturing individuality in organisms and possibly individuals as such is genidentity. As its name implies this criterion allows for change just as long as it is sufficiently continuous. The overall organization of any entity can change but it cannot be disrupted too abruptly.’” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 100; subquote: Hull, David. 1992. “Individual.” In: Keller, E.F. & E.A. Lloyd (eds). Keywords in Evolutionary Biology. pp. 181-7. Harvard UP. p. 182.

“‘Symbiosis’ can be understood here in the very broad sense of any close and lasting interaction between two biological entities belonging to two different species. This is in accordance with the traditional definition of Anton de Bary, formulated in 1879. Adopting this broad definition is important here, as the definition can cover cases that range from mutualism (in which the fitness of the two partners is increased by the interaction) to commensalism (a neutral interaction) and to parasitism (in which the fitness of one partner increases while the fitness of the other decreases). Indeed, all these different cases exist among the recently documented examples of symbioses.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. pp. 102-3.

“Importantly, even a transient interaction between two living things can lead to very significant changes in their respective internal organizations; hence there is no direct link between the robustness and durability of a symbiotic interaction and the extent to which it impacts the internal organization of the partners.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 105.

“In conclusion, the double phenomena of merging and splitting happen successively in many instances of symbiotic interactions, probably reflecting complex physiological, ecological, and evolutionary exchanges between the two partners. From all the examples examined here it can be concluded that symbiotic events of merging and splitting are extremely frequent in nature, which makes Hull’s analyses and diagrams even more useful than they might have seemed when the paper was published in 1978. The ubiquity of symbiosis decisively strengthens Hull’s point that genidentity offers the best way to capture the individuality of biological entities through time.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 105.

“The basic idea at the heart of the genidentity view is to follow a biological process through time. But how does one choose adequately which processes to follow? And how does one follow them in practice?….

“I do not think that it is possible to prove the ontological claim that the biological world is ‘really’ made of processes; and, if this is indeed the claim that process philosophers of biology want to make, then they must give an argument for it. However, it is possible to give good arguments in favour of the adoption of an epistemological process view and to show that, from this epistemological point of view, the decision to interpret the living world in terms of processes makes an important difference to scientific work, because it leads to different perspectives and potentially to different experimental programs.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 105.

“More specifically, I suggest that immunity helps to offer a more precise conception of genidentity applied to organisms. In all species (animals, plants, and also prokaryotes), the immune system plays a decisive role in the delineation of the boundaries of the organism because it constitutes a principle of inclusion-exclusion: the immune system is responsible for the rejection or tolerance of any given entity, which means that the immune system determines which entities will be part of the organism and which won’t.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. p. 106.

“Definition: Organism = a functionally integrated whole, made up of heterogeneous constituents that are locally interconnected by strong biochemical interactions, and controlled by systemic immune interactions.

“This definition means that, when entities interact through regular biochemical interactions and are actively tolerated by the continuous action of an immune system, they are part of a higher-level entity, which should be called an ‘organism’…. This definition rests on the recognition of two layers of interactions (biochemical interactions and immune interactions), which can be seen as a way to make more precise process approaches to the living world…. Thus, an organism can be understood as a local concentration of intertwined biochemical processes under the control of higher-level immunological processes.” Pradeu, Thomas. 2018. “Genidentity and Biological Processes.” In: Nicholson, Daniel & John Dupré (Eds). 2018. Everything Flows: Towards a Processual Philosophy of Biology. pp. 96-112. Oxford UP. pp. 107, 107.

“From the Greeks onward there has been a recognition that our intuitions about the metaphysical primacy of individual organisms is at best programmatic and at worse unjustified.” 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. 186.

“Using Wilson and Sober’s notion of individuality (which is based on functional integration and common fate), I offered a few possible scenarios [for defining individuality for the Hawaiian Bobtail squid that uses symbiotic bacteria for bioluminescence]:

“(a) Considering that the squid can survive without the bacteria, do we have 1 squid and a multitude (109) of V. fisheri = 1 billion and 1 individuals?
“(b) Considering that the bioluminescence, because of the quorum sensing, is a collective property of the bacteria, do we have 1 squid + 1 Vibrio superorganism = 2 individuals?
“(c) Considering that the symbiotic community has its own additional survival potential (i.e. its own emergent common fate), should we say that we have 1 squid + 1 billion Vibrio + 1 Vibrio superorganism + an emergent squid colony superorganism = 1 billion and 3 individuals?

“These scenarios highlight that, because functional integration and common fate can be achieved at various levels of organization, one can have overlapping individuals operating at different temporal scales and with different levels of transiency and continuity.” 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. 190.

“… it becomes obvious that individuality is a matter of degree: if functional integration is the principle of individuality, then we must accept that there are degrees of individuality. Functional integration and common fate are never absolute, in part because evolutionary success is never absolute and depends to a large extent on the external environment in which the individual operates…. Looking at the functional integration of the parts of an individual organism, one also recognizes that the degree to which a part is functionally integrated into the whole will vary from one part to another: my heart is more functionally integrated to me as a whole (and to my fate) than my toes are. Functional integration is a question of degree among the parts themselves.” 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 goal of this chapter is to challenge this view [that macromolecules are not processual] and to argue (a) that macromolecules are fundamentally relational entities; and (b) that this relational nature of macromolecules is of a kind that only a process ontology can account for.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 304.

“This ecological model [of Charles Birch and John Cobb] represents an attempt to formulate a universally applicable process view of the world and states that everything, from atoms to populations, is an ecosystem and has to be treated as such. This means, according to Birch and Cobb, that all entities are fundamentally relational in character, which in turn means that only a process ontology can make sense of them.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 304; reference: Birch, Charles & John B. Cobb. 1981. The Liberation of Life: From the Cell to the Community. Cambridge UP.

“The model [of Birch and Cobb above] is based on two key claims: (1) everything–from atoms to organisms to populations–is an ecosystem, as opposed to some sort of machine or mechanism; and (2) an ecosystem model of the world goes hand in hand with a process ontology, since ecosystems are fundamentally relational in nature.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 304.

“Following the work of William Wimsatt and also Herbert Simon, Bechtel and Richardson distinguish between aggregative systems and composite systems, the latter being further subdivided into component and integrated systems.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 312; reference: Bechtel, W. & R.C. Richardson. 2010. Discovering Complexity: Decomposition and Localization as Strategies in Scientific Research. MIT Press.

“The role of the catalyst is to lower the energy required to reach the transition state, in other words, to lower the activation energy of the reaction. By doing so, the catalyst allows the reaction to take place at a higher rate at a given temperature, since more substrate molecules in the mixture will have the required energy to overcome the activation barrier.

“How do enzymes achieve this feat? Explanations of how proteins function are regularly given using what some refer to as the sequence-structure-function (SSF) paradigm. The SSF has been central to protein biology, roughly, for the past hundred years; it postulates that the function of a protein is determined by its three-dimensional structure, which in turn is determined by its unique amino acid composition and sequence.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. pp. 314-5.

“This [the cycling through conformations of the enzyme] provides a crucial reinterpretation of the way power is attributed to an enzyme: the three-dimensional structure, the only element deemed relevant in the SSF paradigm, is no longer enough to bring about function. What matters for the power of the enzyme to catalyse a reaction is rather the constant change in its polypeptide. Importantly, this change only comes about because of the enzyme’s interaction with the surrounding water.

“To Stein, this is the key change, as the two ‘parts’–the enzyme and the surrounding bulk of water–are now treated as a unit. And it is out of this unit that the capacity to catalyse a chemical reaction arises. As he puts it:

“‘In the end, we will not be able to locate the origins of the catalytic power of an enzyme in a certain 3-dimensional arrangement of active site residues nor in a certain fold of the protein; rather, enzymatic catalysis will have to be analyzed as structurally specific substrates bound to an active site of definite chemical potential embedded in a dynamic protein matrix that is in thermal exchange with the aqueous environment of bulk solvent. This holistic description of enzyme catalysis can be solidly grounded in the metaphysical foundation of Strong Chemical Processism.’

