Authors & Works cited in this section (citations below):
Alberghina, Lilia et al. 2009.
“Molecular networks and system-level properties.”
Citations collected in 2015 (works listed above): "The maximum body volume of organisms preserved in the fossil record has increased by ~16 orders of magnitude over the last 3.5 billion years. Increase in maximum size occurred episodically, with pronounced jumps of approximately 6 orders of magnitude in the mid-Paleoproterozoic (~1.9 Gya) and during the Ediacaran through Ordovician (600-450 Mya). Thus, ~75% of the overall increase in maximum body size over geological time took place during 2 geologically brief intervals that together comprise <20% of the total duration of life on Earth." Payne, Jonathan, Boyer, Brown, Finnegan, Kowalewski, Krause, Lyons, McClain, McShea, Novack-Gottshall, Smith, Stempien & Wang. 2009. "Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity." PNAS. Vol. 106. No. 1. Pp. 24-7. P. 24.
"In particular, the observed episodes of dramatic increase suggest the origins of key evolutionary innovations, the removal of environmental constraints, pulses of diversification, or more likely, some combination of these. The relative stability in maximum size between these episodes of increase suggests the encountering of new environmental or biological upper bounds." Payne, Jonathan, Boyer, Brown, Finnegan, Kowalewski, Krause, Lyons, McClain, McShea, Novack-Gottshall, Smith, Stempien & Wang. 2009. "Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity." PNAS. Vol. 106. No. 1. Pp. 24-7. P. 25.
"Delays between innovation and size increase suggest that increased organizational complexity alone was not sufficient to drive increase in maximum size. Steranes (organic molecular fossils) likely produced by stem-group eukaryotes have been reported to occur indigenously in rocks that predate the earliest macroscopic eukaryotic fossils by as much as 800 My. However, the time gap between the oldest preserved steranes and the oldest eukaryotic body fossils could reflect the sparse nature of the Archean and early Proterozoic body fossil record or contamination of the Archean rocks by biomarkers from younger organic matter. Delay between the advent of eukaryotic multicellularity and subsequent size increase is more clearly defined. The oldest definitive fossil of a multicellular eukaryote–a red alga ~1,200 Myr old–predates the initial Ediacaran increase in maximum size by ~600 Myr." Payne, Jonathan, Boyer, Brown, Finnegan, Kowalewski, Krause, Lyons, McClain, McShea, Novack-Gottshall, Smith, Stempien & Wang. 2009. "Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity." PNAS. Vol. 106. No. 1. Pp. 24-7. P. 26.
"Although increase in maximum size over time can often be accounted for by simple diffusive models, a single diffusive model does not appear capable of explaining the evolution of life’s overall maximum size. Approximately 3/4 of the 16-orders-of-magnitude increase in maximum size occurred in 2 discrete episodes. The first size jump required the evolution of the eukaryotic cell, and the second required eukaryotic multicellularity. The size increases appear to have occurred when ambient oxygen concentrations reached sufficient concentrations for clades to realize preexisting evolutionary potential, highlighting the long-term dependence of macroevolutionary pattern on both biological potential and environmental opportunity." Payne, Jonathan, Boyer, Brown, Finnegan, Kowalewski, Krause, Lyons, McClain, McShea, Novack-Gottshall, Smith, Stempien & Wang. 2009. "Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity." PNAS. Vol. 106. No. 1. Pp. 24-7. P. 26.
"For our purpose of extracting universal logic, it is desirable to study a system that is as simple as possible. Accordingly, we have proposed an approach called constructive biology, in which we set up experimental and theoretical models that possess a certain basic property of life and try to understand the conditions required to possess such a property. "One of the most important steps in constructive biology is the construction of reproducing cells. However, despite considerable efforts and developments toward the experimental construction of artificial cells that reproduce themselves, there remain several difficulties. We need to bridge the gap between ‘simple catalytic reaction networks’ and reproducing cells." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 242.
"In contrast, the reaction kinetics whose catalysts are synthesized by themselves involve nonlinear terms, because the rate of such catalytic reaction is given by the product of the concentrations of the substrate and the catalyst." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 244.
"The deviation from the equilibrium decreases with log t, whereas several plateaus appear successively through the course of relaxation. We have studied a variety of reaction networks to confirm that these two characteristics are universal. How many and which type of plateaus appear depend on the network and initial conditions; however, the existence of several plateaus itself is universal." "Thus, we have revealed a general mechanism for the emergence of plateaus. The plateaus are not metastable states in the energy landscape; rather, they are a result of kinetic constraints due to a reaction bottleneck, originating in the formation of local-equilibrium clusters and suppression of equilibration by the negative correlation between an excess chemical and its catalyst. The existence of such negative correlation depends both on the initial concentrations of chemicals and on the network structures; however, even in randomly chosen networks, there exist several sets of chemicals that satisfy the negative correlation, as long as the number of species is not small (say larger than five)...." "In biochemical reaction processes, the energy variance is rather large, and therefore the above slow-relaxation is observed even if the temperature is not so low. Hence, the slow speed of relaxation to equilibrium is a rather common feature of catalytic reaction networks." "Of course, for the origin of life, initially at least, some nonequilibrium condition has to be supplied externally. Indeed, it is natural that there exists some nonequilibrium condition in nature, as, for example, is provided by a thermal vent. Then, a nonequilibrium condition supplied exogenously is embedded into the internal dynamics so that the relaxation is hindered and the activity is maintained endogenously. "Furthermore, we may expect mutual reinforcement between the sustainment of nonequilibrium conditions, spatial structure with compartmentalization, and reproduction. By taking advantage of nonequilibrium reaction processes, a structure is organized in network and in space, as was also discussed in the case of a dissipative structure. Then, spatial compartmentalization is possible. With such a compartmentalized structure, reproduction in molecules is possible. Such a reproduction process naturally enhances the spatial inhomogeneity in chemical compositions. This inhomogeneity further suppresses the relaxation to equilibrium. "This hindrance of relaxation to equilibrium is important for the origin of life; in addition, it will be relevant to understanding slow processes in present cells. For example, a plant seed, even though it is almost closed with regard to energetic and maternal [material?] flow, is ‘alive’ over a large time span without falling into an equilibrium state. In dormant states that are ubiquitous in bacteria, intracellular processes almost stop but activity restarts when they are put under an appropriate culture condition." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. Pp. 244-5.
"Major chemical species are synthesized and catalyzed by chemicals with slightly smaller abundances. The latter chemicals are synthesized by chemicals with much less abundance, and so forth. This hierarchy of catalytic reactions continues until it reaches the chemical species with minority in number. This power law is confirmed universally for a variety of cell models. "Furthermore, this power law was also confirmed by measuring the abundances of a large variety of mRNAs, over more than a hundred cell types, using microarray analysis. Hence, the statistical law as a result of the recursive production of a protocell is also valid in present cells." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 247.
"Second, we studied the cell-to-cell fluctuations of chemical compositions [as a result of reproductions]. Because the chemical reaction process is stochastic, the number of each type of molecule differs between cells We then studied the distribution of each molecule number ni, sampled over cells, and found that the number distribution is fitted reasonably well by the log-normal distribution, ..." "In general, when successive catalytic reactions for recursive production exist in a biochemical reaction network, fluctuations are multiplied successively through the catalytic reaction cascade. Then, by taking the logarithms of concentrations, these successive multiplications are transformed into successive additions, and the problem is reduced to the addition of random noise. According to the central limit theorem, the distribution of log ni is expected to approach the Gaussian distribution. Hence, the log-normal distribution of ni is derived. This log-normal distribution is also experimentally confirmed for present-day cells." "Note that the power law in abundances and log-normal distribution are a consequence of the reproduction of a cell." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 247.
"In a reproducing system consisting of mutually catalytic molecules, molecule species that [are?] in a minority play the role of heredity carriers, in the sense that they are preserved well and control the behavior of this protocell relatively strongly." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 248.
"In contrast, through stochastic simulation of the present model, the protocell comes to and remains at a state in which only a few active Y and almost no inactive Y molecules exist. Such cells can continue the growth-division process. Probabilistically, such a state is very rare; however, when the number of molecules is small, it can appear due to fluctuation. Once it appears, it is selected, because such a state can continue to grow. Hence, a rare state with a few active Y molecules and no inactive ones is preserved over many divisions of protocells (i.e., a rare initial condition is selected and frozen). Furthermore, these few active Y molecules are shown to control (relatively strongly) the behavior of the protocell, because a slight change in such molecules strongly influences the replication of other molecules. The minority molecule species now acts as a heredity carrier because of the relatively discrete nature of its population, in comparison with the majority species, which behaves statistically in accordance with the law of large numbers. Hence, the kinetic origin of genetic information is demonstrated. "Note that we assumed compartmentalization , that is, chemicals are encapsulated into a membrane that itself grows and divides as in the model of Sect. 10.1.3. The importance of compartmentalization to remove parasitic (inactive) molecules has been discussed for the last few decades. Here, a minority of some molecules (whose number can go to zero frequently) is also essential for the removal of the parasitic molecules." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 249. "Because even the phenotype of isogenic individuals is distributed, the variance of phenotype distribution of a heterogenic population includes both the contribution from phenotypic fluctuations in isogenic individuals and that due to genetic variation." Kaneko, Kunihiko. 2011. "Approach of Complex-Systems Biology to Reproduction and Evolution." Pp. 241-59. From Meyer-Ortmanns, Hildegard & Stefan Thurner (Eds.) Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 251.
