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.
"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. “... viruses and
virus-like selfish elements:
"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." , 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. “(a) Not every type
of highly structured environment favours model-constructing learners.... "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: 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.
"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?" Neuron. 65: 815-30. P. 819. "What happens when a wholly new gesture is employed? Humans are able to relate the form of a gesture to the constraints of the environment: if one’s hands are full, one can ‘point’ with an elbow or foot and be readily understood. Nonhuman primates show the same flexibility, with identical results in cotton-top tamarins, rhesus monkeys, and chimpanzees. When an experimenter, carrying a large object, touched one of two food wells with his elbow, the subjects responded just as if he had used his hand normally, preferentially investigating that place. But when the same experimenter used his elbow, in the same way but with his hands not engaged, the gesture was ignored, just as was a hand-touch that looked unintentional." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 820.
"Based on the evidence currently available, however, we shall distinguish between social complexity that is a matter of degree–knowledge of more social companions, more frequent use of alliances, more complicated manipulative tactics that depend on picking more subtle aspects of behavior, finer and more elaborate categorizations, larger brain (part) sizes that correlate with larger social groups–from social complexity that requires a deeper understanding of mechanism and mind, including the understanding of the self as an entity and perhaps of the false beliefs of others, which is apparently very much more limited. In the case of great apes, there is some evidence for both of these features, in other taxa, it may be that either type of social sophistication can occur without the other–for instance, social carnivores apparently show quantitative social complexity, whereas some corvids give evidence of deeper understanding–so the selective pressures that led to their evolution may be different in kind." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 822.
"Scaling against body size is inappropriate for estimating the intellectual potential of a given brain size, although it has often been used for that purpose. Instead, it is useful as a measure of the brain’s ‘cost’ to the animal." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 822.
"As suggested above, ‘social’ should be seen to include challenges met by information processing in the context of predator/prey interactions, as well as those from living with conspecifics. With this interpretation, linked increases in intelligence and brain size in a much wider range of species may be understood. "But in the great apes, that theory fails: social challenge, as measured by group size, does not differ between ape and monkey species, whereas capacity in some cognitive dimensions–such as understanding cooperation, intention and deception, and mirror self-recognition–do. Instead, what is notable about apes, contra monkeys, is that all genera of living great apes show special skills in manual food processing: Pongo, in accessing spiny rattans and palms and for extracting honey and seeds with tools; Gorilla, for processing physically defended herb resources; Pan, in collecting insect foods with tools, often ones made themselves and sometimes sets of two tools for a more complex task." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 823.
"The suggestion is that the surviving great apes were able to compete by developing skills to reach foods that monkeys could not reach, as shown today in their expertise at extracting insects and dealing with plant defenses: abilities that give them advantages in the domain of physical rather than social cognition. The finding in corvid species, few of which are social, of remarkably similar cognitive skills to those of apes similarly points to physical cognition as the driving function for these capacities." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 823.
"Only in the great apes does it seem that imitation involves learning new skills by assembly of novel actions from components. This difference implies that only great apes, among primates, have behavior-parsing capacities." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 824.
"In summary, we suggest that social cognition is not unique to primates and that primate cognition is not uniquely social. We argue that most demonstrations of cognitive skill can be accounted for by quantitative differences in memory, with the tendency to larger memory most likely being driven by social competition (from conspecifics and from predator/prey interactions). However, some particular skills such as insightful cooperation or deception, perception of intent, imitation of novel skills, and mirror self-recognition, signify a qualitatively different representation of mechanisms and minds. This probably relies on the presence of specific cognitive architecture that allows for behavior parsing and the formation of hierarchically organized programs of action, the selection for which may have been driven by physical constraints." Byrne, Richard & L. Bates. 2010. "Primate Social Cognition: Uniquely Primate, Uniquely Social, or Just Unique?" Neuron. 65: 815-30. P. 825.
"Collective activity as such does not demand a bird’s eye view representation of the activity. Such representations are not needed if there is no role differentiation (as in social carnivores like African wild dogs), or if each agent always takes the same specialized role. But if there is collective action with role specialization, and if agents do not always act in the same role (if sometimes I act to drive the game; if sometimes I am the lookout; if sometimes I wait in ambush), then each team member does need a bird’s eye representation of the collective activity." Sterelny, Kim. 2012. "Language, gesture, skill: the co-evolutionary foundations of language." Philosophical Transactions of the Royal Society: B. 367: 2141-51. P. 2147.
"Dunbar has long argued persuasively that as hominin social worlds became larger and more complex, conflict and social stress would become increasingly difficult to manage through methods inherited from the great apes. Increasingly, vocal grooming would have to replace or supplement physical grooming." Sterelny, Kim. 2012. "Language, gesture, skill: the co-evolutionary foundations of language." Philosophical Transactions of the Royal Society: B. 367: 2141-51. P. 2149. Reference is to Dunbar, R. 2009. "Why only humans have language." From: Botha, R. & C. Knight. The Prehistory of Language. Oxford University Press. Pp. 12-35.
"... the hypothesis about vocal grooming is more plausibly reinterpreted as explaining the evolution of music and song. Music and song are enormously powerful in shaping affect;..." Sterelny, Kim. 2012. "Language, gesture, skill: the co-evolutionary foundations of language." Philosophical Transactions of the Royal Society: B. 367: 2141-51. P. 2149.
"Importantly, selection for song-like social grooming and bonding would not just bring vocalization under top-down control, it would build precise control of vocal performance, performance in response to specific social situations. Once our vocal life was not just under top-down control, but under top-down control that allowed precise execution of a complex vocal sequence, it would naturally be incorporated into mime and gesture. Once that ability is in place, we would expect communicative acts to be a hybrid of manual, bodily and vocal elements." Sterelny, Kim. 2012. "Language, gesture, skill: the co-evolutionary foundations of language." Philosophical Transactions of the Royal Society: B. 367: 2141-51. P. 2149.
"In summary, then, I see the shift from gesture to speech as a four-stage process: an initial stage in which selection for inhibition of emotional response makes vocalization less reflexive; a Dunbarian stage in which minimal top-down control of vocalization expands and becomes much more precise, as vocalization becomes increasingly recruited as a tool of social cohesion and social bonding; a third stage in which the gesture-based system of information sharing and coordination is enriched through recruiting vocal elements; a final stage in which the hybrid system becomes vocal, perhaps driven by the opportunity costs of having one’s hands tied up as communicative tools. This is far from a full theory of the transition, but it is enough to show that it is no insoluble mystery, either." Sterelny, Kim. 2012. "Language, gesture, skill: the co-evolutionary foundations of language." Philosophical Transactions of the Royal Society: B. 367: 2141-51. P. 2149.