“”Stein’s discussion of recent work in enzymology illustrates how the structure of the protein is no longer seen by scientists as the factor that brings about the capacity of an enzyme to catalyse a chemical reaction. It is also no longer the case that the environment is simply treated as the provider of an energy input that then activates the capacity of the enzyme. The interaction between water and enzyme (neither of which is now demoted to the role of mere external environment) is what brings about the capacity to catalyse the reaction…. And what we end up with–once we focus on this question of where the capacity resides and how it comes about–is a picture of integrated rather than component capacities of proteins.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 316; reference (subquote): Stein, R.L. 2004. “Towards a Process Philosophy of Chemistry.” HYLE: International Journal for Philosophy of Chemistry. 10(1):5-22. (p. 15)

“First, it is crucial, I think, to put his [Stein’s; see above] discussion of enzymes into the context of current developments in protein biology more generally, in particular the discovery of intrinsically disordered proteins mentioned earlier [Dunker et al. 2001]. The IDP case convincingly shows that the dynamic nature of the polypeptide has a crucial role to play in the functioning of many more proteins than just enzymes. The prevalence and importance of IDPs for the functioning of the cell undermines the strict link between structure and function that the SSF paradigm postulates, which has important consequences for our understanding of the nature of proteins more generally.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. p. 317; reference: Dunker, A.K., J.D. Lawson, C.J. Brown, R.M. Williams, P. Romero, J.S. Oh et al. 2001. “Intrinsically Disordered Protein.” Journal of Molecular Graphics and Modelling. 19(1):26-59.

“Interestingly, once we dig deeper into the question of how a protein can adopt a particular three-dimensional conformation (or an ensemble of conformations), we are immediately led to talk about forces. … different physical forces are at work when the crucial interactions of a particular conformation of a molecule are formed. One such force that is crucial for the fold of a protein (but also for the double-helix structure of DNA) is the hydrophobic force, a sort of repulsion from water felt by hydrophobic (i.e. apolar) molecules. All structured proteins have a hydrophobic core in which apolar amino acids are ‘buried’, that is, kept away from the protein’s aqueous environment. The formation of this hydrophobic core is an important step in the folding process and is also what to a large extent explains the relative stability of folded proteins….

“The hydrophobic force is interesting for our current discussion because it is not something a single molecule simply possesses, given its intrinsic properties. It is rather a phenomenon that comes about through the interaction of a larger system of (polar and apolar) molecules. It is also not just the mere existence of polar and apolar entities that gives rise to the hydrophobic force. The force only comes about in a context of constant interaction and repulsion; it is a force born out of becoming, and not out of simple being. The structure that the protein adopts is therefore the outcome of a complex process, which takes place within a larger dynamic system. Within this system it is not clearly defined what should be seen as ‘internal’ and what as ‘external’, since the boundaries between the entity of interest and its environment are blurred. The capacity to adopt a particular fold is therefore not something that the protein simply possesses and that is then triggered or activated by some external input from the environment but it is, like the catalytic power Stein discusses, or like the capacities of a termite colony, an integrated capacity that emerges from within an integrated whole.” Guttinger, Stephan. 2018. “A Process Ontology for Macromolecular Biology.” Pp. 303-320. Nicholson, Daniel & John Dupré (Eds). Everything Flows: Towards a Processual Philosophy of Biology. Oxford UP. pp. 317, 318.

“Phylogeny can tell us much about the early evolution of life, but it is not logical to allow the genetics of a highly complex organism with 300-400 genes dictate how chemistry prior to genetics must have proceeded.” Nader, Serge, Lorenzo Sebastianelli & Sheref S. Mansy. 2022. “Protometabolism as out-of-equilibrium chemistry.” Philosophical Transactions A. 380:20200423. 10.1098/rsta.2020.0423. p. 3.

“Surprisingly, less effort has been expended in investigating prebiotic mimics of catabolism…. As with the prebiotic analogues of anabolic reactions, the published prebiotic analogues of catabolic networks frequently feature pyruvate and other α-ketoacids.” Nader, Serge, Lorenzo Sebastianelli & Sheref S. Mansy. 2022. “Protometabolism as out-of-equilibrium chemistry.” Philosophical Transactions A. 380:20200423. 10.1098/rsta.2020.0423. pp. 3-4.

“Instead [of laboratory based anabolic synthesis], metabolism elegantly ties the two branches (i.e. anabolic and catabolic) together through an intermediary process that deposits stores and spends energy to sustain a vast array of endergonic chemistry. That is, life-as-we-know-it plugs into a fuel source with a wire of molecules that consecutively transfers electrons.” Nader, Serge, Lorenzo Sebastianelli & Sheref S. Mansy. 2022. “Protometabolism as out-of-equilibrium chemistry.” Philosophical Transactions A. 380:20200423. 10.1098/rsta.2020.0423. p. 4.

“We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an ‘object’ on which these laws act….

“In AT, objects are not considered as point particles, but are defined by the histories of their formation as an intrinsic property, mapped as an assembly space. The assembly space is defined as the pathway by which a given object can be built from elementary building blocks, using only recursive operations. For the shortest path, the assembly space captures the minimal memory, in terms of the minimal number of operations necessary to construct an observed object based on objects that could have existed in its past. One feature of biological assemblies of objects is multiple realizability wherein biological evolution can produce functionally equivalent classes of objects with modular use of units in many different contexts. For each unit, the minimal assembly is unique and independent of its formation, and therefore accounts for multiple realizability in how it could be constructed.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 321.

“Assembly is a function of two quantities: the number of copies of the observed objects and the objects’ assembly indices (an assembly index is the number of steps on a minimal path producing the object). Assembly captures the amount of memory necessary to produce a selected configuration of historically contingent objects in a manner similar to how entropy quantifies the information (or lack thereof) necessary to specify the configuration of an ensemble of point particles, but assembly differs from entropy because of its explicit dependence on the contingency in construction paths intrinsic to complex objects.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. pp. 321-2.

“An object is finite, is distinguishable, persists over time and is breakable such that the set of constraints to construct it from elementary building blocks is quantifiable.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 322.

“The concept of copy number is of foundational importance in defining a theory that accounts for selection. The more complex a given object, the less likely an identical copy can exist without selection of some information-driven mechanism that generates that object.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 322.

“For any given object i, we can define its assembly space as all recursively assembled pathways that produce it. For each object, the most important feature is the assembly index ai, which corresponds to the shortest number of steps required to generate the object from basic building blocks. This can be quantified as the length of the shortest assembly pathway that can generate the object.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 322.

“A hallmark feature of life is how complex objects are generated by evolution, of which many are functional. For example, a DNA molecule holds genetic information reliably and can be copied easily. By contrast, a random string of letters requires much information to describe it, but is not normally seen as very complex or useful. Thus far, science has not been able to find a measure that quantifies the complexity of functionality to distinguish these two cases. Here we overcome this inherent problem by pointing out another feature of the evolutionary process: the complex and functional objects it generates take many steps to make, and selection allows many identical copies of these objects. Therefore, an evolutionary process can be identified by the production of many identical, or near-identical, multistep objects. The assembly index on its own cannot detect selection, but copy number combined with the assembly index can.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 322.

“Finding more than one identical copy indicates the presence of a non-random process generating the object.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 323.

“We define assembly as the total amount of selection necessary to produce an ensemble of observed objects, quantified using equation (1):

A = ∑i=1N eaini – 1ǀNT

where A is the assembly of the ensemble, ai is the assembly index of object I, ai is its copy number, N is the total number of unique objects, e is Euler’s number and NT is the total number of objects in the ensemble. Normalizing by the number of objects in the ensemble allows assembly to be compared between ensembles with different numbers of objects.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 323.

“Once the pathway for a new object has been discovered, the production of an object (copy number greater than 1) gets easier as the copy number increases because a high copy number implies that an object can be produced readily in a given context. Thus, the hardest innovation is making an object for the first time, which is equivalent to its discovery, followed by making the first copy of that object, but once an object exists in very high abundance it must already be relatively easy to make.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 324.

“The concept of the assembly space allows us to understand how selection and historical contingency impose constraints on what can be made in the future. By aiming to detect ‘selection’, we mean a process similar to selection in Darwinian evolution. We do not, however, model functional differences that selection might act on. Instead, we account only for the specificity of selection–that some objects are more likely to be used to make new things and some are less likely. The only functionality we want to detect or describe is in the memory of the process to generate the object, with examples including a metabolic reaction network or a genome. This allows the three Lewontin conditions for evolution to hold. A key feature of assembly spaces is that they are combinatorial, with objects combined at every step. Combinatorial spaces do not play a prominent role in current physics, because their objects are modelled as point particles and not as combinatorial objects (with limited exceptions). However, combinatorial objects are important in chemistry, biology and technology, in which most objects of interest (if not all) are hierarchical modular structures.” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 324.

“Selection and evolution cannot emerge if new objects are generated on timescales so fast that resources are not available for making more copies of those objects that already exist….”