"In our theory, natural selection is not a consequence of replication, but instead natural selection leads to replication." Nowak, Martin & H. Ohtsuki. 2008. "Prevolutionary dynamics and the origin of evolution." PNAS. V. 105. No. 39. Pp. 14924-27. P. 14926.
"All in all, the loss of heat from the early formation of Earth, as well as a reduction in the heat produced by radioactive decay, should have resulted in a cooling of the planet’s interior through time. This, in turn, should have led to slower rates of mantle convection. Therefore, one can make the case that the rate of H2 release has decreased through time in the face of slower convection." Canfield, Donald. 2014. Oxygen: A Four Billion Year History. Princeton University Press. P. 107.
"The geologic record demonstrates that around 2.3 billion years ago the oxygen content of Earth’s atmosphere increased dramatically. Since cyanobacteria likely evolved much earlier, it does not appear that a well-oxygenated atmosphere is a necessary or immediate consequence of the activities of oxygen-producing organisms. Atmospheric chemistry is a slave to the dynamics of the mantle, as the interior and exterior of the planet are connected in a profound way. Indeed, it took half of Earth’s history for the mantle to quiet to [the] point where oxygen could accumulate." Canfield, Donald. 2014. Oxygen: A Four Billion Year History. Princeton University Press. P. 109.
"The GOE [great oxygenation event] itself seems to have ushered in profound changes in the cycling of nutrients and carbon with surprisingly nonlinear results. First, it appears that the mobilization of nutrients, possibly phosphorus, in a newly oxygenated atmosphere accelerated organic matter production in the oceans, producing high rates of organic carbon burial and the largest positive carbon isotope excursion (the Lomagundi isotope excursion) in Earth history. It also produced a likely elevation in atmospheric oxygen levels beyond those produced during the initial stages of the GOE, perhaps even approaching modern values. A huge oxygen sink was generated as this organic carbon was returned, somewhat later, into the weathering environment; this decreased oxygen to very low values, although apparently somewhat higher than those typically present before the GOE. Some 500 million years after the GOE, the carbon cycle settled into a relatively stable pattern generating oxygen levels that did not exceed 40% of PAL [present atmospheric level], and were more likely in the range of 10% to 15% of PAL, or less." Canfield, Donald. 2014. Oxygen: A Four Billion Year History. Princeton University Press. Pp. 155-6. "The low nutrient requirements of land plants, coupled with their resistant organic matter, would have led to increased organic matter burial and enhanced oxygen liberation to the atmosphere. In this view, the evolution of land plants led to a fundamental reorganization of the carbon cycle, producing much higher levels of atmospheric oxygen, with further cascading effects on biological evolution." Canfield, Donald. 2014. Oxygen: A Four Billion Year History. Princeton University Press. Pp. 157-8.
"In the dynamical systems (DS) approach to adaptive behavior and cognition, agents and their environments are viewed as tightly coupled DS. Nervous systems, bodies, and their environments are considered to have complementary roles in producing a rich range of adaptive behaviors. Accordingly, cognitive agents are not closed systems whose activity can be reduced to the mapping of sensory inputs to motor outputs. In natural agents, the nervous system, body, and environment are not three independent components engaged in a synchronic interaction; rather, natural adaptation is the ongoing result of a global, self-organizing process." Monebelli, Alberto, C. Herrera & T. Ziemke. 2008. "On Cognition as Dynamical Coupling: An Analysis of Behavioral Attractor Dynamics." Adaptive Behavior. V. 16(2/3): 182-195. P. 182.
"Furthermore, the traditional roles that system theory attributes to controller and controlled should be re-examined, as the nature of the mutual relationships among cognitive subsystems can only be contingent and circular. Even the cultural division that traditionally determines the boundary between inside and outside of the body, internal and external, should be critically analyzed in the perspective of cognitive modeling. Even if this distinction might seem quite straightforward in our current artificial agents, obviously developed according to our cultural biases, in biological agents such boundaries appear blurred and highly penetrable, for we are intrinsically extended, permeable, symbiotic biological machines." Monebelli, Alberto, C. Herrera & T. Ziemke. 2008. "On Cognition as Dynamical Coupling: An Analysis of Behavioral Attractor Dynamics." Adaptive Behavior. V. 16(2/3): 182-195. Pp. 192-3.
"In a sharp contrast, viruses exploit effectively all possible combinations of DNA and RNA interconversions:..." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 546.
"... the range of viral genome size’s spans three orders of magnitude, which is similar to the range of genome sizes of cellular life forms." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 548.
"Therefore, it is tempting to think of the virus world as the primordial genomic ‘laboratory’, perhaps the direct descendant of a pre-cellular stage of evolution." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 548.
"Over the last decade, studies of the distinct environmental viromes produced a completely unexpected conclusion: viruses are the most abundant biological entities on earth.... These analyses consistently detect a 10-100 excess of virus particles over cells." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 548.
"The genetic diversity of viruses is no less startling than their physical abundance. In each sequenced virome, the great majority of the sequences represent ‘dark matter’, that is, have no detectable homologs in the current databases, and there is no sign of saturation as sequencing progresses...." "... it is almost certain that a majority of the distinct genes in the biosphere reside in viral genomes. Thus, viruses are likely to represent the principal reservoir of genetic diversity on earth." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. Pp. 548-9.
"The key observation on the viral hallmark genes is that they possess only distant homologs in cellular life forms and yet form a network that connects almost the entire virus world. The parsimonious explanation of these findings appears to be that the hallmark genes became isolated from the cellular genomes at the earliest stages of evolution and ever since comprised the framework of the temporally and spatially continuous, expanding virus world." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 549.
"Furthermore, this ‘ancient virus world’ hypothesis implies the primordial origin of diverse viral replication-expression strategies as opposed to the derivation of these strategies from elements of cellular information processing systems. Specifically, positive-strand RNA, retrotranscribing, ssDNA and dsDNA virus-like elements all can be inferred to have evolved within the primordial gene pool...." "The implications of this conclusion for the early evolution of life are far-reaching. Under this scenario, positive-strand RNA viruses are indeed direct descendants of the primordial RNA-protein world whereas the reverse-transcribing elements provide the means for the transition to the DNA world. The pre-cellular stage of evolution can be envisaged as a pool of small, virus-like genetic elements in which all the genomic strategies evolved and the separation between viruses and cellular life forms was precipitated by the gradual accretion of small dsDNA elements into large molecules." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 550. "This model [virocentric model] goes beyond the notion that viruses coexisted with cells at all stages of evolution by suggesting that evolution of life actually started with a virus-like stage, with the advent of modern-type cells being a comparatively late event." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 551.
"Thus, the virus world is not limited to ‘capsid-encoding organisms’ but rather encompasses a panoply of diverse selfish genetic elements some of which do not possess a capsid. In full prudence, it would have been more appropriate to speak of the ‘world of diverse selfish genetic elements’ but for the sake of brevity and for historical reasons as well, we stick with the original ‘virus world’ designation." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 551.
"The history of life is a story of coevolution of selfish genetic elements and their cellular hosts." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 551.
"The arms race certainly does not end with the host antivirus response: viruses have evolved a great variety of counter-defense measures that go far beyond simple evasion of the host defenses through fast mutation. Large viruses encode multiple proteins that counteract immunity mechanisms or prevent programmed cell death." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 552.
"Mathematical modeling of evolution shows that the emergence of genomic parasites is a fundamental property of any evolving replicator system that exceeds a certain threshold of minimal complexity." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 553.
"In a simple, unstructured host-parasite system, the inevitable outcome is stochastic extinction of both viruses and hosts. However, compartmentalization and, perhaps paradoxically, evolution of defense mechanisms stabilize the coevolving system as a whole. Accordingly, cellular life forms evolved elaborate compartmentalization along with multiple defense strategies, embarking on the perennial arms race. Under this scenario, virus-like genomic parasites and the onset of the arms race far antedate the advent of modern-type cells and were key factors in the emergence of the cellular organization of life." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 553.
"... viruses and virus-like selfish elements: "Taken together, these features of the virus world translate into a ‘virocentric’ view of the history of life under which virus-host coevolution is the principal factor (or in the very least, one of the key factors) that defines the course of evolution of both cells and viruses. This coevolution in all likelihood has started within primitive replicator systems and was essential for the major evolutionary transitions such as the emergence of DNA genomes, cellular organization and later the eukaryotic cell." "Under the virocentric concept, the natural classification of life forms would necessarily include the primary divide between cells and selfish elements (viruses and capsideless elements as well), the major classes of viruses [the seven types of genetic replication cycles] being comparable in status with the three domains of cellular life." Koonin, Eugene & V. Dolja. 2013. "A virocentric perspective on the evolution of life." Current Opinion in Virology. 3:546-557. P. 553-4.
"For example, 37% of the ~23,000 human genes have homologs in the Bacteria and Archaea, and another 28% originated in unicellular eukaryotes [also 16% from animals, 13% from vertebrates, and 6% from primates]." McFall-Ngai, Margaret, M. Hadfield, T. Bosch, H. Carey, T. Domazet-Loso, A. Douglas, N. Dubilier, G. Eberl, T. Fukami, S. Gilbert, U. Hentschel, N. King, S. Kjelleberg, A. Knoll, N. Kremer, S. Mazmanian, J. Metcalf, K. Nealson, N. Pierce, J. Rawls, A. Reid, E. Ruby, M. Rumpho, J. Sanders, D. Tautz & J. Wernegreen. 2013. "Animals in a bacterial world, a new imperative for the life sciences." PNAS. V. 110, No. 9. 3229-3236. P. 3231.