"While network topology discounts metric or spatial relations among network elements, many real-world networks are spatially embedded. Examples are brain networks, transportation networks, the internet and electrical circuits, and even social networks. Spatial embedding may place important constraints on network topology; therefore, the study of network topological features often takes into account the spatial relations." Avena-Koenigsberger, J.Goni, R. Sole & O. Sporns. 2015. "Network morphospace." Philosophical Transactions of the Royal Society: Interface. 12:20140881. Pp. 1-12. P. 3. "It is well known now that in spite of the diverse evolutionary processes that drive the formation of different systems, they all converge towards heterogeneous, modular architectures that show a balance between order and randomness." Avena-Koenigsberger, J.Goni, R. Sole & O. Sporns. 2015. "Network morphospace." Philosophical Transactions of the Royal Society: Interface. 12:20140881. Pp. 1-12. P. 7.
"Rare, serendipitous inventions may make major contributions to fitness, yet they are not heritable because their acquisition depends on many additional factors, such as the constellation of environmental conditions and sheer serendipity. Thus, selection to favour increased cognitive abilities beyond mere conditioning, towards innovative, solutions to problems, i.e. true intelligence, must face a high threshold. "Nonetheless, many species are intelligent. Here, we argue this is largely because socially mediated learning by offspring or other relatives makes inventions heritable, thus lowering the threshold for selection on intelligence." Van Schaik, Carel & J. Burkart. 2011. "Social learning and evolution: the cultural intelligence hypothesis." Philosophical Transactions of the Royal Society: B. 366: 1008-1016. P. 1008.
"A stronger version of the cultural intelligence hypothesis is that social learning not merely increases the set of learned skills, as examined so far, but also affects the asocial-learning ability (intelligence) itself." Van Schaik, Carel & J. Burkart. 2011. "Social learning and evolution: the cultural intelligence hypothesis." Philosophical Transactions of the Royal Society: B. 366: 1008-1016. P. 1010.
"The observations and experiments reviewed above show that individuals with more opportunities for social learning systematically acquire a larger set of learned skills and also become better asocial learners." Van Schaik, Carel & J. Burkart. 2011. "Social learning and evolution: the cultural intelligence hypothesis." Philosophical Transactions of the Royal Society: B. 366: 1008-1016. P. 1011.
"In lineages with opportunities for social learning, a positive coevolutionary process between social-learning ability and brain size may ensue, until increases in brain size no longer provide sufficient additional pay-off in survival or reproduction in the current environment. Different lineages are expected to go different distances in this eco-evolutionary process, with the position of the equilibrium depending on where the fitness costs of continued investment in neural structures begin to balance the benefits." Van Schaik, Carel & J. Burkart. 2011. "Social learning and evolution: the cultural intelligence hypothesis." Philosophical Transactions of the Royal Society: B. 366: 1008-1016. P. 1011.
"The cultural intelligence hypothesis makes plausible assumptions that were empirically supported: (I) social learning is more efficient than individual learning, and (ii) animals appear to rely on it preferentialy. The developmental effects on skill repertoires it predicts were found as well, whereas we also found preliminary support for the predicted evolutionary effects: interspecific correlation between individual and social-learning abilities and a relationship between opportunities for social learning and cognitive abilities across taxa." Van Schaik, Carel & J. Burkart. 2011. "Social learning and evolution: the cultural intelligence hypothesis." Philosophical Transactions of the Royal Society: B. 366: 1008-1016. P. 1012.
"... all hypotheses positing domain-specific benefits must explain how more generalized cognitive abilities, i.e. intelligence, subsequently arose from these specific cognitive adaptations." Van Schaik, Carel & J. Burkart. 2011. "Social learning and evolution: the cultural intelligence hypothesis." Philosophical Transactions of the Royal Society: B. 366: 1008-1016. P. 1013.
"Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life’s complexity to self-replication alone relies on thermodynamically untenable assumptions." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 87.
"According to Polanyi, life in general is characterized by its ‘irreducible structure’. By this he means that, in living matter, all the ordinary laws and mechanisms of chemistry and physics are still valid, but their course of action is now limited by specific constraints, or ‘boundary conditions’." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 88. Reference is to: Polanyi, Michael. 1968. "Life’s Irreducible Structure." Science. 160: 1308-12.
"Given that living organisms represent the highest levels of intermolecular cooperativity existing on this planet, it is not far-fetched to evaluate what kind of potential ‘habitat’‘ for emergent protolife was offering the highest degree of synergy between various environmental factors, acting together in a fortunate and productive combination of cumulative stimuli." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 88.
"From a thermodynamic perspective, for that matter, self-replication of a single sequence is merely a self-terminating run-away reaction, which has no direct means of feed-back influence securing its continuing maintenance in the long run." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 90.
"It is Wicken’s (and others’) most important insight that structural condensation of organic matter is prerequisite in forging the missing link between the thermodynammics of random reactions and the emergence of biological continuity." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 91. Reference is to Wicken, J. 1987. Evolution, Thermodynamics, and Information: Extending the Darwinian Program. Oxford University Press. "After various deep-sea scenarios were considered over time, subaerial volcanism in terrestrial geothermal fields has recently been given a leading role.... "The combination of volcanism with exposition to both sunlight and a dry anoxic atmosphere in terrestrial settings offers significant explanatory power over submarine hydrothermal vents. First of all, the high influx of ultraviolet radiation from the sun, which passed unhindered through the early anoxic/ozone-less atmosphere could actively contribute to life’s emergence in various respects: by mineral-mediated photoactivation of CO2 assimilation, by stimulating robust synthetic pathways and/or minimizing detrimental side reactions, and by selecting for base-paired RNA-like compounds as exceedingly photo-stable products. Moreover, wet-drying and/or freezing cycles at the atmosphere surface may have facilitated polymerizing condensation reactions, such as abiotic peptide synthesis." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. Pp. 92-3.
"The goal is to reintroduce colloid assembly – here understood as the congealing of soft organic compounds by adsorptive forces and consequential phase separation in aqueous medium – as a fundamental principle in biogenic evolution early on." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 93.
"Overall, the photo-heterotrophic pore-space scenario at terrestrial geothermal fields, in line with Mulkidjanian and Galperin, is characterized by robustness and autonomy. By generating ‘photosynthetic pressure’ (photo-dependent accumulation of phase-separated organic compounds) from sub-surface reaction zones, this model provides a recurrent and dependable driving force for progressive evolution." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 97. Reference is to: Mulkidjanian, A. & M. Galperin. 2013. "A time to scatter genes and a time to gather them: evolution of photosynthesis genes in bacteria." Adv Bot Res. 66: 1-36.