“Significant separation of the two timescales of discovery of new objects and (re)production of selected objects results in either a combinatorial explosion of objects with low copy numbers or, conversely, high copy numbers of low assembly objects. In both cases, we will not observe trajectories that grow more complex structures.

“The emergence of selection and open-ended evolution in a physical system should occur in the transition regime where there is only a small separation in the timescales between discovering new objects and reproducing ones that are selected….” Sharma, Abhishek, Daniel Czegel, Michael Lachmann, Christopher P. Kempes, Sara I. Walker & Leroy Cronin. 2023. “Assembly theory explains and quantifies selection and evolution.” Nature. 622:321-328. 10.1038/s41586-023-06600-9. p. 326.

“The opportunity for the new field of systems chemistry is to systematically study how emergent function arises in synthetic, simplified mixtures obtained through bottom-up approaches with the ultimate objective of rationalizing emergent properties and integrating them to design novel systems that show life-like characteristics.” Kroiss, Daniela, Gonen Ashkenasy, Adam B. Braunschweig, Tell Tuttle & Rein V. Ulijn. 2019. “Catalyst: Can Systems Chemistry Unravel the Mysteries of the Chemical Origins of Life?” Chem. 5:1917-1923. p. 1917.

“According to Mumford, Galileo’s real crime was: ‘[t]hat of trading the totality of human experience, not merely the accumulated dogmas and doctrines of the Church, for that minute portion which can be observed within a limited time-span and interpreted in terms of mass and motion, while denying importance to the unmediated realities of human experience, from which science itself is only a refined ideological derivative.’ This is how Galileo broke human experience up into the objective and subjective spheres, leaving the latter out of science altogether.” Muursepp, Peeter, Gulzhikhan Nurysheva, Aliya Ramazanova & Zhamilya Amirkulova. 2021. “Chemistry as the basic science.” Foundations of Chemistry. 23:69-83. 10.1007/s10698-020-09357-5. p. 71.

“Let us remember that for Galileo, the method itself prevailed over the experimental part, not to speak about the applications. Finding out general objective relationships became much more important for the early modern scientists than direct application of research findings. Francis Bacon was an exception here but even he did not have very good ideas, how to make an actual use of the first scientific results.” Muursepp, Peeter, Gulzhikhan Nurysheva, Aliya Ramazanova & Zhamilya Amirkulova. 2021. “Chemistry as the basic science.” Foundations of Chemistry. 23:69-83. 10.1007/s10698-020-09357-5. p. 71.

“We do not have any other option rather than to reiterate the five theses of practical realism [from work of Rein Vihalemm] that say the following:

“1. Science does not represent the world ‘as it really is’ from a god’s-eye point of view. Naive realism and metaphysical realism have assumed the god’s-eye point of view, or the possibility of one-to-one representation of reality, as an ideal to be pursued in scientific theories, or even as a true picture in the sciences.
“2. The fact that the world is not accessible independently of scientific theories–or, to be more precise, paradigms (practices)–does not mean that Putnam’s internal realism or ‘radical’ social constructivism is acceptable.
“3. Theoretical activity is only one aspect of science; scientific research is a practical activity and its main form is the scientific experiment that takes place in the real world, being a purposeful and critical theory-guided constructive, as well as manipulative, material interference with nature.
“4. Science as practice is also a social-historical activity which means, amongst other things, that scientific practice includes a normative aspect, too. That means, in turn, that the world, as it is accessible to science, is not free from norms either.
“5. Though neither naive nor metaphysical, it is certainly realism, as it claims that what is ‘given’ in the form of scientific practice is an aspect of the real world. Or, perhaps more precisely, science as practice is a way in which we are engaged with the world.’” Muursepp, Peeter, Gulzhikhan Nurysheva, Aliya Ramazanova & Zhamilya Amirkulova. 2021. “Chemistry as the basic science.” Foundations of Chemistry. 23:69-83. 10.1007/s10698-020-09357-5. pp. 75-6; reference: Lohkivi, E. & R. Vihalemm. 2012. “Guest editorial. Philosophy of science and practical realism.” Stud. Philos. Est. 5(2):1-6.

“Chemistry really has a dual character, seeking laws of nature as well as describing reality in the style of natural history. The example of the periodic law is a perfect illustration to most if not all theses of practical realism.” Muursepp, Peeter, Gulzhikhan Nurysheva, Aliya Ramazanova & Zhamilya Amirkulova. 2021. “Chemistry as the basic science.” Foundations of Chemistry. 23:69-83. 10.1007/s10698-020-09357-5. p. 78.

“This might be a slightly exaggerated comparison but the high valuation of theoretical scientific knowledge may really be a modern counterpart of scholasticism. The deeply rooted influence of Christian culture makes itself felt even in the most objective human activity of today, exact science. The practical realist account of science helps us to get rid or at least suppress this kind of postscholasticism and reorient ourselves to the most valuable any branch of science can offer, practical results.” Muursepp, Peeter, Gulzhikhan Nurysheva, Aliya Ramazanova & Zhamilya Amirkulova. 2021. “Chemistry as the basic science.” Foundations of Chemistry. 23:69-83. 10.1007/s10698-020-09357-5. p. 79.

“As it has been revealed from different angles, chemistry is a special kind of science because of its dual character. This philosophical discovery supports the practice-based approach in the philosophy of science and opens up new developments like analysing philosophically the special position of physics as the only science proper and the role of biology as a possible competitor of chemistry for securing leadership as an interesting case of dual character.” Muursepp, Peeter, Gulzhikhan Nurysheva, Aliya Ramazanova & Zhamilya Amirkulova. 2021. “Chemistry as the basic science.” Foundations of Chemistry. 23:69-83. 10.1007/s10698-020-09357-5. p. 81.

“Construing the status of the chemical bond as an issue of existence is, perhaps, an unfortunate formulation. What exists are entities such as molecules, atoms and electrons, whereas bonding is something they do. The question is How?” Needham, P. 2014. “The source of chemical bonding.” Stud. Hist. Philos. Sci. 45:1-13. Quoted in: Scerri, Eric R. 2023. “A commentary on Weisberg’s critique of the ‘structural conception’ of chemical bonding.” Foundations of Chemistry. 25:253-264. 10.1007/s10698-022-09454-7. p. 263.

“… the existence of the stable H2+ molecule ion refutes the notion that electron pairing is essential for covalent binding. Throughout much of the twentieth century the dominant idea was that covalent bonding is distinguished from ionic bonding by a build-up of electron density between the nuclei. More recent work by Klaus Ruedenberg and co-workers … has shown that this view is incorrect. On this view, the fall in potential energy at the equilibrium internuclear distance is due to the contraction of the wave function around the nuclei, as well as an every-increasing kinetic energy pressure that resists further contraction. Whilst this view entails some build-up of electron density midway between the nuclei, it clearly emphasizes other regions as being as least as significant. These other regions would have to be taken into account in further attempts to find a material element corresponding to the bond. If there is any sense in which the bond can be said to ‘exist’ it is far more complex than anything imagined in classical chemistry or even the earlier quantum mechanical accounts thereof.” Scerri, Eric R. 2023. “A commentary on Weisberg’s critique of the ‘structural conception’ of chemical bonding.” Foundations of Chemistry. 25:253-264. 10.1007/s10698-022-09454-7. p. 263.

“Reversibility in common discourse is thus essentially a question of whether or not the reverse reaction proceeds at an appreciable pace under the given conditions. But this (‘appreciable pace’) is a subjective term. To a femtosecond spectroscopist, a millisecond is too long, whereas to a chemist studying reactions in interstellar space, a million years is, metaphorically, but the blink of an eye. The chemical reaction that is too slow to be of any practical use to a synthetic organic chemist may be the one that created the precursor molecules of life in interstellar space or giant molecular clouds. Thus time scales effectively distinguish chemical substances from chemical reactions, and reversible reactions from irreversible ones.” Sukumar, N. 2020. “Ontological status of time in chemistry.” Foundations of Chemistry. 22:353-361. 10.1007/s10698-020-09370-8. p. 356.

“I argue that whether we choose to reduce a science to physics or to biology ultimately reduces to which kinds of questions we hold to be more fundamental: material or efficient causes, instrumental or functional causes.” Sukumar, N. 2020. “Ontological status of time in chemistry.” Foundations of Chemistry. 22:353-361. 10.1007/s10698-020-09370-8. p. 358.