"An ecological perspective influences not only our understanding of animal-microbiome interactions but also their greater role in biology. The ecosystem that is an individual animal and its many microbial communities [i.e., the holobiont] does not occur in isolation but is nested within communities of other organisms that, in turn, coexist in and influence successively larger neighborhoods comprising ever more complex assemblages of microbes, fungi, plants, and animals." McFall-Ngai, Margaret, M. Hadfield, T. Bosch, H. Carey, T. Domazet-Loso, A. Douglas, N. Dubilier, G. Eberl, T. Fukami, S. Gilbert, U. Hentschel, N. King, S. Kjelleberg, A. Knoll, N. Kremer, S. Mazmanian, J. Metcalf, K. Nealson, N. Pierce, J. Rawls, A. Reid, E. Ruby, M. Rumpho, J. Sanders, D. Tautz & J. Wernegreen. 2013. "Animals in a bacterial world, a new imperative for the life sciences." PNAS. V. 110, No. 9. 3229-3236. Pp. 3233-4. "Animals are directly or indirectly dependent on bacteria for extracting energy and cycling biomolecules, whereas animals actively contribute to bacterial productivity through bioturbation, nutrient provisioning, and as habitats for colonization and shelter." McFall-Ngai, Margaret, M. Hadfield, T. Bosch, H. Carey, T. Domazet-Loso, A. Douglas, N. Dubilier, G. Eberl, T. Fukami, S. Gilbert, U. Hentschel, N. King, S. Kjelleberg, A. Knoll, N. Kremer, S. Mazmanian, J. Metcalf, K. Nealson, N. Pierce, J. Rawls, A. Reid, E. Ruby, M. Rumpho, J. Sanders, D. Tautz & J. Wernegreen. 2013. "Animals in a bacterial world, a new imperative for the life sciences." PNAS. V. 110, No. 9. 3229-3236. P. 3234.
"These new data [bacterial influences and symbioses with viruses, Archaea, animals, plants and fungi] are demanding a reexamination of the very concepts of what constitutes a genome, a population, an environment, and an organism." McFall-Ngai, Margaret, M. Hadfield, T. Bosch, H. Carey, T. Domazet-Loso, A. Douglas, N. Dubilier, G. Eberl, T. Fukami, S. Gilbert, U. Hentschel, N. King, S. Kjelleberg, A. Knoll, N. Kremer, S. Mazmanian, J. Metcalf, K. Nealson, N. Pierce, J. Rawls, A. Reid, E. Ruby, M. Rumpho, J. Sanders, D. Tautz & J. Wernegreen. 2013. "Animals in a bacterial world, a new imperative for the life sciences." PNAS. V. 110, No. 9. 3229-3236. P. 3234.
"One such difficult domain [in common research for robotics engineering and psychology] is our feeling that there is a steady world and an underlying space around us. In developmental psychology, the issue of ‘the child’s construction of reality’ was raised more than 70 years ago by Piaget; philosophical and mathematical investigations, by authors like Husserl and Poincare, go even farther back in some cases. The question can be stated as follows: How is it that, given our diverse sensors that are moving at any moment, we get to the idea that there is a more or less permanent world around us that contains objects and living beings and that is endowed with spatial and temporal properties? This is a difficult question because it does not seem trivial to extract these properties from our sensors." Sigaud, Olivier, M. Butz, G. Pezzulo & O. Herbort. 2013. "The anticipatory construction of reality as a central concern for psychology and robotics." New Ideas in Psychology. 31: 217-20. P. 218.
"Action representation is also central to Action Simulation Theory (AST).... One of the key ideas in AST is that the representation of an action is not a static content stored in a memory register – as would be the case for the representation of a variable in a computer – but rather a dynamic process involving the re-enactment of the action." Sigaud, Olivier, M. Butz, G. Pezzulo & O. Herbort. 2013. "The anticipatory construction of reality as a central concern for psychology and robotics." New Ideas in Psychology. 31: 217-20. P. 219.
"Anyone who has ventured into the world of complexity knows that it is a wild jungle that is growing much faster than it is being mapped. There is only one way to be linear but there are many ways to be non-linear." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 2.
"Llinas argues that the control of movement is the prime evolutionary driving force in the development and perfection of the brain. To illustrate the case, he tells the story of the seq squirt that moves around in the water and once it finds a spot with favorable conditions where it can plant itself and not move for the rest of its life it eats its brain." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 2. Reference: Llinas, R. 2001. I of the Vortex: From Neurons to Self. MIT Press.
"First, the brain is massively distributed and parallel. In this sense it resembles a high-dimensional network. Network is what one calls a dynamical system when it starts having many degrees of freedom. The brain is nonlinear in at least two different ways: the response of at least some neurons to pre-synaptic potentials is a nonlinear (sigmoid) function and the brain is full of feedback loops, instantiating a recurrent network. A neuron is an analog machine because even the slightest pre-synaptic activity changes the distance of the neuron state from the action potential threshold. Hence, the brain is a real-time continuous-state recurrent network. The spreading of activation takes time. Dynamical systems theory has delay equations for that. Like everything in biology, neurons too are messy; they do not run on ideal trajectories like machined mechanical devices. Whether one should call this stochastic dynamics or chaos is not so clear yet but there are dynamics for both types. To conclude, the brain is a continuous state high-dimensional recurrent nonlinear stochastic and/or chaotic dynamical system, among other things. A Turing machine is neither of these." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 3.
"The technical term that Haken uses for low-dimensional patterns emerging at the level of collective behavior is order parameter. Reduction of dimensionality is an essential marker of self-organization." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 3. Reference: Haken, H. 1988. Information and Self-Organization: A Macroscopic Approach to Complex Systems. Springer.
"Described very cursory, strong anticipation deals with the ability of chaotic dynamical systems to synchronize with other systems, to do so in an anticipatory manner when the coupling has a delay, and to maintain the synchronized trajectory some time after the coupling is removed. In very few words, statistical prediction is replaced with dynamical anticipation." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 5. "A good synthesis of the ecological and synergetic theory is provided by Warren. In his schematic, the dynamics of perception and action consist of a closed loop that couples agent dynamics and environment dynamics. In the one direction the coupling consist of a mapping from body movement to forces acting on the environment. In the other direction, the coupling consists of an optic array specifying the state of environment relative to the agent. All of this makes a dynamic field embedding multiple parts (eyes, musculoskeletal system, nervous tissue, ground, surfaces, light reflected from those surfaces, optic flow, and all the rest). The emergence of an order parameter (a behavioral dynamic pattern), i.e., a certain type of movement of the agent across the environment, means that the parts as a collective have entered a collaborative mode." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 6. Reference: Warren, W. 2006. "The dynamics of perception and action." Psychological Review. 113: 358-389.
"If one can make sense of this reconceptualization of the way the parts of the body serve behavior, one will discover that it leads to a range of unintuitive realizations. First, an agent does not think the behavior, prepare the pattern, and then perform it. Instead, the behavior grabs the agent because the suitable conditions happened to occur. A necessary member of these conditions is that a match exists between abilities of the agent and affordances of the environment, also known as duality of constraint between animal and environment." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 6.
"In this sense, the brain, as the thing that sits between most sense organs and the muscles, has to be enslaved by a higher-order dynamic pattern for motor behavior to occur and be sustained." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 8.
"Accordingly, the main job of the brain, at least in the context of on-line control of movement, tracking danger and prey, etc., is merely to close that circuit of a given dynamical field spanning a configuration of brain, agent, and environment." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 8.
"The claim in the previous section was that an essential aspect of the functionality of the brain is to allow itself to be enslaved by a dynamic field spanning the animal and its surroundings.... To avoid becoming locked in a potentially unfavorable mode of behavior, the brain has to be sensitive simultaneously to multiple threats and opportunities in the environment and switch among them.... In order for the agent to possess behavioral stability the order parameter needs to sit on an attractor. In order to quickly switch, it needs to sit on a repeller, or change attractors frequently. Such a hypothetical regime where the system seems to occupy multiple points in phase-space simultaneously has been labeled metastability." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 8.
"Some 20 years ago, in defining the notion of the organism-environment system, Jarvilehto suggested that a number of problems faced by modern psychology and neuroscience could be due to the very assumption of two separate systems. He pointed out that the two-systems assumption in psychology was largely due to pre-scientific common-sense intuition: our experience with the world seems to suggest a very strong dualism between inside the head and outside the head." Dotov, Dobromir. 2014. "Putting reins on the brain. How the body and environment use it." Frontiers of Human Neuroscience. V. 8. Art. 795. Pp. 1-12. P. 9. Reference: Jarvilehto, Timo. 1998. "The theory of the organism-environment system: I. Description fo the theory." Integr. Physiol. Behav. Sci. 33: 321-34.
"... neuroscientific studies with humans have revealed that active tool-use can change the representation of space, in particular inducing an extension of the near space." Borghi, Anna, C. Scorolli, D. Caligiore, G. Baldassarre & L. Tummolini. 2013. "The embodied mind extended: using words as social tools." Frontiers in Psychology. V. 4. art. 214. Pp. 1-10. P. 3.
"The view we will present is slightly different. We agree that the computational role of inner language, intended as a guide for action, has not been considered enough. However, we intend to stress the role of other aspects of words that, despite the novel burst of interest for social neuroscience, have been neglected: the social and public role words possess." Borghi, Anna, C. Scorolli, D. Caligiore, G. Baldassarre & L. Tummolini. 2013. "The embodied mind extended: using words as social tools." Frontiers in Psychology. V. 4. art. 214. Pp. 1-10. P. 4.