"Though not impossible, it is considered fairly difficult to form peptides abiotically under early-Earth conditions. Thus the rate of prebiotic peptide formation may have been one of the most stringent limiting factors for early evolution." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 98.
"Most notably, an innate ‘polyphosphate-peptide synergy’ may have been instrumental at an early stage of biogenesis. Small peptides, with little regard to side chain composition and even including those rich in glycine, can form tight coordination complexes with metal ions, phosphate groups or iron-sulfur clusters, where the stabilizing ligands are partially encircled by several main-chain contacts with the peptide. Such so-called ‘nest’, ‘niche’ and ‘catgrip’ configurations supposedly represent some of the earliest evolutionarily relevant types of peptide, which still reside at active centers of many ancient enzymes." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 99.
"In the context of mineral-nucleated colloid films and microspheres, originally randomized peptides may have become subject to selection for intra- and intermolecular fit in structurally stabilized configurations, which differentially affected their survival. This formed the structural and functional foundation on which rudimentary peptide catalysis started to evolve, together with various non-peptide cofactors, so as to gradually optimize their catalytic activities supporting the entire system." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. Pp. 99-100.
"Incidentally, the intrinsic reactivity of ribose phosphate derivatives includes the potential of amino acid activation, as it is still used today in ribosomal protein synthesis. This in turn may have had direct repercussions on the rate of prebiotic peptide synthesis. Repeating the preceding argument, emergent tRNAs can thus be understood as more bulky handles for ribose phosphate-activated amino acids as a facile means of making nonribosomal peptide synthesis more efficient, and it now appears possible to bridge the conceptional gap between nonribosomal and ribosomal protein synthesis." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 100.
"In the foregoing it was surmised that coevolution of proteins and RNA commenced from relatively small oligomers with random sequences, some of which happened to interact affinitively and productively. From this platform it seems natural to apply the notion of cross-catalytic and collectively autocatalytic networks to mixed collections of abiotic peptides and oligonucleotides simultaneously." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 101.
"The classical microsphere hypothesis of Fox and Oparin is here extended to mineral-attached confluent composite films, depending on spontaneous microphase separation (or colloid assembly) as a realistic and experimentally demonstrable possibility. This sheet-like spreading naturally connects to the general concept of mineral-associated surface metabolism by adding to the solid-liquid interface a third dimension of very limited extent for further reactivity and the buildup of organic compounds." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 104. References are to: Fox, S.W. 1980. "Metabolic microspheres: origins and evolution." Naturwissenschaften 67: 378-83. Oparin, A. 1965. "The origin of life and the origin of enzymes." Adv Enzymol 27: 347-80. "As modeled and substantiated by computer simulation studies, ‘nonmetabolic replicators’ require rich resources, but these are rapidly outcompeted by ‘metabolic replicators’ in more typical resource-poor environments. It is my conjecture that such metabolic replicators in turn can have evolved from the yet more primitive stage of ‘metabolic accumulators’, as represented by confluent and not regularly dividing composite colloidal films." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 104.
"The fundamental principle of phase-separated colloidal adhesion is here considered together with two supplementary conditions of potential import to life’s emergence: photo-catalyzed organic syntheses at mineral reaction centers and recurrent dehydration cycles – respectively aiding in the retention of photosynthetic organic products close to the site of energy conversion and in the polymerization of mobile subunits into colloidally interacting macromolecules." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 104.
"Presumably, amino acids could be activated for polymerization by certain cofactor-active compounds, ribonucleotides in particular, which may in turn have led directly to a molecular coevolution of proteins and nucleic acids – perhaps the most fundamental pair of co-emergent properties in living matter. An additional supportive spoke conceivably emerged from affinity interaction between lipids and hydrophobic peptides. It is apparent, therefore, that peptides and proteins are positioned most strategically at the center of this self-organizing spinning wheel, ..." Egel, Richard. 2014. "Origins and Emergent Evolution of Life: The Colloid Microsphere Hypothesis Revisited." Orig Life Evol Biosph. 44: 87-110. P. 105.
"The analog of the set of polymers is the set of items encoded in associative memory. The analog of M, the maximum polymer length, is the maximum number of features of an item encoded in memory when one attends that item, and the analog of P the probability of catalysis, is the probability that one thought brings about associative recall of another. So long as exposure to highly similar items or events causes the formation of abstract concepts that connect these instances, an associative memory that meets certain criteria is expected, sooner or later, to reach a critical percolation threshold such that the number of ways of forging associations amongst items in memory increases exponentially faster than the number of items in memory. This is an entropy-minimizing process and the outcome is that the worldview achieves a more stable equilibrium state that has been referred to as conceptual closure. "If the probability of associative recall is low, the network is subcritical. The resulting worldview will tend to be stable but may have difficulty incorporating new information. If the probability of associative recall is high, the network is supra-critical. The resulting worldview will incorporate new information readily but it risks destabilization. In Kauffman’s origin of life model, each polymer was composed of up to a maximum of M monomers, and assigned a low a priori random probability P of catalyzing each reaction. The lower the value of P, the greater M has to be, and vice versa in order for closure to be achieved." Gabora, Liane. 2013. "An evolutionary framework for cultural change: Selectionism versus communal exchange." Physics of Life Reviews. 10: 117-45. P. 133. Reference is to Kauffman, S. 1993. Origins of Order. Oxford University Press.
"Child language is highly context dependent, and, as mentioned, one of the directions of language learning and sophisticating is coming to be able to address broader and broader audiences–to reduce context dependencies. But another direction is to become more and more skilled at making use of contexts, in conversation, discussions, arguments, meetings, community-addressed communications, and so on. That is, one of the directions is to increase the ability to deploy and exploit the natural context sensitivities of language, both those within language itself and those between language and its broader situated contexts." Bickhard, Mark. 2007. "Language as an interaction system." New Ideas in Psychology. 25: 171-87. P. 177.