“Let us now briefly turn to the epistemology of time. If there were no periodic processes in the universe, no days, no years, no ticking clocks, we could not tell the passage of time. If, on the other hand, the universe [were] comprised of only periodic processes, with no death, no ageing, no learning, we could not tell the passage of time either. So time can be perceived only through co-existence of periodic (cyclical) and acyclic processes. Of course, this co-existence of periodicity and aperiodicity is not just true of time: Restrepo et al. have argued that the formal structure of the Periodic Table is the result of two separate organizing principles: similarity and sequential ordering. Elements in the Periodic Table are not just copies of the ones above them in the group. This combination of periodicity and order is at the heart of richness of chemistry.” Sukumar, N. 2020. “Ontological status of time in chemistry.” Foundations of Chemistry. 22:353-361. 10.1007/s10698-020-09370-8. p. 359; reference: Restrepo, G. 2017. “Building classes of similar chemical elements from binary compounds and their stoichiometries.” In: Benevenuto, M.A. & T. Williamson (eds.) pp. 95-110. Elements Old and New: Discoveries, Developments, Challenges, and Environmental Implications, ACS Symp Ser. vol. 1263. American Chemical Society, Washington, DC.

“Such notions of periodicity are employed by Earley to develop the theory of Process Structural Realism: ‘Stability is achieved only when relationships internal to each item demonstrate such closure that states of the system repeatedly re-occur, so that the system persists through time.’ According to Earley, it is this closure that allows a substance to have ontological significance. ‘Stability constitutes a closure of relationships that makes it possible for each chemcial entity to retain its self-identity while undergoing interactions with the rest of the world.’” Sukumar, N. 2020. “Ontological status of time in chemistry.” Foundations of Chemistry. 22:353-361. 10.1007/s10698-020-09370-8. p. 359; subquotes: Earley, J.E. 2008. “Process structural realism, instance ontology and societal order.” In: Riffert, F. & H.J. Sander (eds.) pp. 190-211. Whitehead’s Process Philosophy: System and Adventure in Interdisciplinary Research, Discovering New Pathways. Berlin: Alber.

“But the time and length scales are epistemologically relevant, because if an observer does not have access to the said time or length scales, then (s)he has no way of distinguishing between a chemical substance and a collision that takes place on a time scale too long to be observable. So from an epistemological standpoint, the distinction between a chemical substance and a chemical reaction would depend upon the time scale of this temporal closure. A process with a very long time scale for closure would be described by the observer as a (stable or metastable) chemical substance.” Sukumar, N. 2020. “Ontological status of time in chemistry.” Foundations of Chemistry. 22:353-361. 10.1007/s10698-020-09370-8. p. 359.

“… there are two lines in modern acidity, which we might call ‘electronism’ and ‘protonism.’ The former, introduced by Gilbert Lewis, emphasizes mechanistically the role of the outer electrons, the latter, in the tradition of Arrhenius and Bronsted/Lowry, depicts a substantial entity, the hydrogen ions, as the cause of acidity. Do both approaches speak of the same phenomenon? Obviously not….

“… the protonist is closer to the notion of substance….

“Hacking uses the well-chosen expression ‘bifurcating kinds’ for the departure of the electronists from the protonists around 1923. Intriguingly, both concepts are still in use, and nobody seems really to care about the conceptual difficulties our chemistry students may run into when the established experts use the word ‘acid’ in different meanings, experimental settings and explanatory applications without further ado….

“‘….a basic substance is one which has a lone pair of electrons which may be used to complete the stable group of another atom, and that an acid substance is one which can employ a lone pair from another molecule in completing the stable group of one of it[‘s] atoms.

“The quotidian basis of the protonist approach no longer plays any significant role in this extreme generalization. According to Lewis, the hydrogen cations (H+), for example, are acidic (as any other cation) and the hydrogen anions (H-) basic (as any other anion). In this utterly structuralist way of theoretical description the peculiarities of acidity, if not the contact to substance reality are weakened…. there is a vantage point of the bifurcation, initiated by Lewis in order to advocate modern chemical theory, because to him protonism was a kind of old-fashioned dogma.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. pp. 414-5; reference and second subquote (p. 142): Lewis, G.N. 1923. “Valence and the Structure of Atoms and Molecules.” NY: The Chemical Catalog Company; first subquote: Hacking, Ian. 1983. Representing and Intervening. Cambridge UP. p. 85.

“The talk about electrons is a talk about (chemical) unobservables, as is the talk about atomic numbers in chemistry too.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. p. 415.

“According to the prevailing meaning of observability in physics, electronegativity is not observable, that is there is no ‘direct’ path to measure it. It is a quantified concept, but at the same time not precisely defined…. The capability of atomic entities to attract electrons is a highly abstracted instance. It can be described by a multitude of methods, but direct measurement is not possible. Electronegativity is relational. There is no absolute single value for elements.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. p. 415.

“Scientific pluralism, the view that there is more than one way to success in methodology and theory, is inevitable in chemistry.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. p. 416.

“The different concepts of element, one physical and the other chemical, show that the non-exact-scientific or non-mathematical (non-numeric) description is viable and necessary in chemical laboratory practice, whereas the atomic number-based definition/identification is restricted to theoretical discourses.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. p. 416.

“Acidity in turn seems to be a hybrid example, where a single term is applied to very different concepts–different with respect to their practical import.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. p. 416.

“… it [chemical science] certainly cannot be reduced to physics as a more fundamental science, that is to its basic entities, theories and methods. Chemistry is a very practical science in that it makes its own epistemic entities, and this practice must be accounted for on its own terms. Such account, which is our main conclusion, must entail pluralistic ideas.” Ruthenberg, Klaus & Ave Mets. 2020. “Chemistry is pluralistic.” Foundations of Chemistry. 22:403-419. 10.1007/s10698-020-09378-0. p. 417.

“Rather than a potentialist form of micro-predeterminism, our analysis ultimately supports a relational-construction-based view of protein development and potentialities formation, which requires an indispensable analysis of the dynamical interplay between the micro-level of the parts and the macro-level of the relational structures of their systems.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 363.

“Biochemically speaking, a proper conceptualisation of protein development needs to account for each of its relevant stages, from the formation of the peptide bond between residues to the acquisition of topological and architectural features through the folding process, from the formation of native structure to post-folding modifications, etc. It is within this multi-step developmental process that the characteristic structural features of proteins, such as active sites and interfaces, are formed.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 364.

“Indeed, if reduction is a real unilateral or asymmetric relation between a reducing and reduced term, microstructuralism can only be coherently defined as the view that all properties of a system are fully produced or determined by–thereby being fully explainable or reducible to–the properties and capacities that each part instantiates independently of being a part of that very system. Microstructuralism thus implies the notion that any system is micro-determined by the intrinsic or system-independent properties of its parts. Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 364.

“More generally, it is today well known that protein folding – like many other biological processes – is a regulated process whose robustness depends exactly on the causal role played by a variety of molecular factors like chaperones and quality control systems.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 366. This quote is referencing or possibly quoting: Anfinsen, C.B. 1973. “Principles that govern the folding of protein chains.” Science. 181(4096):223-230.

“And what are the relevant causal factors at play in such constraining process [for protein folding]? The difficulty in interpreting the nature of the thermodynamic hypothesis is that it mixes two kinds of answer to the above questions. The first answer appeals to thermodynamic and energetics considerations: the native structure is the configuration with minimal free energy, which means that it is the most chemically stable configuration. The second answer is the causal hypothesis according to which primary structure determines native structure. We shall call this latter determination hypothesis, a causal hypothesis concerning the causal role of folding factors, which are reduced to those characterisable in terms of primary structure. Thus, Anfinsen’s thermodynamic hypothesis mixes a principle of physico-chemical stability with the primary structure determination claim.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. pp. 366-7.

“The insufficiency of primary structure for determination of native structure is particularly evident in cases of incorporation of ‘additives’ or environmentally available components. Often the polypeptide ‘entrenches’ extrinsic components present in the environment in order to acquire and maintain native structure. These components are often necessary for such acquisition and maintenance. This process of entrenchment during folding and post-folding modifications is a variant of the more general process of ‘developmental entrenchment’, which is basically the phenomenon whereby phenotypes do not ‘emanate’ spontaneously from DNA taken by itself.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 368.

“Another important example concerns the role of chaperones, which play an active causal role by generating correct microenvironments in order for proteins to reach their native structure and avoiding the formation of incorrectly folded states…. In this respect, additive and entrenched extrinsic factors, chaperoness and quality control systems cannot be considered as abnormal elements of the physiological environment in any meaningful sense.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 369.