"Words and physical tools share an important feature: both can be used to accomplish goals via external means, respectively, other people and objects, resulting in a change of the current state of the world and in an extension of our capabilities." Borghi, Anna, C. Scorolli, D. Caligiore, G. Baldassarre & L. Tummolini. 2013. "The embodied mind extended: using words as social tools." Frontiers in Psychology. V. 4. art. 214. Pp. 1-10. P. 4.
"When performing activities which require coordination, such as lifting very heavy objects, we need to possess the sophisticated ability to understand others’ action plans, others’ willingness to collaborate, etc. Similarly this ability should be present during language use as well, otherwise words, even if referentially correct, are not effective. In this respect, words constitute a bridge between ourselves, the environment and the others." Borghi, Anna, C. Scorolli, D. Caligiore, G. Baldassarre & L. Tummolini. 2013. "The embodied mind extended: using words as social tools." Frontiers in Psychology. V. 4. art. 214. Pp. 1-10. P. 4.
"Here we propose that words and tools share a further similarity: we consider the possibility that when we use words to reach for something, word use expands the near space, modifying the representation of the relationship between our own body and the objects in space, similarly to what happens afer tool use. The argument behind this hypothesis is the following: if words are similar to tools, then their use should lead to an extension of the bodily space, as it happens with real tools." Borghi, Anna, C. Scorolli, D. Caligiore, G. Baldassarre & L. Tummolini. 2013. "The embodied mind extended: using words as social tools." Frontiers in Psychology. V. 4. art. 214. Pp. 1-10. P. 4.
"EG theorists [embodied-grounded view of mind] demonstrated that comprehending words activates the motor system. EM theorists [extended mind] propose that, as tools extend our body schema, ‘language extends our capacities for thought and therefore can be treated as extending our mind schema.’ In fact, it has been shown that language modifies cognition, for example influencing perception and categorization, in a flexible manner." Borghi, Anna, C. Scorolli, D. Caligiore, G. Baldassarre & L. Tummolini. 2013. "The embodied mind extended: using words as social tools." Frontiers in Psychology. V. 4. art. 214. Pp. 1-10. P. 4. Subquote is from Noe, A. 2009. Out of Our Heads: Why You Are Not Your Brian, and Other Lessons from the Biology of Consciousness. Hill and Wang.
"Third [traditional assumption about language], to most linguists ‘language’ is treated like a semiotic system that permits the ‘language users’ to communicate, i.e. in describing linguistic interaction, they posit a ‘language’ as an ontologically real phenomenon in its own right. Proponents of the third wave [of cognitive science] deny that ‘language’ is a proper ontologically given object; rather, they emphasize its materiality, embodiment, and co-actionality." Steffensen, Sune V. 2012. "Care and conversing in dialogical systems." Language Sciences. 34: 513-31. P. 516.
"Lexicogrammatical structures, i.e. the usual object of linguistics, are not denied in this view; rather they are seen as virtual patterns that constrain the dynamics of languaging persons engaged in interactivity." Steffensen, Sune V. 2012. "Care and conversing in dialogical systems." Language Sciences. 34: 513-31. P. 516.
"‘We speak of structural coupling whenever there is a history of recurrent interactions leading to the structural congruence between two (or more) systems’. "Through structural coupling, two (or more) systems constitute a dynamic whole with a relatively high degree of stability." Steffensen, Sune V. 2012. "Care and conversing in dialogical systems." Language Sciences. 34: 513-31. P. 517. Subquote is from Maturana, H. & F. Varela. 1987. The Tree of Knowledge: The Biological Roots of Human Understanding. New Science Library. P. 87. "The process of structural coupling can be found between all sorts of systems: For instance, the relation between the living system and its environment is a case of structural coupling whose ‘history of recurrent interactions’ consists of the material flow between the two." Steffensen, Sune V. 2012. "Care and conversing in dialogical systems." Language Sciences. 34: 513-31. P. 518.
"Agency thus points to an interactional asymmetry between the organism and the environment, and this asymmetry is partly related to the idea that "Agents have goals or norms according to which they are acting’ which environments do not." Steffensen, Sune V. 2012. "Care and conversing in dialogical systems." Language Sciences. 34: 513-31. P. 518. Subquote is from Barandiaran, X., M. Rohde & E. Di Paolo. 2009. "Defining agency: individuality, normativity, asymmetry and spatio-temporality in action." Adaptive Behavior. 17: 367-86.
"The dialogical system refers to the situated behavioral coordination between individualities, while the social system refers to the subsequent trans-situational coordinated behavior of the participants. A dialogical system is thus defined as a whole where the participants perform social coordination; and a social system is defined as a whole where the participants are socially coordinated." Steffensen, Sune V. 2012. "Care and conversing in dialogical systems." Language Sciences. 34: 513-31. Pp. 519-20.
"What Grasse discovered in the coordination and regulation of termite colonies, is the phenomenon of indirect communication mediated by modifications of the environment – which he termed ‘stigmergy’.... In other words, the environment acts as a kind of distributed memory system." Doyle, Margery. 2013. "Stigmergy 3.0: From ants to economies." Cognitive Systems Research. 21: 1-6. P. 2. Reference: Grasse, P. 1959. "La reconstruction du nid et les coordinations interindividuelles chez Bellicositermes natalensis et Cubitermes sp. La theorie de la stigmergie: Essai d’interpretation du comportement des termites constructeurs." Insectes Sociaux. 6(1): 41-83.
"...‘the human analog of the insects’ pheromone is the expenditure of money in market exchanges.’" Doyle, Margery. 2013. "Stigmergy 3.0: From ants to economies." Cognitive Systems Research. 21: 1-6. P. 3. Quoting Lavoie, D. 1985. National economic planning: What is left? Ballinger. P. 72.
"The diverse theorists [of situated cognition] invoked are bound together by the idea of informational flow between generations and the idea of cooperation conceived as distributed cognition. Stigmergy can also be understood as informing these downstream coordination systems writ large. In short, since mind is intrinsically constrained in its computational capacity to assimilate the infinitely fine-grained and perpetually dynamic characteristic of human experience, sociality functions as a kind of distributed ‘extraneural’ memory store manifest as dynamic orders. Furthermore, mind and the broad manifold of sociality are in effect co-evolved spontaneous orders." Doyle, Margery. 2013. "Stigmergy 3.0: From ants to economies." Cognitive Systems Research. 21: 1-6. P. 4.
"Even the simplest known cells are exquisitely organized agglomerates of intricate macromolecular complexes. The two classes of such complexes that define the cellular state and clearly separate cells from virus-like entities are (1) membrane embedded energy transformation and molecular transport systems and (ii) translation system that makes all the proteins required for the cell function. A fundamental and striking feature of cells is that formation of a cell de novo has never been observed." Koonin, Eugene. 2014. "The origins of cellular life." Antonie van Leeuwenhoek. 106: 27-41. Pp. 27-8.
"The emergence of the cellular organization is the central problem in the study of the evolution of life, so much so that all the subsequent evolution, even such major transitions as the emergence of eukaryotes, can be viewed as ‘mere history.’" Koonin, Eugene. 2014. "The origins of cellular life." Antonie van Leeuwenhoek. 106: 27-41. Pp. 36-7.
"Work this decade has shown that 1/f scaling (a.k.a., 1/f noise or pink noise or long memory) is ubiquitous in smooth cognitive activity. 1/f scaling is temporal long-range dependencies in the fluctuations of a repeatedly measured behavior or activity. Analogous to spatial fractals, 1/f scaling denotes a fractal or self-similar structure in the fluctuations that occur over time (within a time-series of measurements). This is, higher frequency, lower amplitude fluctuations are nested within lower frequency, higher amplitude fluctuations as one moves from finer to courser grains of analysis. 1/f scaling indicates that the connections among the cognitive system’s components are highly nonlinear." Anderson, Michael, M. Richardson & A. Chemero. 2012. "Eroding the Boundaries of Cognition: Implications of Embodiment." Topics in Cognitive Science. 4: 717-30. P. 719.
"They [see Reference] found that learning a new strategy for solving a problem coincides with the appearance of 1/f scaling, as measured in eye movements. This indicates that even leaps of insight do not occur in the brain alone–the eye movements are part of the cognition." Anderson, Michael, M. Richardson & A. Chemero. 2012. "Eroding the Boundaries of Cognition: Implications of Embodiment." Topics in Cognitive Science. 4: 717-30. P. 722. Reference [‘They’]: Stephen, D., J. Dixon & R. Isenhower. 2009. "Dynamics of representational change: Entropy, action, cognition." Journal of Experimental Psychology: Human Perception & Performance. 35: 1811-22.
"For example, Dotov, Nie, and Chemero ... describe experiments designed to induce and then temporarily disrupt an extended cognitive system. Participants in these experiments play a simple video game, controlling an object on a monitor using a mouse. At some point during the 1-minute trial, the connection between the mouse and the object it controls is disrupted temporarily before returning to normal. Dotov et al. found 1/f scaling at the hand-mouse interface while the mouse was operating normally, but not during the disruption. As discussed above, this indicates that, during normal operation, the computer mouse is part of the smoothly functioning interaction-dominant system engaged in the task; during the mouse perturbation, however, the 1/f scaling at the hand-mouse interface disappears temporarily, indicating that the mouse is no longer part of the extended interaction-dominant system. These experiments were designed to detect, and did in fact detect, the presence of an extended cognitive system, a synergy that included both biological and non-biological parts. The fact that such a mundane experimental setup (using a computer mouse to control an object on a monitor) generated an extended cognitive system suggests that extended cognitive systems are quite common." Anderson, Michael, M. Richardson & A. Chemero. 2012. "Eroding the Boundaries of Cognition: Implications of Embodiment." Topics in Cognitive Science. 4: 717-30. Pp. 722-3. Reference: Dotov, D, L. Nie & A. Chemero. 2010. "A demonstration of the transition from readiness-to-hand to unreadiness-to-hand." PLoS ONE. 5. e9433.