"All sciences have gone through a historical period in which the basic phenomena have been understood in terms of some sort of substance. This could be in the form of some postulated divisible stuff, or indivisible atoms, or more complex structural units. Virtually all sciences have progressed beyond this phase and realized that the basic phenomena are phenomena of process; fire is no longer modeled as the release of the substance phlogiston, but as a process of combustion; heat is no longer conceptualized in terms of the substance caloric, but as a random kinetic energy; life is no longer rendered in terms of vital fluid, but as complex thermodynamic process; matter is no longer modeled in terms of indivisible atoms, but in terms of organizations of quantum field processes; and so on. "Studies of mental phenomena, however, are still caught in a substance framework. Perception is supposed to be grounded in the transduction of light in the retina into representational elements or vectors; cognition is supposed to be the manipulation or processing of symbolic units or vectors; and language is the encoding of cognitive contents into formally well-formed strings of sound and meaning units. "Substance conceptions are just as inappropriate in the study of mental phenomena as they were in all other sciences but, nevertheless, have remained dominant much longer than in other sciences. The historical shift to process, however, is now underway, even with regard to language, a redoubt of formal atomistic thinking. It is about time." Bickhard, Mark. 2007. "Language as an interaction system." New Ideas in Psychology. 25: 171-87. Pp. 185-6.
"At small body sizes, the diapsids [snakes, lizards, birds] still rule the day and the mammals rule the night, now as in the Cretaceous." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 27.
"‘Natural selection’ for example [as a useful but limited metaphor], is an oxymoron, equivalent to ‘mechanical choice.’ This sort of ‘selection’ does not involve any actual choosing. Likewise, ‘competition’ in evolution involves no competitors and no contests." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 52.
"Everything we know or can infer about early mammals suggests that they were shrew-like creatures that had managed to survive in a reptile-dominated world by becoming diminutive, warm-blooded, largely nocturnal predators that lived and fed in dense cover. They were uniquely suited to this special way of life. Their high internal temperatures gave them an advantage over cold-blooded reptiles during the cool night time hours. Their reliance on senses other than vision in hunting also gave them an edge over the vision-guided diapsids in darkness and shadows." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 73.
"The early mammals faced little competition for their new niche because it was a difficult way of life to maintain, bordering on the physically impossible. A tiny animal finds it hard to sustain a constantly elevated body temperature.... To stay warmer than its surroundings, a shrew has to eat almost continuously around the clock every day of its short, frenzied life." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 73.
"Faced with these allometric problems [conserving heat in small bodies], early mammals were under intense pressure to come up with ways of processing both food and oxygen as rapidly and efficiently as possible. Most of the distinctive peculiarities of mammals originally evolved to serve those ends, either directly or indirectly. It is easy to see the connection when we look at such mammalian features as the diaphragm (to help pump air in and out faster), fur (to minimize heat loss), a four-chambered heart (to prevent the oxygen-rich blood from the lungs from mixing with the oxygen-depleted venous blood coming back to the heart from the rest of the body), and dental occlusion (to speed digestion by slicing and grinding food into smaller bits)." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 73.
"But the upper and lower molar teeth of mammals have reciprocal surfaces that need to fit against each other with precision. If a new molar grew in to replace an old one, it would be of little use until it had erupted into full occlusion. Even when it got there, it would not fit properly at first, because it would lack the ground-down wear surfaces that had developed reciprocally between its predecessor and the teeth opposed it during chewing. "Mammals therefore do not replace their complicated molars, and they replace their other, simpler teeth–incisors, canines, and premolars–only once, if at all." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 74.
"This [laying many eggs to allow for infant mortality] was not an option for early mammals. They were living so close to metabolic bankruptcy that they could not afford to lay a lot of large-yolked eggs at once. Their only recourse was to make a smaller number of eggs and then invest additional energy in each offspring more gradually by helping the hatchling to survive until it grew big enough to survive on its own. "Mammalian motherhood came into existence to address these problems. Early mammals must have laid and incubated their eggs in a protected nest, probably in a burrow in the ground (Burrowing could have evolved out of the reptilian habit of burying the eggs in a shallow hole.)" Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 75.
"Warm-blooded animals face difficulties with respiratory water loss. The air expelled from any animal’s lungs is always saturated with water vapor. Because warm air can hold more water vapor than cool air, a warm-blooded animal loses more water vapor from its lungs in every exhalation. Warm-blooded animals also have high metabolic rates, and thus have to breathe faster than cold-blooded ones. As a result, mammals tend to become dehydrated just by breathing." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. Pp. 76-7.
"Birds, the other group of small warm-blooded vertebrates, have independently come up with their own ways of dealing with some of these problems, evolving four-chambered hearts, high-turnover respiratory apparatus, nest-building and incubation of eggs, fluffy feathers (instead of fur), gizzards (instead of dental occlusion), and maternal feeding of blind, naked babies with insects or regurgitated stomach contents (instead of milk). The independent appearance of such mammal-like traits in birds supports the notion that these features are functionally linked to warm blood and small body size–though both birds and mammals appear to have inherited some of them from larger-bodied synapsid or diapsid ancestors." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 78.
"The combination of shearing, crushing, and grinding functions in a single occlusal package made the tribosphenic molar not only an important evolutionary advance in itself, but also a versatile point of departure for evolving new dietary adaptations." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 79.
"This habit of viviparity or ‘live birth’ has some obvious advantages. It makes eggshells unnecessary, and thus saves the energy and materials that would go into making them. It allows the mother to keep her eggs warm inside her body and protect them from predators 24 hours a day, even while she runs around foraging.... "But retaining the eggs internally poses certain problems. The body of the offspring is foreign tissue, genetically different from that of the mother, and it is likely to be attacked by her immune system if she keeps it inside her too long. An embryo developing inside the mother also faces respiratory problems, since there is not much oxygen available in her oviducts." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 80.
"Compared with other mammals, primates have unusually keen vision. As noted earlier, the ancestral mammals evidently had small eyes and a dim sense of sight. Primates, however, have moved back toward the sharper-eyed reptilian condition, re-evolving large eyeballs, color vision, and mechanisms for focusing the retinal image. The visual centers of the brain are big and complicated in even the most primitive living primates; and in the so-called ‘higher’ primates (monkeys, apes, and humans), they attain levels of size and complexity not achieved by any other mammals." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 84.
"The increase in body size seen in the early Erectines is striking,..." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 261.
"Second, increasing body stature would have yielded benefits in locomotion. Longer limbs result in a longer stride, and increase in stride length allows an animal to cover more ground in a given amount of time." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 262.
"But because our large brains are coupled to small guts, a workable human diet has to center on foods that are both high in energy and relatively easy to digest. And since Erectines appear to have had relatively larger brains and smaller guts than Australopithecus, they must have been eating more of such foods than their predecessors–and probably using new technologies to relieve their guts of some of the work of processing and digesting food. "The skull and teeth of Erectines bear independent witness to this change. Erectine chewing muscles, facial buttresses, and cheek teeth are markedly reduced compared to those of Australopithecus." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 263.