“Part of the explanation [for “memory” or conservatism in protein structure despite changes in amino acid sequence] is that some residues are more important than others: for example, the residues forming the hydrophobic core of the protein are fundamental for architecture conservation while the active sites residues are fundamental for function conservation. Thus, not all amino acid changes have equal effect on native structure and function, with the majority producing no effect on them and a minority producing major changes, e.g., changes in what Anfinsen called macromolecular geometry and/or functional ones.

“Moreover, multiple realisation of function could be unrelated to folding robustness: there are many cases where neither primary nor native structures determine function. For instance, E. Coli possesses two different proteins performing phosphofructokinase activity, i.e. Pfk1 and Pfk2. These proteins are not evolutionary [sic] related and are very different in terms of primary and native structure.

“This means that function, diachronically speaking, is neither determined by the primary nor by the native structure, being rather relationally constructed by the cell or the organism according to its physiological needs within a particular organismal and environmental context.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. pp. 371-2.

“While multiple realisation refers to the fact that from different primary structures the same native structure and function can be realised (i.e., a many-one relationship), plasticity refers to the fact that the same primary structure can lead to different native structures and functions (i.e., a one-many relationship)…. An interesting case concerns bifunctional proteins, whereby same primary structure develops into the same native structure but the protein, in the same environment, performs two different functions…. Other forms of plasticity, such as so-called moonlighting proteins, have already attracted considerable philosophical attention. These plastic proteins possess same primary structure and (sometimes) same native structure while exhibiting different functional roles in different environments (e.g., intra vs. extra-cellular environments).” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 372.

“Thus, according to potentialist predeterminism, the causal role of molecular, cellular and organismal contexts and environmental conditions is only to select the potentialities that will actually be instantiated by the developing polypeptide. However, the potentialities are given from the outset by the primary structure.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 375.

“In summary, we do not deny the crucial importance of the micro-constituents for the explanation of the development of any system. rather, we criticise the predeterminist potentialism associated to microstructuralism insofar as it is committed to the view that the (structural and functional) nature of a developing polypeptide can be reduced to the set of its micro-constituents independently, first, of the fact that at least some of those micro-constituents are affected by the macrostructure of the relations of their systems and, secondly, of their specific global or macro-structural organisation.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. pp. 377-8.

“Many post-folding modifications generating transformer, plastic and bifunctional proteins produce compositional structural changes to the developing polypeptide that are not in any sense predetermined or ‘contained’ in the primary structure.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 378.

“Ultimately, it is much simpler to hypothesise, as the relational-construction-based potentialism we endorse makes clear, that this prediction failure is due to the fact that the often unpredictable cellular, organismal and, more generally, environmental context is causally relevant in polypeptide development in generating new potentialities on the part of the developing polypeptide.” Santos, Gil, Gabriel Vallejos & Davide Vecchi. 2020. “A relational-constructionist account of protein macrostructure and function.” Foundations of Chemistry. 22:363-382. 10.1007/s10698-020-09373-5. p. 379.

“A powerful partner of supramolecular chemistry, for instance, may be nanotechnology. Nanotechnology actually establishes creation and fabrication of nanoscale and submicron-scale structures that are visibly observed under incredibly high resolution. Combination of the bottom-up approach for assembling functional molecules in supramolecular chemistry with the top-down approach to build organized materials in the nanoscale level leads to a novel scientific concept, nanoarchitectonics, which aims to construct functional systems and materials like molecular devices and molecular sensors.” Komiyama, Makoto, Keitaro Yoshimoto, Masahiko Sisido & Katsuhiko Ariga. 2017. “Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics.” Bulletin of the Chemical Society of Japan. 90:967-1004. 10.1246/bcsj.20170156. p. 968.

“Nanoarchitectonics possesses one distinct difference from nanotechnology. It is a way of thinking about precision. In the methodology of nanotechnology, higher structural precision corresponds to more successful nanotechnology. In contrast, nanoarchitectonics may not put important focus on the structural precision. In the nanoscale world, the dynamic nature of actions and events sometimes tends to result in uncontrollable situations and unpredictable features. Various kinds of disturbances and fluctuations including thermal and statistical fluctuations cannot be ignored in the precisely assembled architectures, which could be further perturbed through mutual interactions between unit components. These features in organization of materials systems from nanoscale units, often destroy simple one-to-one correspondence between input and output. Therefore, nanoarchitectonics may require particular care in dealing with well-defined sequential processes and controls in assembling functional systems. Instead, wise harmonization (well-balanced consideration on all possible factors) of multi-kinds of interactions becomes crucial in nanoarchitectonics. Indeed, such harmonized mechanisms are well accomplished in biological systems because biological systems are ultimately organized with a huge number of components that function even under unavoidable and substantial thermal fluctuations. Therefore combination of molecular assemblies with biological systems including DNAs or living cells will be the utmost strategy for bio-nanoarchitectonics.” Komiyama, Makoto, Keitaro Yoshimoto, Masahiko Sisido & Katsuhiko Ariga. 2017. “Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics.” Bulletin of the Chemical Society of Japan. 90:967-1004. 10.1246/bcsj.20170156. p. 969.

“Broad [early philosopher of emergentism, 1887-1971] also stressed that if mechanistic chemistry were true it should be possible to deduce the chemical behaviour of any element from the number and arrangement of such particles, without needing to observe a sample of the element in question, which is something that is clearly not the case. Against this position, McLaughlin maintains that the coming of quantum mechanics and the quantum mechanical theory of bonding has rendered those emergentist claims untenable….

“Granted that the quantum mechanical theory of bonding that McLaughlin appeals to does provide a more fundamental account of chemical bonding than the classical, or Lewis’s, theory. Nevertheless, it does not permit one to predict in advance the behaviour of elements or the properties that a compound might have once any two or more elements have combined together….

“Why then should we accept McLaughlin’s claim that pioneer quantum chemistry, or even today’s version of the theory of bonding, can so decisively deal a death blow to any notions of emergence and downward causation?” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. p. 21.; references: Broad, C.D. 1925. The mind and its place in nature. London: Kegan Paul,Trench and Trubner; McLaughlin, B. 1992. “The rise and fall of British emergentism.” In: Emergence or reduction? Essays on the prospect of a nonreductive physicalism. Beckerman, A., H. Flohr & J. Kim (eds). pp. 49-93. Berlin: de Gruyter.

“Hendry argues that according to the current state of quantum chemistry, there is at least as much evidence for emergence as there is for ontological reduction of chemistry but actually goes a little further in favouring emergence.” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. p. 22; reference: Hendry, R.F. 2010. “Ontological reduction and molecular structure.” Stud. Hist. Philos. Mod. Phys. 41:183-191. 10.1016/j.shpsb.2010.03.005.

“The first reason that Hendry gives [to distinguish between epistemological or theoretical approaches to reduction in chemistry] concerns the application of a theory like quantum mechanics to actual cases. Whereas the theory is highly abstract, any case in question is rather specific and necessitates the use of approximations of all kinds. It is possible that any failure of reduction can be blamed on this move. This being the case, a reduction would have failed on epistemological or inter-theoretical grounds. One cannot conclude, Hendry argues, that there is a lack of ontological reduction.

“The second reason Hendry gives is that two scientific disciplines such as chemistry and physics typically develop independently as history unfolds, and that there is no guarantee that the two sciences mesh together in such a way that reduction can be demonstrated. If this is the case, then once again any apparent lack of reduction can be attributed to inter-theoretical issues and one cannot rule out the ontological reduction of one level to another one.” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. p. 22; reference: Hendry, R.F. 2010. “Ontological reduction and molecular structure.” Stud. Hist. Philos. Mod. Phys. 41:183-191. 10.1016/j.shpsb.2010.03.005.

“On a more general point, it might be well to take account of Hendry’s earlier warning to the effect that ontological considerations should not be anchored to the present state of our theoretical understanding. Why should we suppose that the failure of present-day quantum mechanics to recover molecular structure is a reflection of the ontological situation rather than just a deficiency that will be removed as the theoretical treatment is improved. By attaching so much importance on the Born-Oppenheimer approximation and its philosophical consequences, if any, Hendry is falling into the very trap that he warns us against falling into.” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. p. 24; reference: Hendry, R.F. 2010. “Ontological reduction and molecular structure.” Stud. Hist. Philos. Mod. Phys. 41:183-191. 10.1016/j.shpsb.2010.03.005.