"For instance, Chang et al. investigated the perception of aperture passability for an interpersonal perception-action system, which comprised an adult perceiver with a child as a companion. The results demonstrated that the adult-child dyads perceived the minimum aperture width that they could pass through on the basis of the body-scaled information defined by the adult-child dyad together (i.e., not by the adult or child alone). Knowing when to pass through the aperture or not was a functional relation of the agent-agent system as a whole. Isenhower et al. obtained complementary findings for pairs of participants performing a plank-lifting task. Participants were required to lift and move wooden planks of various sizes from one side of a room to another. The participants in a pair were free to choose whether to move the planks alone or together, although approximately 2/5 of the planks were sufficiently large that they required that pairs lift the planks together. By presenting the planks in ascending and descending size, the authors found that pairs transitioned between solo and joint action abruptly (bifurcated), at a ratio of the pairs’ collective action capabilities relative to plank size. Accordingly, the implicit commitment to act as a ‘plural subject’ of action, that is, the ‘decision’ to choose to cooperate (or not) was something that occurred as a dynamic response to a meaningful relation defined across an agent-agent system. As with rhythmic interpersonal synchrony, the coordinated behavior resulted from the functional relations inherent to the social system as a whole; the coordination arose and dissolved spontaneously, dependent on the system parameters and functional task constraints." Anderson, Michael, M. Richardson & A. Chemero. 2012. "Eroding the Boundaries of Cognition: Implications of Embodiment." Topics in Cognitive Science. 4: 717-30. P. 725. References: Chang, C., M. Wade & T. Stoffregen. 2009. "Perceiving affordances for aperture passage in an environment-person-person system." Journal of Motor Behavior. 41: 495-500. Isenhower, Robert, M. Richardson, C. Carello, R. Baron & K. Marsh. 2010. "Affording cooperation: Embodied constraints, dynamics, and action-scaled invariance in joint lifting." Psychonomic Bulletin & Review. 17: 342-7.
"In contrast, several of the more progressive elements to emerge within evolutionary biology in the last decade or so emphasize, in different ways, how developmental processes, traditionally disregarded as solely relevant to proximate questions, are in fact highly germane to evolutionary issues. These include the ‘developmental bias’ arguments emerging from evo-devo, the ‘genes are followers, not leaders, in evolution’ argument emerging from the study of developmental plasticity, related arguments deriving from the theory of ‘facilitated variation’, and niche construction theory. The arguments from developmental bias, developmental plasticity and facilitated variation have in common the view that developmental processes systematically channel the generation of phenotypic variants along certain pathways, and thereby bias the direction and rate of evolution by, in part, determining the variants that are subject to selection.... "Niche construction theory makes a related argument: it emphasizes how developing organisms modify external environments in a manner that systematically biases the selection pressures acting on the constructing population, their descendants, and other populations (including other species) that inhabit their local environment. The parallels are self-evident: niche construction is a manifestation of an externally expressed developmental bias, or conversely, developmental bias is the outcome of an internal constructive process." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2414.
"The term ‘constructive development’ is designed to capture the idea that the developing organism shapes its own developmental trajectory by constantly responding to, and altering, internal and external states." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2414.
"Developmental systems respond flexibly to internal and external inputs, most obviously through condition-dependent gene expression, but also through exploratory behaviour (among microtubular, neural, muscular and vascular systems), which enables somatic selection of diverse functional states in response to local demands." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2414.
"Turner points out that many of the structures built by animals do physiological work, capturing and channelling chemical and physical energy. Earthworms’ soil environment, termite mounds and countless animals’ burrows effectively function as externalized organs of physiology." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2414. Reference: Turner, Scott. 2000. The Extended Organism: The Physiology of Animal-Built Structures. Harvard University Press.
"Indeed, organisms do not just modify environments, they confer their own physiology on their local environments. In order to survive, organisms must act on their environments and, by doing so, change them. One consequence of this imperative is that all living organisms must engage in ‘niche construction’ – that is, they must modify their environment to some degree, however small-scale and transient." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2415.
"Much of the reasoning underpinning NCT (niche construction theory) can be derived from Ashby’s ‘Law of Requisite Variety’. This law specifies that, if it is to be stable, the number of states of the control mechanism of a system (e.g. the variant states available to an organism) must be greater than or equal to the number of states in the system being controlled (e.g. the variant environmental states with which the organism must cope).... This is germane to living organisms: if it experiences an environmental state or states with which it is unable to cope, it will die." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2416. Reference: Ashby, W. 1956. An Introduction to Cybernetics. Chapman & Hall.
"Where the organism is able to counteract or exploit environmental variation, either by responding to it adaptively or by changing the environment to suit itself, then that enhances the organisms’s capacity to survive and reproduce and contributes to the subsequent evolution of its population. Hence, through this niche construction, the fundamental niche itself may be adjusted. "In practice, this adaptive regulation demands not just the protection of multiple variables simultaneously and successively, but also their adjustment towards values that maximize fitness, which makes it a niche management problem. If adaptive regulation is successful, and the multi-dimensional organism-environment relationship (henceforth ‘niche relationship’) is successfully protected by the organism, then we end up with a dynamic and evolvable homeostatic relationship between the organism and its environment." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2416.
"To sustain an internal environment of, say, high sodium concentration implies that work is being done to concentrate sodium from the environment. Doing so means that the external environment must, to a degree, be depleted of sodium. It follows that sodium homeostasis in an organism’s internal environment imparts changes in sodium concentrations to the external environment as well. Therefore, an organism’s ‘internal physiology’ can imply a degree of ‘external’ physiology, as in some, but not all, cases such environmental changes are themselves regulating and homeostatic. This means that extended physiology is both nestable and scalable in ways that are not readily accountable under the gene-selectionist scheme of the MS (Modern Synthesis). Thus, physiology is both intensive and extensive. It is more proper, therefore, to speak of an organism’s extended physiology, and to conceive of the organism, not as a physiological entity embedded in a physical environment, but as an extended organism, consisting of environments partitioned by adaptive interfaces that control the flow of matter and energy across them, including through niche construction." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. Pp. 2417-8.
"In conventionally defined organisms, these adaptive interfaces constitute the various epithelial boundaries that manage the flows of matter and energy between the ‘internal’ and ‘external’ environments: the epithelia of the gastrointestinal and urogenital tracts, the lungs (or gills) and skin. Extended physiology in these instances is embodied in the internalization of the external environment: the ‘interiors’ of the lungs and the gastrointestinal and urogenital tracts are topologically ‘external’ environment, albeit enfolded ‘internally.’" Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2418.
"Niche construction is the physiological expression of the extended organism. The logic also leads to an intriguing hypothesis: that there is no outward boundary to the extended organism and to niche construction, save the boundaries of the biosphere itself." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2418.
"It can be seen that niches and environments exist inside the body, whilst physiological processes operate outside it." Laland, Kevin, J. Odling-Smee & S. Turner. 2014. "The role of internal and external constructive processes in evolution." The Journal of Physiology. 592: 11. Pp. 2413-22. P. 2420.
"The concept of ‘horizontal genomics’ involves an internal contradiction because the notion of horizontal gene transfer (HGT) inherently implies the existence of a standard of vertical, tree-like evolution, and most of the existing methods for HGT detection are based on the comparison of gene trees to a standard ‘species tree,’ in practice often the rRNA tree. If the vertical standard does not exist, the concept of HGT becomes effectively meaningless, so all we can talk about is a network of life." Puigbo, Pere, Y. Wolf & E. Koonin. 2013. "Seeing the Tree of Life behind the phylogenetic forest." BMC Biology. 11:46. P. 1.
"The analyzed FOL [forest of life] consisted of 6,901 maximum likelihood phylogenetic trees that were built for clusters of orthologous genes from a representative set of 100 diverse bacterial and archaeal genomes.... Although the FOL includes very few trees with exactly identical topologies, we found that the topologies of the trees were far more congruent than expected by chance. The 102 Nearly Universal Trees (NUTs; that is, the trees for genes that are represented in all or nearly all archaea and bacteria), which include primarily genes for key protein components of the translation and transcriptions systems, showed particularly high topological similarity to the other trees in the FOL. Although the topologies of the NUTs are not identical, apparently reflecting multiple HGT events, these transfers appeared to be distributed randomly.... Thus, although the NUTs cannot represent the FOL completely, they appear to reflect a significant central trend, an attractor in the tree space that could be equated with the STOL [statistical tree of life].... Thus, the ubiquity of HGT notwithstanding, this central tree-like trend reflects a major aspect of genome evolution and hence has a legitimate claim to represent the STOL." Puigbo, Pere, Y. Wolf & E. Koonin. 2013. "Seeing the Tree of Life behind the phylogenetic forest." BMC Biology. 11:46. Pp. 1-2.