"The loss of body hair and the multiplication of eccrine sweat glands in Homo presumably represent adaptations to increased daytime activity levels in a hot climate." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 264.
"But the role of a diurnal hunter/scaveneger was pretty much there for the taking by early Erectines. The available evidence from comparative anatomy and physiology strongly suggests that they succeeded by meeting the physiological challenges of this diurnal niche." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 265. "Taken together, all these sources of information point to a very inclusive subsistence strategy for ESA [Early Stone Age] Homo, in which new technologies were employed to secure a wide range of food items by hunting, scavenging, gathering, and collecting." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 267.
"From a biological perspective, Homo sapiens is a uniquely generalized species. Generalized species tend to exploit wider geographic and ecological ranges, show more intraspecific variation, and exhibit less of a tendency to branch off new species than do more specialized species, which exploit narrower ecological niches." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 272.
"In a series of papers on Homo erectus, Cachel and Harris suggest that Erectines were such successful colonizers and able to spread so quickly and broadly because they acted as a ‘weed species.’ Plant and animal ‘weeds’ that quickly colonize new regions thrive on environmental disruption caused by a variety of agents, and benefit by moving into vacant niches in regions that lack species with a similar adaptation." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 273. Reference: Cachel, S. & J. Harris. 1998. "The lifeways of Homo erectus inferred from archaeology and evolutionary ecology: A perspective from East Africa." From: Petraglia, M. & R. Korisettar (Eds.) Early Human Behaviour in Global Context. Routledge. Pp. 108-32.
"One curious aspect of the Erectine period in Indonesia is the relative paucity of stone tools." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 277.
"According to W. Loomis, depigmentation of human skin would be a necessity for humans to successfully adapt above 40 N latitude. Above this ‘pigment line,’ which runs through present-day northern Turkey, Greece, Italy and Spain, dark pigmentation would preclude absorption of sufficient UVR. Without adequate dietary sources of vitamin D, dark-skinned humans north of this line would risk all the ills associated with vitamin D deficiency." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 288. Reference: Loomis, W. 1967. "Skin-pigment regulation of vitamin-D biosynthesis in man." Science. 157: 501-6.
Foley suggests that once Homo achieved its status as a broad exploiter of many different sorts of resources, including meat, it was unlikely that the human lineage would speciate extensively. Broad resource exploitation would make later hominins a classic example of a generalized species, and such species show very low rates of speciation. Foley argues that speciation events would have been far less common in Homo than in earlier hominins with narrower ecological niches. This would be especially true in nontropical regions, where speciation rates tend to be reduced for all mammalian lineages. "We suggest that increasing human dependence on culture would also have inhibited speciation–not because culture is an ecological niche, as some theorists have suggested, but precisely because culture is a way of escaping from any ecological niche. By allowing humans to opportunistically exploit any resources that become available, cultural adaptations lead to more encompassing exploitation of all resources and therefore to greater niche breadth–which would be expected to inhibit speciation." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 289. Reference: Foley, R. 1991. "How many species of hominind should there be?" JHE. 20: 413-27.
"Cranial-capacity reduction in recent humans may likewise reflect trends toward smaller and more gracile bodies in post-Pleistocene human populations." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 420.
"In Europe, the first evidence of anatomical modernity is coupled to the first clear signs of modern behavior. But this is not true anywhere else. The earliest anatomically modern specimens in Africa and the Near East occur in cultural contexts that differ little from those associated with earlier, more archaic humans in these areas." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. Pp. 421-2.
"Several geneticists and population biologists have accordingly espoused what is called the ‘Mostly Out of Africa’ model. This model suggests that the majority of human genetic diversity is traceable back to an African root, but that the exceptions noted above provide evidence of non-African contributions to the recent human gene pool." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 468.
"Advocates of both AM [assimilation model] and MRE [multiregional-evolution] hold that local archaic peoples contributed significantly to early modern human populations in various regions of Eurasia. Both resist the assignment of any of these archaic groups, including the Neandertals, to species other than Homo sapiens." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 470.
"Following the initial expansion of modern humans out of Africa, continued gene flow from the larger African populations would be expected to have enforced greater proportions of African genes everywhere else. In time, continuing gene flow out of Africa could have produced a genetic picture indistinguishable from one of near-total population replacement." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 474.
"...a ‘chemistry conservation principle’: the chemical traits of organisms are more conservative than the changing environment and hence retain information about ancient environmental conditions. Chemistry conservation is manifest, for example, in the highly reduced state of the cell interior even in those organisms that dwell in oxygenated habitats." Mulkidjanian, Armen, A. Bychkov, D. Dibrova, M. Galperin, & E. Koonin. 2012. "Origin of first cells at terrestrial, anoxic geothermal fields." PNAS. Feb 13, 2012: E821-E830. P. E821.
“Hence a major
conundrum:
"The absence of any enzymes related to autotrophy in the ubiquitous protein set suggests that the protocells were heterotrophs, i.e., their growth depended on the supply of abiotically produced organic compounds." Mulkidjanian, Armen, A. Bychkov, D. Dibrova, M. Galperin, & E. Koonin. 2012. "Origin of first cells at terrestrial, anoxic geothermal fields." PNAS. Feb 13, 2012: E821-E830. P. E825.
"... a 5mm layer of ZnS-containing precipitates would give the same UV protection as a greater than 100 m water column.... Hence, a stratified system could be established within geothermal ponds, where the illuminated upper layers would be involved in the ‘harvesting’ and production of reduced organic compounds, whereas the deeper, less productive but better protected layers could provide shelter for the protocells." Mulkidjanian, Armen, A. Bychkov, D. Dibrova, M. Galperin, & E. Koonin. 2012. "Origin of first cells at terrestrial, anoxic geothermal fields." PNAS. Feb 13, 2012: E821-E830. P. E826.
"Remaining almost independent of the ambient climate, inland geothermal fields could exist for millions of years, long enough to serve as incubators not only for the protocells but also for the preceding life forms." Mulkidjanian, Armen, A. Bychkov, D. Dibrova, M. Galperin, & E. Koonin. 2012. "Origin of first cells at terrestrial, anoxic geothermal fields." PNAS. Feb 13, 2012: E821-E830. P. E826.
"The dramatic difference between the ionic compositions of the cytosol and seawater implies that cellular organisms could invade the ocean only after the emergence of ion-tight membranes." Mulkidjanian, Armen, A. Bychkov, D. Dibrova, M. Galperin, & E. Koonin. 2012. "Origin of first cells at terrestrial, anoxic geothermal fields." PNAS. Feb 13, 2012: E821-E830. P. E827.