“In the molecular case, the apparent breaking of symmetry is, I suggest, entirely epistemological/theoretical. There is little doubt that the molecule of HCl should be asymmetrical, given that it is formed from two unlike atoms. The fact that the current quantum mechanical treatment does not capture this structure in an ab initio manner is, I claim, a theoretical rather than an ontological issue.” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. pp. 24-5.

“If all cases of symmetry breaking reveal downward causation this would mean that the phenomenon is rather rampant including the cases of symmetry breaking to yield a predominance of matter over anti-matter, the predominance of laevo amino acids over dextro isomers in the biological world and many other cases.” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. p. 25.

“My own conclusion is that just as McLaughlin has failed to rule out the occurrence of emergence and downward causation, so Hendry has failed to make a case in their favour. I suggest that the best attitude to adopt towards the concepts of emergence and downward causation is one of agnosticism.” Scerri, Eric R. 2012. “Top-down causation regarding the chemistry-physics interface: a sceptical view.” Interface Focus. 2:20-25. 10.1098/rsfs.2011.0061. p. 25; references (see citations above).

“The organization identified by proponents of viewing organisms as autonomous systems is not productive continuity within a mechanism but the organization of components (parts, subsystems or mechanisms) and processes within an organism that is required for the organism to construct, repair, and reproduce itself as a far from equilibrium system. This often requires adaptive behavior in which individual components operate as needed by the whole organism.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 96.

“However, we argue, biological control processes are not organized hierarchically, but heterarchically. Heterarchy is a complex relationship which can be situated between flat distribution and full-fledged hierarchy.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 97.

“The search for mechanisms does not begin with the parts, but with a phenomenon for which the mechanism is responsible, where phenomena are understood … as regularities identified in the course of research. Some examples of biological phenomena include alcoholic fermentation, the generation of action potentials, and the synthesis of proteins. Phenomena are often closely associated with experimental protocols in which researchers can themselves elicit a given phenomenon and characterize it in detail. The characterization of the phenomena directs the search for mechanisms–only those entities that contribute to the production of a phenomenon count as parts of a mechanism. In this sense, mechanism proceeds top-down. Developing a mechanistic explanation, as opposed to just describing the phenomena, requires going down; decomposing it into parts and operations, which are often identified through different research techniques, and then localizing operations in the different parts.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 97.

“The crucial assumption, articulated by Simon, is that natural systems are nearly decomposable into components whose operations can be understood independently of the rest of the mechanism. The modifier nearly signifies that there may be some effects of other components on the operation of a given component but that these can be ignored in developing a first account of the mechanism. These other effects can then be incorporated in a more elaborated account of the mechanism. Simon offers arguments that not only would processes like natural selection result in biological systems being nearly decomposable, but that we would not be able to understand systems that were not decomposable. That near decomposability is an assumption is made clear by holists who reject it and maintain instead that living systems are so highly integrated that one cannot understand their constituents when detached from the whole.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 97.

“Decomposition, however, is only the first step in developing a mechanistic explanation –researchers must also recompose it and resituate it in the context in which it operates. This may involve actually putting the parts back together, but it may also involve doing so conceptually (e.g., developing a diagram showing how the parts relate to one another) or computationally (creating a simulation of the whole mechanism from equations characterizing the activities of the components)…. Research on mechanisms thus proceeds both top-down from the phenomenon to the constitution of the mechanism and bottom-up to reconstruct the phenomenon for which the mechanism is responsible.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 97.

“A feature of mechanisms emphasized by the new mechanists is that the process of decomposition can be iterated. The parts of mechanisms can often be treated as mechanisms in their own right, each responsible for its own phenomenon–the operation/activity it performs in the larger mechanism….

“Just as one can go down levels within a mechanism, one can ascend to higher levels. The phenomenon associated with one mechanism may figure in a larger-scale mechanism in which its output is input to another mechanism that further transforms it…. However, it is important to point out that in ascending from lower to higher levels in which one can identify larger and more comprehensive mechanisms that carry out higher-level activities, one will not arrive at an account of the organism as an autonomous system. At best, one will arrive at a phenomenon exhibited by autonomous organisms, such as procurement of energy as reproduction. Rather, mechanistic accounts top out where they began–with a phenomenon that a researcher has singled out for study.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 98.

“The autonomy framework was built upon pioneering work by Jean Piaget, Robert Rosen, Humberto Maturana & Francisco Varela, among others. Recently it was further developed by Stuart Kauffman, Cliff Hooker and collaborators, and Alvaro Moreno and collaborators. The core feature of the account, also known as the ‘organizational account’, is the identification of topological relations between the operations of components and between processes of transformation within a system. It is important to point out that this account of organization differs from mechanistic accounts in that it emphasizes the relations between activities that contribute to the maintenance on the system, rather than between the component activities that mechanists treat as giving rise to phenomena. Moreover, it treats the organism as a whole as the starting point and the main focus when addressing what is distinctive about living organisms. In doing so, the early work on autonomy did not engage in decomposition as described by the mechanists. In particular, the autonomy tradition privileged approaches that focused on functional relations of the whole organism. When it did reference parts of organisms, it did so functionally in terms of their contribution to the organization of system that they together realize, rather than in terms of material properties. As a consequence, the autonomy tradition has been characterized by a high degree of generality and abstraction from materiality.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 98.

“… there is a core sense in which the autonomy tradition contrasts with that of the new mechanists: mechanist research is invested in unpacking the details of a mechanism whereas the autonomy tradition abstracts from these to focus on the system as a whole.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 98.

“The main objective of the autonomy research tradition is to identify and characterize aspects common to all actual and possible manifestations of life, thereby revealing the features of living systems that distinguish them from other classes of natural and artificial systems. According to the autonomy framework, these features cannot be found in the basic components of living systems but in the ways they are related. The reasons are two: (1) the same components can participate in other kinds of systems and (2) biological systems are characterized by the fact that components are constantly produced, transformed, and degraded while the system as a whole persists. Therefore, rather than delving into the details of how any particular organism maintains itself, the autonomy framework has characterized the required biological organization in general terms. It recognizes the differentiation of functional roles among the parts of a system and emphasizes how they must be integrated and coordinated if they are to contribute to the production and maintenance of the system that harbors and synthesizes them. The autonomy tradition thus emphasizes a generative framework in which there is a mutual dependence between components of the organism, such that the very existence of each component depends on its relationship with the others and with the system as a whole.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. pp. 98-9.

“In Maturana’s words ‘The living organization is a circular organization which secures the production and maintenance of the components that specify it in such a manner that the product of their functioning is the very same organization that produces them’. Note, insofar as this concept of circular organization underlies autonomy–the maintenance, repair, and replication of the organized system itself–it is different from cyclic organization found in mechanisms such as the Krebs cycle.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 99; reference: Maturana, H.R. 1980. “Biology of cognition.” In: Maturana, H.R. & F.J. Varela (eds). Autopoiesis and cognition: The realization of the living. pp. 1-58. Dordrecht: Reidel. p. 48.

“Constraints, as understood in the autonomy tradition, are components that figure causally in the generation of processes: a component C acts as a constraint on process P iff: (1) at a time scale characteristic of P, C is locally unaffected by P and (2) exerts a causal effect on P. As a result of this causal influence of C, there is a difference between free P, and P under the influence of C.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 99.

“Since constraints contribute to the maintenance of the biological system, they are viewed by the autonomy tradition as serving biological functions: a function is identified as the contribution a constraint makes to the realization and maintenance of the organization that produces it.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 99.

“The mechanist tradition has been concerned with explaining how components of a mechanism give rise to the phenomena exhibited by the mechanism, but not how the mechanism comes to be or is maintained in the organism or is invoked on a given occasion. Accordingly, most new mechanists have not addressed the autonomy tradition.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 99.

“Neither mechanists nor autonomy theorists deny that there is variability in how even individual living organisms behave over time, hut neither addresses it in their accounts….

“Yes, in living organisms, regular behavior, stability, and continuity might be the exception rather than the rule…. Recognizing this, recent theorists in both traditions have focused on the importance of regulation and control. This common recognition provides the foundation for a constructive bridge between the two traditions, a bridge that on one end connects to the dynamic autonomy of organisms and on the other end to the mechanisms employed by the organism. We will begin to construct the bridge from the autonomy side by focusing on the critical importance of regulation for achieving autonomy and then link it to mechanism by introducing a special type of mechanism, a control mechanism, that is external to but operates on and alters the behavior of other mechanisms.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 100.

“Regulation entails an architecture of constraints that satisfies three main requirements: (1) Some constraints are higher order in that they modulate the activity of other constraints instead of directly channeling metabolic processes, as first-order constraints do; (2) These constraints must be sensitive to variation and capable of performing different activities; (3) These constraints must contribute to the maintenance of the system (i.e., they are functional).” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 100.