"Empirical studies of vertebrates and invertebrates have demonstrated that animals typically form groups for one or more of five functional reasons: (I) predator avoidance; (ii) resource acquisition; (iii) mate acquisition; (iv) offspring care; and (v) homeostasis." Hofmann, Hans, A. Beery, D. Blumstein, I. Couzin, R. Earley, L. Hayes, P. Hurd, E. Lacey, S. Phelps, N. Solomon, M. Taborsky, L. Young & D. Rubenstein. 2014. "An evolutionary framework for studying mechanisms of social behavior." Trends in Ecology & Evolution. V. 29. No. 10. P. 584.
"If representation is inherently agentive itself, however–inherently interactive–then the way is open to understanding persons as agents that are inherently related to their knowledge in and of the world. If representation is an emergent of interactivity, then persons have agency and cognition as aspects of the same underlying ontology, rather than having those aspects split into two fundamentally different kinds of phenomena." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 108.
"If it is assumed that representation can be impressed into a passive mind, like a signet ring into wax, then it is tempting to conclude that perception and learning take place via phenomena such as transduction and induction. In such a framework, there is little work for development to do. "If, however, representations, thus cognition, are emergents of interaction systems, then there is no temptation to conclude that interactive systems can be impressed by the environment into a passive mind. Interaction systems must be constructed. "Furthermore, such constructions cannot be prescient, so they must be fallible trials in a variation and selection process: an action-based model of representation forces an evolutionary epistemology." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 112.
"An interactive system represents characteristics of its environment via the implicit presuppositions of (indications of the potentiality of) its interactions. Such a system might itself have properties that would be worth representing–e.g., the fact that one of the heuristic strategies in that system instantiates the number three in its organization of ‘try three times before switching to another procedure.’ Properties of this first level system can be represented by a higher level system that interacts with it in essentially the same manner–via implicit presuppositions of interactive anticipations–as the first level system represents its environment. "Such a second level system might itself, in turn, have properties that could be represented at a third level, and so on There is no in-principle bound on these levels of knowing, though in practice we rarely find more than three or perhaps four. "One immediate consequence is that, together with the evolutionary, epistemological constructivism that an action-based model forces, the knowing levels impose a sequence on development: it is not possible for an interactive system to be constructed at level N + 1 if there is nothing at level N for it to interact with. Therefore, the levels must be developmentally ascended one at a time within any given domain of construction: the knowing levels force a kind of stage sequence of development, one that we find in the developmental data." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 113.
"There are, however, strong ontological candidates [on the nature of the self or identity] that emerge from the knowing levels model. "I will outline three directly relevant properties that emerge from the knowing levels: (1) Interactions and interaction indications involve presuppositions concerning the conditions that would support them. So also do broader and more persistent manners of functioning in the world, and the presuppositions involved are correspondingly broader and more persistent. (2) Furthermore, such presuppositions can be reflexive–about the organism or agent. And, finally, (3) presuppositions can themselves have presuppositions. "General ways of interacting in the world, thus, involve presuppositions about the agent, and perhaps at multiple levels." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 113.
"As infant and toddler develop, ways of dealing with the physical and the social world are organized and constructed. These will involve presuppositions about those physical and social worlds, as well as about the toddler within them. In this sense, the toddler becomes an emergent agent, a self in a restricted sense." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 114.
"At second and third knowing levels–second and third levels of reflection–goals will be about the organization and activities of the individual. They will guide interactions, learning, and development of that individual. In that sense, they constitute values. They can also be about other values: second and third order desires." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 114.
"... coherence is a meta-value, functioning at least implicitly in the normative value-guided development of the individual." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 114.
"An important class of values is those that are reflexive: that are about the entire person. I may have a value of being kind or being fearless, for example. One crucial property of such reflexive values is that they cannot be consistently approached in an instrumental fashion. I can decide to get to the store on one route rather than another, or to use this tool rather than that tool in some task, but I cannot similarly simply decide to be in the world in a kind of fearless manner. Instrumentality requires a distinction between the agent and the (means toward the) task, while reflexive values do not permit that distinction. To attempt to instrumentally approach a reflexive value is to command oneself to spontaneously be kind or fearless–but to command oneself to be spontaneous in any sense is to impose a contradiction, a double bind." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. Pp. 114-5.
"Agents with goals and values, interacting with and developing within their environments, sounds like a psychological ontology. And so it is. So where is the socio-cultural ontology? How does that integrate? "I will argue that the person develops as an agent, but as a special emergent kind of agent, generated within the societies and cultures within which the individual develops. The person, then, is psychological (and biological) as an agent, with interactive abilities, goals, values, and so on, but is social with respect to the kind of agent. Agency per se can be biological and psychological, but the facts, origins, contents, values, and ontologies of higher level agency as persons are inherently social. Social realities are constituted in multiple interactive and potential interactive relationships among persons as social agents, but the developmental emergence of such persons, as well as the ongoing functioning of such persons, is possible only within and with those social realities. Social persons and the social realities that they co-constitute are metaphysically dual to each other: they can exist only with respect to each other." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 115.
"In particular, for one agent to characterize a situation that involves another agent requires characterizing that other agent, but the interactive potentialities afforded by that agent will depend on aspects of that other agent that are not readily perceptually apperceivable. These include the agent’s mood, beliefs, and so on, and, most especially, that other agent’s characterization of his or her situation–including their characterization of the first agent. "The problem of interactively characterizing the situation, thus, is reciprocal and symmetric, and must be resolved jointly. Such a joint interest in a resolution to a symmetric problem constitutes a coordination problem, and Lewis proposed that a convention be modeled as a solution to a coordination problem. In the class of cases outlined, the coordination problem, thus the conventionality of a solution, is about the joint situation, and I accordingly call such solutions, such joint and interactively consistent situation knowledge, situation conventions–conventions about the nature of the (social) situation. "Within the category of situation convention, there are those that are momentary and not likely to ever be repeated, such as the common understanding of an utterance in a conversation, and those that are more general, across repeated situations and perhaps large numbers of people, which are called institutionalized conventions. Language is itself a convention–a specialized kind of convention, for the construction of conventional utterances, which transform situation conventions." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. Pp. 115-6. Reference: Lewis, D. 1969. Convention. Harvard University Press.
"The infant develops as a biological and psychological agent, but that agency is progressively adapted to the society and cultural environment in which the individual is developing. The social realities of society and culture are themselves emergent in the relationships among the participating and constituting persons, and the social persons that developmentally adapt to those realities are similarly emergent–a developmental emergence of a socio-cultural agent, a kind of agent that cannot develop and cannot exercise its interactive capabilities except in the context of the realities of the socio-cultural processes which it comes to co-constitute along with other participant persons." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 116.
"Persons, however, are not metaphysically independent. Instead, they are deeply dependent on and formed within and together with their socio-cultural environments." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 116.
"The development of values, then, is inherent in the functioning of interaction, learning, and the knowing levels. Which values are developed, however, is the product of a dialectic between the developing person and the potentialities outlined and enabled by the socio-cultural circumstances of that person. New values unfold values that are already implicit in the manner of being in the world that the person has thus far developed, but that ‘unfolding’ relation does not fully determine what those values must be. The culture presents various value possibilities in its narratives, religions, ideologies, and presuppositions, and society enables or inhibits living those values in various ways. Value development, then, emerges in a dialectic between the potentialities and presuppositions of the person and the possibilities of society and culture. "Furthermore, as with goals in general, values can guide interaction, but they can also guide learning and development. The dialectic, then, is multiform, with values unfolding what is already implicit in the person, into the space of possibilities framed by the social and cultural environment, which, in turn, participate in guiding the further activity and development of the person." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 117.
"Persons, then, are both self-generated and socially constituted." Bickhard, Mark. 2012. "A process ontology for persons and their development." New Ideas in Psychology. 30: 107-119. P. 118.
"... generally speaking, more slowly changing dynamics constrain faster dynamics, not vice versa. In self-organization, a key distinction between control and order parameters versus state dynamics is based on how fast one changes with respect to the other. Order parameters are defined to be particular configurations of state dynamics, which means they must change more slowly than state dynamics." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 1.
"The most widely held conventional belief is that the brain controls behavior, not the other way around. Yet, when compared with the lightening fast changes in the brain, the typically more slowly changing body suggests the exact opposite broad-stroke outline of control. The brain appears to take direction from the body, just as old school blue-collar workers took direction from white-collar counterparts in the front office." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 1.
"Multicellular living things comprise nested structures.... Toes and fingers are nested within the next scale of rigid bones of arms and legs that are coupled by larger articulating joints. Arms and legs in turn sprout from the trunk of the human body and are connected to the trunk by rotating joints at the hips and shoulders.... "The anatomy of blood vessels throughout the body, the detailed anatomy of a kidney, and the airways of a lung all comprise nested tree-structures across multiple scales–an arrangement called fractal structure that is studied using the mathematical tools of fractal geometry. The scaling relations that define the spatial organization of living things indicate their fractal composition. In a scaling relation, the size of a structure is inversely proportional to how often structures of that same size recur. For example, within limits, the diameter of each blood vessel is inversely proportional to the total number of blood vessels of that same diameter that will be found in the body." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 2.
"Event times of both human physiology and human behavior compose temporal scaling relations. In the scaling relations of event times, the magnitude of changes in the duration of event times is inversely proportional to how often a change of that magnitude recurs." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 2.
"Repeatedly measured data values, whether from brain activity or behavior, are generally scale-free with exponents a~1 ...." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 4.