"The two most important and successful mechanistic, reductionist approaches to living systems are molecular biology and non-equilibrium thermodynamics.... Prigogine, Eigen, Kauffman, and others have noted that all self-ordering systems are internally coupled. What none of these theoreticians have explained is what gives rise to the coupling." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 448.
"Physicists, chemists, and biologists often use this term [system] in very different ways, depending on whether they are looking at the thermodynamic, structural, or functional properties of an ensemble.... Weiss suggests that a system is an aggregate of components, the interactions of which can be characterized by what he calls ‘variance’. By variance, Weiss means the range of possible states that the components of the system could take on. We define system as an aggregate of components in which the variance of the features of the whole collective (Vs) is significantly less than the sum of the variances of its independent constituents (Va, Vb, Vc...Vn) and significantly greater than zero: 0<<Vs<<sum (Va+Vb+Vc+...Vn) In other words, systems must be able to vary (Vs>>0) in order to perform a function but, as Weiss says, ‘the basic characteristic of a system is its essential invariance beyond the much more variant flux and fluctuations of its elements or constituents.’" Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 451. Reference: Weiss, P. 1970. Life, Order, and Understanding: A Theme in Three Variations. University of Texas Press.
"We define complementarity as non-random, reversible coupling of the components of a system.... Molecular complementarity refers specifically to non-random, non-covalent interaction between molecules. Thus, van der Waals forces, hydrogen bonds, pi-pi stacking bonds, ionic bonds, charge-transfer complexes, and similar reversible chemical interactions can all be involved in molecular complementarity. Higher order levels of complementarity are also possible in living systems; cell organelles, cells, tissues, organs, and organisms all couple non-randomly. One can even think of symbiosis as being complementarity between organisms, and ecological niches as being complementarity between environment and organism.... "Complementarity is what leads to the reduction in variance in an aggregate of components that defines their interactions as a system." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 452.
"A hierarchy is defined following Simon, Pattee and Weiss to exist within a system when it is possible to ignore the properties of individual elements of some subset of the system in favour of an aggregate property or measure. To take an extremely simple example, every atom has kinetic energy, but no single atom has the property of temperature." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 452. References: Simon, H. 1981. The Sciences of the Artificial. MIT Press. Pattee, H. 1973. "The physical basis and origin of hierarchical control." Pp. 71-108. From Pattee, H (Ed.). Hierarchy Theory: The Challenge of Complex Systems. George Braziller. Weiss, P. 1971. Hierarchically Organized Systems in Theory and Practice. Hafner.
"We use the term coupling to mean the non-random linking of two or more processes. Careful consideration of the concept of coupling reveals that there are four basic types: (1) thermodynamic coupling, in which two or more energy processes are linked; (2) physical coupling, in which two or more mechanisms or objects are linked; (3) conversion coupling, in which one or more mechanisms are linked to a thermodynamic process in order to convert energy to work; and (4) transformational coupling, in which energy is used either to make or break molecular (or higher order) structures. "All four forms of coupling are found in living systems. For example, thermodynamic coupling occurs when the energy in sunlight is converted to chemical bond energy. Physical coupling is apparent within the structure of DNA, its transcription into RNA, and translation into protein, thereby allowing the storage, replication and translation of genetic information. Conversion coupling is evident in the active transport of ions. And transformational coupling occurs when ATP is broken down into ADP to release energy used to catalyse the synthesis of a protein." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 453. "We stress that complementary systems are a subset of all possible coupled systems, in which non-random interaction of the parts of the system are essential to the coupled process(es). For example, molecular complementarity plays fundamental roles in thermodynamic processes such as catalysis; in physical coupling, such as DNA structure, replication, and transcription; in conversion coupling, as in channelling within mitochondrial energy systems; and in transformational coupling, as in the synthesis of proteins. It is possible, however, to imagine different types of non-reversible couplings, such as those found between the gears of a clock, or the transformation of egg proteins by heating in a pan, that do not have the useful characteristics necessary to life." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. Pp. 453-4.
"For the moment, we will simply note that we consider a sperm that never inseminates an egg, terminally differentiated neurons, and sterile human beings to be living systems. The evolutionary advantages of systems that can replicate are obvious, but that should not blind us to the fact that such advantages need not be a prerequisite either to the origins or definition of life." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 454.
"If we have an open non-equilibrium system composed of any set or subset of ‘buttons’ (chemicals) and all possible threads (chemical interactions and reactions) that can chemically exist between them, then we will find that any type of coupling process (most especially molecular complementarity) will allow only a subset of buttons to be linked. Of all of the linked-button sub-assemblies, those that are (1) most strongly coupled and (2) most capable of making further linkages to other sub-assemblies will, through the sub-assembly formation described by Simon, eventually undergo the transformation to a super-cluster of reaction-interaction processes (i.e. they will form a ‘watch’)." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 456. Reference: Simon, H. 1981. The Sciences of the Artificial. MIT Press.
"In short, coupling in the form of complementarity is the form in which natural selection was first manifested in nature." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 456.
"One need not assume,... that the system is either physically closed (in terms of its components) or that linkages form randomly between the components of the system, for a self-assembling system to evolve. To the contrary, it is more reasonable to assume that the system is open not only thermodynamically but structurally as well; that some components of the system can interact (and remain localized and stabilized in both time and space) and some cannot; and that some will form sub-assemblies having new, emergent properties or hierarchical organizations, while others will not. Molecular (and higher order) complementarity provides a mechanism for doing just these things." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 457.
"Modular evolution in turn alters the picture we have of evolution. The standard model results in tree or bush-like structures representing divergence from a single, functional precursor. A system driven purely by the assembly of complementary modules, on the other hand, would result in an inverted tree or bush-like structure. Evolutionary trees and assembly trees are, in many ways, inversions of one another. The evolutionary tree begins with a functional precursor; the assembly tree results in one. The evolutionary tree diverges; the assembly tree converges." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 458.
"If for example, every duplex could interact with monomers, and every triplex with every duplex and every monomer, and so forth, there would obviously be a combinatorial explosion. The problem of dealing with all of the possible ways of putting together a system of a large set of monomers becomes overwhelming. If, however, there is specificity of interaction at every level of interaction, huge sets of possibilities are once again eliminated. If duplexes can only bind up a very small proportion of monomers, triplexes only a handful of duplexes and monomers, etc., then the number of possible outcomes for the system remains relatively small. The specificity intrinsic in molecular complementarity thus represents a constant mechanism for winnowing viable, functional interactions from the astronomically large number of interactions that would be possible if any molecule could interact functionally with any other." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 461.