“Whereas the autonomy tradition arrives at the need for regulation in organisms from the perspective of the need to shift between different possible regimes in order to achieve self-maintenance, the mechanist tradition starts from individual mechanisms and the observation they are subject to control by other mechanisms that are external to them and operate on them.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 100.

“Following Pattee and Hooker, they borrow the conception of constraints from classical mechanics in which constraints impose limits on what are otherwise degrees of freedom through which the states of a physical system can change in time…. While limiting, constraints are also enabling–by limiting how the components of the system can change, constraints enable the system itself to change in ways that it would not otherwise. A pipe, for example, constraints the flow of water, but enables it to direct water to locations it would not otherwise reach.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 100; references: Pattee, H.H. 1973. “The physical basis and origin of hierarchical control.” In: Pattee, H.H. (ed). Hierarchy theory: the challenge of complex systems. pp. 71-108. NY: George Brazillier; Hooker, C.A. 2013. “On the import of constraints in complex dynamical systems.” Foundations of Science. 18(4):757-780.

“To understand how one mechanism can be controlled by another, Winning and Bechtel distinguish stable and flexible constraints within the controlled mechanism.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 100; reference: Winning, J. & W. Bechtel. 2018. “Rethinking causality in neural mechanisms: Constraints and control.” Minds and Machines. 28(2):287-310.

“The account of control mechanism bridges the mechanist and autonomy accounts by connecting on one end to the operation of production mechanisms and on the other to the organism as an autonomous system that acts to maintain itself.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 101.

“We characterize heterarchy in terms of three distinctive features. First, as argued before, at any level, there may be more control mechanisms operative than controlled mechanisms. Second, there are, even at the highest level, such as it[=is?] usually ascribed to the nucleus of the cell or the nervous system, multiple controllers operating relatively independently. Third, in many cases, control mechanisms form cycles, in which the output of one mechanism exercises control over a component of the second, while the output of the second in turn exercises control over a specific component of the first. This undercuts a single ordering of levels. In addition, control relations, such as those performed in the mammalian lateral hypothalamus, may link together seemingly independent activities such as digesting food and maintaining alertness. A further complication is that different control processes may act on different timescales. The result may be an imbricated network manifesting complex dynamics.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 103.

“Integrating multiple sources of information does not require centralization. One way different nuclei [areas of a brain] inform each other is through the release of volume transmitters (e.g., serotonin, dopamine). Unlike classical neural transmitters, which are released and reabsorbed at individual synapses, volume transmitters disseminate widely from where they are released. For each volume transmitter there are numerous different receptors that enable different brain regions to respond in different ways to a common signal. Although these volume transmitters enable large-scale coordination across the organism, what they accomplish is integration of activity, not the creation of a central executive.” Bich, Leonardo & William Bechtel. 2022. “Organization needs organization: Understanding integrated control in living organisms.” Studies in History and Philosophy of Science. 93:96-106. 10.1016/j.shpsa.2022.03.005. p. 104.

“However, by challenging the individuality and the separate existence of physical systems, quantum mechanics offers no friendly conceptual framework for a classical notion such as that of chemical atom, conceived as a component of a molecule.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 108.

“From a strongly reductionist, eliminativist view, Bader advocates for replacing the concepts of chemistry by their quantum counterparts. According to him, QTAIM [quantum theory of atoms in molecules developed by Richard Bader] supports ‘the view that chemistry has been reduced to physics and that the existing language of chemistry stated in terms of models based on valence bond and molecular orbital theories and related actions such as electronegativity, resonance, Coulson’s overlap integral, non-bonded and steric interactions as well as ‘Pauli repulsions’, is to be replaced in its entirety by physics’….

“By pointing out the limitations of Bader’s strong reductionism, and the ontological independence of much of chemistry’s own concepts such as electronegativity, aromaticity, etc., an emergentist stance is adopted here according to which the domain of chemical entities at the molecular level emerges from the quantum basal realm.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 108; reference: Bader, Richard F.W. 1990. Atoms in Molecules: A Quantum Theory. Oxford UP.

“But all the quantum state vectors of the system, ground and excited wavefunctions [not measurable], can, in principle be mapped to the measurable ground-state electron density, which is a real three-dimensional scalar function of the ordinary coordinate space [according to Bader’s work in QTAIM to connect quantum mechanics to chemical properties]. Therefore, the ground-state electron density contains, in principle, the same information as that contained in the wavefunction. This is the basis of numerous empirical quantitative structure-to-property relationships, that connect properties obtained from the electron density with all sorts of physicochemcical and biological properties of molecules, even when the direct causal link is not known.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 111.

“On this basis [using the electron density to map probable locations of nuclei of atoms in the electron density mapping], a topological atom is defined as the union of the nucleus and its associated basis, where the basin is the region of space traversed by the set of trajectories of ∇ρ(r) that terminate at the nucleus, the nucleus acting as an attractor in the gradient vector field. Therefore, in this theory atoms do not overlap: The nuclear space is exhaustively partitioned into mononuclear regions and, as a consequence, into atoms….

“The Laplacian of the electronic density, ∇2ρ(r), determines how the electronic density is locally distributed: It is depleted where ∇2ρ(r) > 0 and concentrated where ∇2ρ(r) < 0. The Laplacian ∇2ρ(r) defines the lines along which the density is a maximum with respect to any neighboring line; when one of those lines links a pair of nuclei it is called bond path. This means that bonded atoms are linked by lines of maximum electron density. This way of conceiving the phenomenon of bonding transcends all particular bonding schemes and endows the different kinds of bonding with a common physical origin. In turn, the linked set of bond paths defines a molecular structure.

“This presentation, although very brief, is sufficient to understand the reductionist program underlying QTAIM: Molecules are composed of atoms, and the atom’s properties, even those induced by externally applied fields, are determined by its form in physical space, that is, by its distribution of charge encoded in the electronic density as described by quantum mechanics. In turn, all bonded interactions-all interactions that bind one atom to another thus requiring a force to separate them—have a common physical basis and are universal in character. For these reasons, the theory proposes to extract all chemistry from electronic density.

“The reductionist view regarding molecular structure has been challenged from different perspectives, both in physics and in philosophy.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 112.

“By admitting the possible difficulties of a reductionist reading of QTAIM, we will approach the relation between molecular chemistry and quantum mechanics from an emergentist perspective, in order to elucidate the role played by QTAIM in that relation and to circumvent those potential problems.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 113.

“An important distinction in this field [study of emergence] is that between diachronic and synchronic emergence. Diachronic emergence is a time process through which a novel item arises from a pre-existent domain: a novel (emergent) item comes into existence at a certain time as the result of previous events. By contrast, in the synchronic case the time variable is irrelevant: Emergence refers to the relationship between a certain item and a lower level: a novel (emergent) item arises from an underlying domain. In both cases, novelty is neither reducible nor predictable from the basal domain.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 114.

“In principle, we will admit the possibility of emergence of properties, substantial entities, laws as regularities in nature, events, processes, etc. In order to embrace all these cases, we will use the term ‘item’ to denote whatever belonging [sic] to the realm of reality, without specifying its ontological category.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 114.

“Finally, it is worth stressing the relationship between emergence and reduction. As stated above, emergence is traditionally understood as non-reductive, i.e., emergent items cannot be reduced to the basal level. Nevertheless, more recently, some authors have raised the novelty of claiming the compatibility between reduction and emergence (Butterfield 2011)…. In this paper we will not follow this strategy since we will focus on ontic relationships” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 114; reference: Butterfield, J. 2011. “Less is different: emergence and reduction reconciled.” Found Phys. 41:1065-1135.

“Virtually all emergentists hold a hierarchical view, according to which reality is organized in different ontic levels or strata. Pace those recent claims about the compatibility between reduction and emergence, emergence is traditionally conceived as the symptom of a failure of reduction. Moreover, emergence is an asymmetric relation: if A emerges from B, then B does not emerge from A. This means that emergence does not involve mere correlations, but requires something else: Ontic dependence, that is, the fact that each level depends for its existence on the lower level. In other words, if A emerges from B, then if B didn’t exist, A would not exist either.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 115.