"... the priority of control, as we mentioned already rests on relatively slowly changing constraints and the scale-free behavior of the body includes several orders-of-magnitude slower changes than the co-occurring brain activity." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 4.
"Before complexity science the variation in measured values was divided exclusively between the regular changes of explainable variance and the random changes of measurement error, signal versus noise. But pink noise is neither signal nor noise, or it is both, as already noted, and so it cannot be classified within the conventional dichotomy. Pink noise is a third category of behavior, a widely acknowledged game-changing phenomenon of complexity science. It is the simultaneous presence of instability together with stability that defines a critical state. "Thus our thesis: if white-collar control can be said to exploit the instability of a critical state then blue-collar work depends upon stability. Brain-to-body control by the faster changing dynamics of the brain exploits the instability near a critical state to change the course of the slower dynamics of the body. Blue-collar work exploits constraints supplied by the more slowly changing ‘ghost’ parameter dynamics of criticality that lend stability to the faster changing dynamics of the brain." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 7.
"Organism-wide synergies emerge across a tensegrity structure. The tensegrity structure is formed by a taught [=taut?] web of muscles and fascia to fully connect the parts of the skeleton, appearing to wrap it like a mummy. Similar to tensegrity structures in architecture or robotics and biology, the skeleton supplies the struts while the muscles, ligaments, and fascia form the tension lines eliminating slack from the tensegrity structure. The taught [taut] web of tension lines ensures that movement at any one place in the tensegrity structure has consequences throughout the structure, creating a robust mechanical holism that even survives damage that has left the body paralyzed. The neuromusculoskeletal structure of the body, in the guise of this tensegrity structure, is an excitable medium of self-organizing constraints to sustain the coordinated movements of the body." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 8. "... there exist incalculably more possible configurations of the possible states of the body than there are smoothly and appropriately coordinated ways to make behavior. Tensegrity structure and synergies reduce the degrees of freedom of the body, limiting the possible configurations to task, and context appropriate ‘symphonies’ of movement for coordinated change in behavior." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 9.
"... the reduced degrees of freedom observed of one process may anticipate the reduced degrees of freedom of another process not yet enacted. Raising an arm requires anticipation by remote muscles on the opposite side of the body prior to any change in the arm’s position – else the body would tip over. If the arm movement were made to signal a cognitive choice then the preflex of the remote muscles would ‘signal’ the same choice. If so then the fact of the reduced degrees of freedom in the anticipatory preflex corroborates the synergy of the soft-assembled choice response. "One widely used cognitive task includes a judgment of whether a visually presented letter string correctly spells a word in a reference language – that is, standing before a screen on which letter-strings will appear, raise one arm for each American English ‘word’ and the other arm for ‘non-words.’ Event times as ‘response times’ by anticipatory preflexes can be measured in the onset of change in electromyographic activity in the right or left thigh, the right or left paraspinal muscles of the lower back, or the right or left shoulder muscles.... "Moreno et al. conducted this experiment, and the side of the body of the preflex reliably distinguished the word from the non-word letter-strings. The observed reduced degrees of freedom in the corresponding preflexes corroborated synergetic control.... On average, the preflex ‘word’ response times preceded the arm ‘word’ response time by 120 ms at the shoulder, 189 ms at the trunk, and fully 225 ms at the thigh. Synergies appear to have soft-assembled a multilevel whole-body ‘American English word versus non-word judgment device’." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 9. Reference: Moreno, M.A., N. Stepp & M. Turvey. 2011. "Whole body lexical decision." Neurosci. Lett. 490: 126-9.
"The blue-collar contribution brings together the concepts of timescale, constraint, synergy, and criticality to understand how the brain supports on-going behavior, to anticipate forthcoming behavior. Constraints that reduce the degrees of freedom for behavior unfold on different timescales, and the more slowly changing constraints have priority over faster change constraints. Control in this sense in non-specific, a practically unlimited set of possible actions is reduced to a smaller subset, shaped by the contemporary states of physiological processes, environmental regularities, and the idiosyncratic history of the organism. The smaller subset is sustained in a state of criticality, lacking only a contingent discriminating circumstance to enact one of the possible actions." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. Pp. 9-10. "Cognitive science is well underway as complexity science, with wide implications for how to conceptualize and investigate human nature." Van Orden, Guy, G. Hollis & S. Wallot. 2012. "The blue-collar brain." Frontiers in Physiology. V. 3. Article 207. Pp. 1-12. P. 10.
"... [Wild systems theory] WST conceptualizes organisms as natural, wild agents. Not in the sense that smaller scale internal dynamics code for larger scale dynamics, as is the case in internalist approaches to agency. But rather, in the sense such systems constitute a nesting of multi-scale self-sustaining dynamics. It is the inherent end-directedness of these self-sustaining systems that, according to WST, qualifies such systems as agents." Jordan, J. Scott. 2008. "Wild agency: nested intentionalities in cognitive neuroscience and archaeology." Philosophical Transactions of the Royal Society: B. 363: 1981-91. P. 1984.
"... wild agents are naturally and necessarily ‘about’ the multi-scale energy-transformation contexts in which they sustain themselves." Jordan, J. Scott. 2008. "Wild agency: nested intentionalities in cognitive neuroscience and archaeology." Philosophical Transactions of the Royal Society: B. 363: 1981-91. P. 1984.
"The notion of embodied context should not be confused with internalism. Rather, it is more consistent with Oyama’s notion of a developmental system, the idea being that organisms inherit not only their genes but also the multi-scale contexts in which the interactions necessary to the emergence of a phenotype are possible (e.g. the persistence of contexts entailing available food, clothing, shelter and other organisms)." Jordan, J. Scott. 2008. "Wild agency: nested intentionalities in cognitive neuroscience and archaeology." Philosophical Transactions of the Royal Society: B. 363: 1981-91. P. 1984. Reference: Oyama, S. 1985. The ontogeny of information: developmental systems and evolution. Cambridge University Press.
"Given that wild agents constitute embodiments of context, they can be conceptualized as world-in-world. That is, the natural homology of organisms and the contexts they embody indicates that wild agents do not need to be ‘informed’ about the context in which they are embedded (i.e. their environment) in order to be about it. They are naturally and necessarily about it." Jordan, J. Scott. 2008. "Wild agency: nested intentionalities in cognitive neuroscience and archaeology." Philosophical Transactions of the Royal Society: B. 363: 1981-91. P. 1984.
"Instead of the concepts perception, action and cognition, WST conceptualizes psychological functionality in terms of scales of sustainment. "The concept scales of sustainment provides a gradient-oriented approach to psychological functionality, versus the trichotomy-driven approach (i.e. perception, action and cognition) of internalism. In this gradient-oriented framework, the distinguishing feature of an architecture is the distality of the time scales in which a wild agent can sustain coordinations.... "In addition to proximal and distal sustainment, humans are further able to engage in virtual sustainment. For example, in order to switch from dancing a tango to a samba, one must constrain one’s distal sustainment towards producing a samba-like distal pattern versus a tango-like pattern. The switch from one possible distal pattern to another constitutes virtual sustainment: the system is able to reconfigure and constrain the possible distal patterns it works to sustain." Jordan, J. Scott. 2008. "Wild agency: nested intentionalities in cognitive neuroscience and archaeology." Philosophical Transactions of the Royal Society: B. 363: 1981-91. P. 1984.
"Effective control of behaviour on the part of an animal requires at least a minimal grasp of the structure of the ecological niche in which it is situated. For many species, the requisite knowledge can be quite sophisticated. Thus, a forager can benefit from a representation of the spatial layout of its range, a social animal–of the dominance hierarchy in its group, and a tool user–of the cascading effects of the various actions that the tools afford. While such representations are clearly beneficial when fully in place, their acquisition–both over evolutionary time and in individual learning–presents a problem: intermediate steps in the acquisition process may not be useful and in any case are not necessarily incrementally reinforced. In this paper, we examine such learning, in which a learner continuously attempts to learn all regularities in its environment regardless of their immediate value. We refer to this mode of learning as continuous, and focus on its relationship with reinforced learning in the context of a foraging task. We chose to refer to the learning mode of interest as ‘continuous’ because the alternative (‘unreinforced’) would be misleading in that occasional reinforcement does occur in the tasks that we explore." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 1.
"We used agent-based computer simulations to compare three learning strategies: local reinforcement learning(LR) that associates environmental cues with food only if they are experienced in the same locality as the food; reinforcement learning with chaining (RL-chain), which supports construction of a world model through backward chaining; and CL [continuous learning], which uses not only the same associative mechanisms as the first two strategies, but also seeks statistical regularities in the relations among all items in the environment, regardless of initial association with food." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 2.
"... when there are no cues or other regularities in the environment that can aid foraging, learning by all three models is not adaptive." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 5. "We identified two main factors favouring the evolution of CL [continuous learning]: structured environment and limited time for training. The structured environment gives advantage to model-constructing learners that can then predict the presence of food more than one step ahead. Thus, a structured environment favours both CL and RL-chain. However, the limited time for training gives CL an advantage over RL-chain because CL learners construct their world model much faster; they acquire data and construct a network right from the outset, without waiting for multiple encounters with food. As expected and confirmed by our simulations, this advantage increases when food or its most reliable predictors are rare." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 8.
"In nature, we believe, many environments are structured and may be best characterized as directed network environments. Yet, it is quite possible that many of these networks are not sufficiently structured to make model construction sufficiently effective. Moreover, given that model construction may also incur costs in terms of memory and computation, not every structured environment would favour it; the environment must be sufficiently structured that the predictive power of the model improves foraging success to the extent that it outweighs the costs of constructing and managing a world model." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 9.