"Eliminating possibilities, however, requires us to recognize the ‘negative space’ between the branches or the ‘holes’ in the network that one does not see in order to ‘observe’ the choices that are not available.... "The recognition that the ‘negative space’ in evolutionary and developmental trees represents non-viable ‘space’ leads necessarily to the conclusion that evolution is not a random process. All possible random choices are not available." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 461.
"The simplest test of the theory is that virtually all components of living systems will be multiply- and specifically interactive with other components. One cannot look at current work in any area of molecular biology or biochemistry, ranging from virus self-assembly to second-messenger systems and transcription control mechanisms to metabolite channelling, without noting the correctness of this prediction. Specific intermolecular binding often resulting in relatively complex aggregates is the rule, not the exception in living systems. "We stress the unexpectedness of this observation. There is no theory, and no set of observations that pre-dates the molecular biology revolution, that would have led (or did lead) any scientist to predict the incredibly high degree of physico-chemical integration or complex ordering that occurs between the molecular components of living systems. For much of this century, protoplasm was considered to be an unorganized colloidal mixture of components. Biochemical pathways were linear or cyclical affairs composed solely of enzyme-substrate interactions." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 469.
"The solubility of molecular complexes differs markedly from the solubility of the individual components. For example, insulin and glucagon are both virtually insoluble in aqueous solution at pH 7. They are physiologically useless unless they bind to a carrier molecule. The insulin-glucagon complex, however, is substantially more soluble than the individual components. The insulin-glucagon example is once again simply one instance of a more general principle: Complexation alters the physico-chemical properties of the molecular components taking part in the complex, and in order for living systems to take advantage of these novel properties, the molecules forming the complex must be co-localized anatomically." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 472.
"In short, molecular complementarity leads to complexes with chemical and physiological properties substantially different than those found in the individual molecules that comprise the complex." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 473.
"We maintain that living things are less than the sum of their parts because complementarity reduces the possible states a system can achieve thereby making possible the harnessing of free energy fluxes into ordered sets of functions." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 476.
"Because complementarity is necessary for system formation and selects among possible components, complementarity itself becomes one of the driving forces of evolution, and perhaps the primordial manifestation of natural selection itself." Root-Bernstein, Robert & P. Dillon. 1997. "Molecular Complementarity I: the Complementarity Theory of the Origin and Evolution of Life." Journal of Theoretical Biology. 188: 447-479. P. 476.
"We cannot expect to explain cellular evolution if we stay locked into the classical Darwinian mode of thinking." Woese, Carl. 2002. "On the evolution of cells." PNAS. V. 99. No. 13. Pp. 8742-7. P. 8742.
"The central question posed by the universal tree is the nature of the entity (or state) represented by its root, the fount of all extant life. Herein lies the door to the murky realm of cellular evolution." Woese, Carl. 2002. "On the evolution of cells." PNAS. V. 99. No. 13. Pp. 8742-7. P. 8742.
"Cellular componentry can be roughly classified according to the degree to which it is connected to the rest of the cell. Loosely connected, or modular, elements define one extreme of the spectrum. Such components tend to be largely self-defining in their structure/function, interacting minimally with other elements in the cell, and are, therefore, obvious candidates for horizontal gene displacement by alien homologs. At the other extreme are the tightly coupled elements, which have extensive, specific, and constraining physical and chemical ties to others of the cellular componentry and, therefore, could seldom, if ever, be sufficiently mimicked by an alien homolog to be displaced by it. The remarkable difference between the HGT profiles of the aminoacyl-tRNA synthetases and others of the translation componentry is thus explained by the loosely coupled, modular nature of the former and the tightly coupled nature of the latter." Woese, Carl. 2002. "On the evolution of cells." PNAS. V. 99. No. 13. Pp. 8742-7. Pp. 8743-4.
"The difficulty with the classical Darwinian outlook, as Alfred North Whitehead long ago pointed out, is that it sees evolution as a ‘procession of forms,’ when the focus should instead be on the process that produces them–on the gem, not the reflections from its facets." Woese, Carl. 2002. "On the evolution of cells." PNAS. V. 99. No. 13. Pp. 8742-7. P. 8745. Reference: Whitehead, Alfred. 1929. Process and Reality. Collier-Macmillan.
"The Mirror System Hypothesis (MSH) proposes that this primitive action-matching system underwent successive evolutionary modifications to support imitation, pantomine, manual ‘protosign’ and ultimately vocal language, thus providing a neural underpinning for ‘gestural hypotheses’ of language origins. The MSH does not specify the evolutionary pressures leading these adaptations, but the specific response of monkey F5 and human Broca’s area to hand-object interactions, the predominance of object manipulation and tool-use behaviours among putative learning, and the importance of complementary gesture and speech in the human transfer of tool skills are all directly compatible with earlier hypotheses identifying the transmission and coordination of tool use as a likely context for the evolution of intentional communication and language." Stout, Dietrich & T. Chaminade. 2012. "Stone tools, language and the brain in human evolution." Philosophical Transactions of the Royal Society: B. 367: 75-87. P. 76.
"The archaeologically attested ability of Late Acheulean hominins to implement hierarchically complex, multi-stage action sequences during handaxe production thus provides evidence of cognitive control processes that are computationally and anatomically similar to some of those involved in modern human discourse-level language processing. This provides a second behaviourally and chronologically grounded functional/anatomical link between technological and linguistic capacities, further extending the plausible context for co-evolutionary interactions (e.g. behavioural, developmental and/or evolutionary co-option)." Stout, Dietrich & T. Chaminade. 2012. "Stone tools, language and the brain in human evolution." Philosophical Transactions of the Royal Society: B. 367: 75-87. P. 81.
"Accumulating evidence is increasingly supportive of technological hypotheses of language origins, and goes a long way towards allaying concerns that the similarity in the hierarchical, combinatorial organization of the two domains is a superficial one or that the ‘imitative’ learning of toolmaking skills is fundamentally distinct from intentional communication. In particular, evidence of intention attribution during the observation of stone toolmaking provides support for a ‘technological pedagogy’ hypothesis, which proposes that intentional pedagogical demonstration could have provided an adequate scaffold for the evolution of intentional vocal communication. This hypothesis is consistent with the widespread view that increasing reliance on social learning and pedagogy was a key factor in hominin brain and cognitive evolution and removes one of the major motivations for positing a transitional pantomine stage as seen in current formulations of the MSH." Stout, Dietrich & T. Chaminade. 2012. "Stone tools, language and the brain in human evolution." Philosophical Transactions of the Royal Society: B. 367: 75-87. P. 82.