“Another salient feature of emergent items, which can be traced back to the British tradition, is that they have novel causal powers or are causally autonomous, meaning that they are capable of producing genuinely novel effects that are not reducible to the causal powers of the basal level. If one prefers to avoid the talk about causal powers, it might be said that emergents are actively involved in new regularities in their ontic domain. For Kim, the reason for endowing emergent items with causal efficacy in their own right is that this would ensure they are not to be merely epiphenomenal. The level at which such novel causal powers are exerted is matter of debate. Some authors would consider emergent items to be efficacious at their own level, while others have considered such causal efficacy to be exerted downwardly.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 115; reference: Kim, J. 1999. “Making sense of emergence.” Philos. Stud. 95:3-36.

“Downward causation consists in the emergents’ capability of affecting the basal level from which they arise: Not only do emergents have novel causal powers; moreover, such powers are not restricted to the emergent level and affect the basal one. The main problem with downward causation is that it leads to a dilemma: Either causal over-determination, because one event has two distinct and sufficient causes, one in its own level and the other coming from the emergent level, or reduction, because the two causes of the event are identical. For this reason, in the philosophy of physics and the philosophy of chemistry, many authors prefer to leave downward causation aside and to try to make sense of emergentism without appealing to this notion…. In the next sections we will follow this trend, insofar the argumentation will be independent of the notion of downward causation.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 115.

“Let us consider two items I1 and I2, denoted by the terms t1 and t2, respectively, which belong to certain theories. Let us also suppose that I2 emerges from I1. Two cases can be distinguished:

“• Inter-domain emergence The terms t1 and t2 belong to two different theories T1 and T2, respectively. From an ontic point of view, this means that the items I1 and I2 belong to different ontic domains, those referred to by the theories T1 and T2. So, the emergence of I2 from I1 expresses the fact that there is a relation of ontic dependence between the two domains, or at least between some items belonging to them.

“• Intra-domain emergence The terms t1 and t2 belong to the same theory T. From an ontic point of view, this means that the items I1 and I2 belong to the same ontic domain, that referred to by the theory T. In this case, the emergence of I2 from I1 expresses the fact that two levels can be identified within the same domain, in such a way that the level corresponding to I2 depends ontically on the level corresponding to I1.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 116.

“If the task is to elucidate the emergence of chemical items from physical items, the first step is to clearly identify the domains involved in the relationship. The emergent level is constituted by the molecular domain, in which chemical explanations are valid: These explanations describe ‘matter as an assembly of molecules or crystals themselves composed of elemental atoms. The mutual interaction of these elemental atoms (bonding) is ruled by the location of the involved elements in the periodic table which determines their ‘atom in molecules’ properties such as electronegativity, valence, ionic and covalent radii.’ The basal level, in turn, is the quantum domain, described by a theory expressed in Hilbert space, with its particular concept of state and its peculiarities regarding factorizability and statistics….” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 117; subquote: Causa, M., A. Savin & B. Silvi. 2014. “Atoms and bonds in molecules and chemical explanations.” Found. Chem. 16:3-26. p. 4.

“… A supervenes on B just in case two things cannot differ with respect to A-properties without also differing with respect to their B-properties. In other words, a difference in A-properties requires a difference in B-properties. In turn, supervenience holds when there is multiple realizability, that is, when the relation between the lower subvenient level and the higher supervenient level is many-to-one: A single property of the higher level can be realized by many different lower level properties.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 119.

“… in general emergentists conceive supervenience as an ingredient of emergence, or even as the concept that makes the notion of emergence precise. For instance, Putnam conceives supervenience as emergence because, given that it is possible that subvenient properties be different but supervenient properties be the same, it cannot be said that the latter reduce to the former in the sense that they describe the same features from a different perspective. In the same line, McLaughlin defines emergence as supervenience of properties plus supervenient fundamental laws, and Alexander Rueger conceives emergence as supervenience defined in terms of stability or robustness.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. pp. 119-120; references: Putnam, H. 1975. “Philosophy and our mental life.” In: Putnam, H. (ed). Mind, Language, and Reality: Philosophical Papers. pp. 291-303. Cambridge UP; McLaughlin, B. 1997. “Emergence and supervenience.” Intellectica. 2:25-43; Rueger, Alexander. 2000. “Physical emergence, diachronic and synchronic.” Synthese. 124:297-322.

“In summary, the concept of electron density, central to QTAIM, is–hence–defined exclusively in quantum terms, independently of chemical notions. However, when considered from standard quantum mechanics, it turns out to offer a coarse description of the quantum system under study. Therefore, not only the electron density, but also the concepts defined in terms of it, such as topological atom and bond path, can be conceived as denoting emergent items.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 120.

“In other words, chemical atoms and chemical bonds are items that ‘populate’ the ontic domain described by molecular chemistry, whereas topological atoms and bond paths are items that ‘inhabit’ the realm of QTAIM. There are neither topological atoms nor bond paths in the domain of molecular chemistry to the extent that the quantum concept of electron density is not defined in it. Conversely, there are neither chemical atoms nor chemical bonds in the realm of QTAIM since they are essentially classical items.” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 120.

“Since QTAIM is placed in the intermediate position between molecular chemistry and quantum mechanics, two different relationships have been analyzed:

“• In the case of the relation between QTAIM and quantum mechanics, we have pointed out that the concept of electronic density, although defined in quantum mechanical terms, supplies a coarse description of the quantum level.
“• In the case of the relation between QTAIM and molecular chemistry, we have stressed the difference between analogous concepts defined in the chemical and the QTAIM contexts. So, only a non-theoretically supported metaphysical assumption would allow identifying the two kinds of concepts and, with this, reducing chemical items to the quantum items defined in the QTAIM framework.

“In other words, the inter-theoretic link between molecular chemistry and quantum mechanics through QTAIM involves two steps: One from quantum mechanics to QTAIM, defined by the coarse-grained description supplied by the electronic density, the other from QTAIM to molecular chemistry, constituted by the analogical association between the concepts of QTAIM and the chemical concepts at the molecular level.

“Once these two steps are clearly distinguished, it is not difficult to see that they can be understood as the manifestation of emergence in its two forms [intra-domain emergence and inter-domain emergence]….” Matta, Cherif F., Olimpia Lombardi & Jesus Jaimes Arriaga. 2020. “Two step emergence: the quantum theory of atoms in molecules as a bridge between quantum mechanics and molecular chemistry.” Foundations of Chemistry. 22:107-129. 10.1007/s10698-020-09352-w. p. 121.

“If the Anthropocene is constituted as a convergence of scales–the human and the geological–then the image of the sword in the stone would seem to be the best example. The human has ruptured linear temporality. He has stuck his ‘blade’ deep into the tectonic layers of polytemporality.

“Arthur takes the sword out of the stone in order to fight and prove his kinship–his ‘dominance’ over other beings. Perhaps, then, we should put the sword back in the stone, letting it fossilize and become a monumental reminder of this time when we cut ourselves off from the land, the animals, the plants, and our interrelated ways of knowing.” Strand, Sophie. 2022. The Flowering Wand: Rewilding the Sacred Masculine. Rochester, VT: Inner Traditions. p. 7.

“Male chefs exist now in the realm of celebrity, treating food as if it were another country to exploit and master. Men own fashion companies and real estate. They own homes. But what does it mean to embody a home? To become that sacred space that calls in community and conversation and family? How often do we see the masculine as a freshly cleaned kitchen with a bowl of strawberries and whipped cream on the windowsill? A wide expanse of untilled land, gone to seed, humming with native wildflowers and pollinators?” Strand, Sophie. 2022. The Flowering Wand: Rewilding the Sacred Masculine. Rochester, VT: Inner Traditions. p. 34.

“We have no more time for abstraction. And we have no more time for moralizing. Species collapse every day, bringing down other beings they have been mututalistically involved with for millennia. But, conversely, the emergency of our situation does not call for the manic techno-narcissistic death dance of trying to ‘fix’ the world. It calls for slowing down. For sitting next to the pool. And looking into the water.

“If we are lucky, we will see ourselves.

“But not as an isolated subject in the abstracted blank space of phenomenological ontology. Or in the metaverse of digital binaries. We will see that we are in the pool. We are not outside of the life forms that we are damaging and polluting. We are intimately of them. The real narcissism is to believe we can stand apart philosophically, or morally. And yes, let us, like Narcissus, fall in love with this more complex reflection. A reflection that contextualizes our being inside of, and dependent on, many other modes of being.” Strand, Sophie. 2022. The Flowering Wand: Rewilding the Sacred Masculine. Rochester, VT: Inner Traditions. p. 55.

“We could all use more animal instinct. We need to put our horns back on and start thinking less as individuals and more as patchy, contaminated relationships to other peoples, e