"... our results suggest that given a certain level of environmental complexity, CL is always faster than chaining, implying that it is likely to succeed under a wider range of changing environments." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 9.
"Moreover, the acquisition of continuous streams of data presents the challenges of segmenting the input into the most useful units and of constructing the model in a way that would facilitate efficient search, as well as appropriate decision-making and planning. It is therefore expected that right from the start, the evolution of CL [continuous learning] would give rise to new selective pressures acting towards reducing the costs of memory and computation, improving the management and use of the model, and minimizing the acquisition and storage of unnecessary data. In short, the transition to CL selects for the evolution of relatively advanced cognitive mechanisms." Kolodny, Oren, S. Edelman & A. Lotem. 2014. "The evolution of continuous learning of the structure of the environment." Journal of the Royal Society: Interface. 11: 20131091. P. 9.
"... agents can still behave coherently despite certain levels and types of perturbations by exploiting systemic features like situatedness, embodiment, and agent-environment coupled dynamics. Situatedness, or being situated in the environment, means that agents (biological or artificial organisms) use their surroundings to directly influence their future actions. Embodiment refers to the physical existence of an organism or robot having a co-related, but essentially different, dynamics from the environment. The concept of coupled dynamics will refer forefront to the active interaction between the neurocontroller (‘brain’), body, and environment systems." Fernandez-Leon, Jose. 2012. "Behavioral robustness: An emergent phenomenon by means of distributed mechanisms and neurodynamic determinacy." BioSystems. 107: 34-51. Pp. 34-5.
"The accepted understanding of what produces robust and adaptive behavior is gradually changing from being generated by isolated control mechanisms within organisms toward dynamical processes occurring over multiple and distributed systemic components." Fernandez-Leon, Jose. 2012. "Behavioral robustness: An emergent phenomenon by means of distributed mechanisms and neurodynamic determinacy." BioSystems. 107: 34-51. P. 35.
"By understanding emergent dynamics at an organism-to-environment systemic level, aside from the practicality of finding such an interface in biological organisms, this paper serves as a baseline from which to understand the causally connected interplay between structure and behavior in organisms. Proposed experimental results from ‘silico’ demonstrate clearly that a dynamical interface is possible by means of distributed processes in a coupled system." Fernandez-Leon, Jose. 2012. "Behavioral robustness: An emergent phenomenon by means of distributed mechanisms and neurodynamic determinacy." BioSystems. 107: 34-51. P. 49.
"Basa, just like bahasa in Classical Malay, meant ‘language’, but it always included in its broad semantic field the notions of civility, rationality, and truth. This conceptions of ‘true’ language meant that in the profoundest sense Javanese (or in their local habitats, Sundanese, Balinese and Buginese) was isomorphic with the world, as it were glued to it. It was this isomorphism, this inherence, that made for the efficacy of mantra. Because words or particular combinations of them contained Power, like kinds, krisses, banyan-trees and sacred images, their utterance could unleash the Power directly on, and in the world." Anderson, B. 1990. "Language, fantasy, revolution in Java, 1900-1945." Prisma. 50: 25-39. P. 28. Cited in Nash, Joshua & P. Muhlhausler. 2014. "Linking language and the environment: the case of Norf’k and Norfolk Island." Language Sciences. 41: 26-33. P. 28.
"This type of
ecologically embedded language [as opposed to disconnected languages]
exhibits properties such as: "Writers on cultural evolution have in recent years commented on a (largely anecdotal) literature suggesting that, contrary to claims that teaching makes human culture distinctive, teaching plays only a minimal role in hunter-gatherer culture, by comparison with observational learning." Whiten, Andrew, R. Hinde, K. Laland & C. Stringer. 2011. "Culture evolves." Philosophical Transactions of the Royal Society: B. 366: 938-48. P. 945.
"Empirical studies of language acquisition have revealed two preponderant learning styles: the synthetic style, children emphasize single words for primarily referential functions and acquire the exposed language by combining elements into multiword utterances; and the gestalt style, children produce unanalyzed language forms or chunks with little appreciation of their internal structures or specific meanings." Gong, Tao, L. Shuai & B. Comrie. 2014. "Evolutionary linguistics: theory of language in an interdisciplinary space." Language Sciences. 41: 243-53. Pp. 247-8.
"In short, if a system has multiple coexisting attractors and noise is sufficiently strong to cause switching among stable states, it may be said to be multistable." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 906.
"First and foremost is the need to recognize that complex biological systems at all relevant scales are degenerate. Degeneracy means that at every conceivable level of description, the same outcome or function can be achieved in many ways using different components." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 907.
"Synergies are exquisitely context-sensitive functional groupings of elements that are temporarily assembled to act as a single coherent unit. Depending on context, synergies may accomplish different functions using some of the same components (e.g. the jaw, tongue and teeth to speak and chew) and the same function using different components (e.g. ‘hand’ writing with a pen attached to the big toe)." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 907.
"Multistability confers a tremendous selective advantage to the brain and to nervous systems in general: it means that the brain has multiple patterns at its disposal and can switch among them to meet environmental or internal demands." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 910.
"Multistable coordination dynamics confers a capacity on the brain to lock in to one of several available patterns. Locking in and switching capabilities can be adaptive and useful, or maladaptive and harmful. "Another kind of mechanism called metastability is becoming recognized as an important dynamical mechanism for understanding brain and behavioural coordination.... It is the simultaneous realization of two competing tendencies: the tendency of the individual components to couple together and the tendency for the components to express their independent behaviour. In coordination dynamics, metastability corresponds to a regime near a saddle-node or tangent bifurcation in which stable and unstable coordination states no longer exist, but attraction remains to where those fixed points used to be. This gives rise to a dynamical flow consisting of phase trapping and phase scattering." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 913.
"What does coordination behaviour look like in the metastable regime? Although all the fixed points have vanished, a key aspect is that there are still some traces of coordination, ‘ghosts’ or ‘remnants’ of where the fixed points once were. Despite the complete absence of phase-locked attractors, the behaviour of the component parts in the metastable regime is not totally independent. Rather, coordination takes the form of dwellings (phase gathering) near the remnants of the fixed points and phase scattering, where the individual components act quasi-independently, expressing their autonomy. In the metastable regime, successive visits to the remnants of the fixed points are intrinsic to the time course of the network, and do not require any additional sources of input." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 914.
"In the metastable brain, the activity of individual elements obeys neither the intrinsic dynamics of the elements nor the dynamics dictated by the assembly. A delicate balance between the two poles of integration (coordination between individual elements in transiently synchronized ensembles) and segregation (expression of individual behaviour in diverging neural ensembles) is thus achieved. This design plays out in space and time, with ensembles of various sizes coming together and disbanding incessantly." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 914.
"In short, metastability guarantees that the living brain (and complex, goal-directed systems in general) never finds itself frozen for any length of time in a particular coordination state: no energy barriers need to be crossed to visit self-organized metastable tendencies." Kelso, J.A. Scott. 2012. "Multistability and metastability: understanding dynamic coordination in the brain." Philosophical Transactions of the Royal Society: B. 367: 906-18. P. 914.
"In contrast to primates, most nonprimate vertebrate taxa are found in groups where the membership is inconstant, and there is no evidence that individuals recognize each other as distinct and base their interactions on this individuality: they are ‘herd animals,’ but not truly social." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 816.
"Where groups are inconstant aggregations, relationships between brain size and typical group size are lacking, adding further support to the idea of a close relationship between brain enlargement and semipermanent social living...." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 816.
"Although primate-like sociality is infrequent among other mammals, some species of carnivore, equines, certain dolphin and whale species, and all species of elephant live in groups where they are part of a semipermanent network rather than an amorphous herd." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 817.
"As well as good evidence that primates recognize individuals, kinship, rank, and the third-party relationships between others, there is now extensive evidence that many species of primate regularly deploy subtle or manipulative social tactics during intragroup competition with these individuals." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 817.
"Although in general monkeys have failed to give evidence of cooperative abilities, cotton-top tamarins, a cooperatively breeding species, not only performed well in a two-role task but showed similar capacities to chimpanzees in understanding the role of the other. These studies suggest that temperament may be more important that [sic] cognitive architecture in whether or not a species is able to cooperate efficiently." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 818.
"Scrub jays react to others’ seeing them cache their food, by recaching it once they get the chance, in private–but only if they themselves have prior experience of pilfering the caches of others." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 818.
"Gaze following is known in many species of animal (e.g., great apes, goats, ravens, ibises) and is often taken to be an automatic, almost reflexive tendency. However, research on monkeys has found gaze following to depend on the particular facial expression of the model ...." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 818.
"In the great apes, there is evidence for ‘triadic’ interactions, in which two individuals interact both with each other and with an object, paying attention to the nature of the other’s interaction with the object." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 819.
"As with gaze following, shared attention to objects and the ‘intersubjectivity’ shown in triadic interactions over objects have been suggested to be important developmental precursors to theory of mind in humans." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 819.
"The general lack of pedagogical teaching among all nonhuman primates supports this conjecture [that nonhuman primates lack ostension or ‘natural pedagogy’]. Functionally defined teaching has been recorded in several species of animal, including ants, babblers, meerkats, cheetahs, and several callitrichid primates. But none of these data suggest that the teacher understands the (lack of) knowledge of the learner; in contrast, observations suggesting deliberate pedagogy are very rare and, consequently, hard to interpret." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" |