"We would contend that at early stages in cellular evolution, ambiguous translation was tolerated (there being no alternative) and was an important and essential part of the evolutionary dynamic. What we imply by ambiguity here is inherent in the concept of group codon assignments, where a group of related codons is assigned as a whole to a corresponding group of related amino acids. From this flows the concept of a ‘statistical protein,’ wherein a given gene can be translated not into a unique protein but instead into a family of related protein sequences." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10696.
"Thus, we may speculate that the emergence of life should best be viewed in three phases, distinguished by the nature of their evolutionary dynamics. In the first phase, treated in the present article, life was very robust to ambiguity, but there was no fully unified innovation-sharing protocol. The ambiguity in this stage led inexorably to a dynamic from which a universal and optimized innovation-sharing protocol emerged, through a cooperative mechanism. In the second phase, the community rapidly developed complexity through the frictionless exchange of novelty enabled by the genetic code, a dynamic we recognize to be patently Lamarckian. With the increasing level of complexity there arose necessarily a lower tolerance of ambiguity, leading finally to a transition to a state wherein communal dynamics had to be suppressed and refinement superseded innovation. This Darwinian transition led to the third phase, which was dominated by vertical descent and characterized by the slow and tempered accumulation of complexity." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10697.
"Here, we present an alternative; the universality of the genetic code is a genetic consequence of the communal evolution of early life. HGT [horizontal gene transfer] of protein coding regions and HGT of translational components ensures the emergence of clusters of similar codes and compatible translational machineries. Different clusters compete for niches, and because of the benefits of the communal evolution, the only stable solution of the cluster dynamics is universality. Within clusters, concerted optimization of codes is possible. These mechanisms are consistent with two macroevolutionary scenarios. (i) The code stayed nearly universal at all times. (ii) The codes diverged at first but then gradually became universal." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10697.
"One of the advantages of communal evolution is that universally good traits and refinements can spread through HGT to organisms occupying different niches, preserving their diversity. In a world increasingly dominated by protein, most innovations would involve them, and correspondingly HGT will be most effective between organisms having the same genetic code. In this way, the organisms sort into communities sharing related genetic codes." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10697.
"The larger the community and diversity of organisms sharing sufficiently related genetic codes, the larger the pool of protein innovations accessible to everyone. This leads to faster evolution among the larger communities than the smaller ones and therefore a greater potential to invade niches occupied by organisms with different incompatible genetic codes. With this dynamics larger communities will tend to become even larger at the expense of smaller ones." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10697.
"On the long scale, the direction of change is to reduce ambiguity, but on the short scale, the code must be able to tolerate a greater level of ambiguity while ingesting new genes." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10698.
"With this work, we have revisited the largely overlooked problem of genetic code universality and the conceptual difficulties associated with it. These difficulties can all be avoided if one takes, as we do, the stance that evolution was essentially communal from the very beginning. We have argued that there are three distinct stages of evolution, which we might classify as (i) weak communal evolution, which gave way via development of an innovation-sharing protocol and the emergence of a universal genetic code to (ii) strong communal evolution, which developed exponential complexity of genes, finally leading via the Darwinian transition to (iii) individual evolution–vertical, and so, Darwinian." Vetsigian, Kalin, C. Woese & N. Goldenfeld. 2006. "Collective evolution and the genetic code." PNAS. V. 103. No. 28. Pp. 10696-10701. P. 10701.
"In dynamic networks, not only do strategies evolve but also the network topology is under evolutionary selection pressure. Recent theoretical work shows that such co-evolution of behaviour and network structure favours the evolution of cooperation. In particular, the ‘active-linking’ models of Pacheco et al. Show that when individuals playing prisoner’s dilemma are allowed to control their interactions, i.e. to break existing links and to form new links with random partners, cooperation evolves." Fehl, Katrin, D. Van der Post & D. Semmann. 2011. "Co-evolution of behaviour and social network structure promotes human cooperation." Ecology Letters. 14: 546-551. P. 546. Reference: Pacheco, J., A. Traulsen, H. Ohtsuki & M. Nowak. 2008. "Repeated games and direct reciprocity under active linking." J. Theor. Biol. 250: 723-31.
"Hence, utterance-activity rises from our bodily experiences and emotions, our actions, activities and interpersonal relations. With Love and Thibault, we can refer to the lived activity as first-order languaging, i.e. ‘Whole-body sense-making activity that enables persons to engage with each other in forms of coaction and to integrate themselves with and to take part in social activities that may be performed either solo or together with other agents’. In contrast, ‘what most people, including linguists, think of as language’ is second-order language, i.e. ‘Stabilized cultural patterns on longer, slower cultural timescales’. These lexicogrammatical patterns function as attractors for our first-order languaging, and they are hence ‘integrated with the first-order dynamics in ways that facilitate coordination between persons and between persons and aspects of their worlds and interpretation.’" Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 42. References: Love, N. 1990. "The locus of language in a redefined linguistics." In: Davis, H.C. & T. Taylor (Eds). Redefining Linguistics. Routledge. Thibault, P. 2011. "First order languaging dynamics and second-order language: the distributed language view." Ecological Psychology. 23 (3) 210-245. Subquotes from Thibault.
"Thus, any natural fractal defines a range of timescales where the same organizing principle is operating. We refer to such a ‘range of timescales’ as a temporal range. Accordingly, the extension of the temporal range (i.e. the section of nested timescales comprised by the temporal range) is determined by an organizing principle.... "What this model illustrates is that with each additional organizing principle, the temporal range is narrower (i.e. it comprises fewer timescales) and more complex (i.e. it is governed by more organizing principles)." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 44.
"In general, each emergent temporal range presupposes the previous one(s), and it defines a domain within which processes are more complex because they abide a higher number of organizing principles. Unsurprisingly, complexity is thus the order parameter of evolution. In other words, the increasingly narrowing of the temporal range entails still more complex (physical, biological and behavioral) processes to be observed, i.e. processes with a higher degree of variability, because they are increasingly unconstrained by very slow and very fast timescales." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 45.
"While the traditions of ethnomethodology and Conversation Analysis limit themselves to the microsocial timescale by using as a methodological criterion how participants orient to what happens in the interaction, newer developments in applied CA widen the perspective by showing how interaction is part of situated events. The same focus is also found in dialogism and in distributed approaches, e.g. in Cognitive Event Analysis. These traditions also edge towards the social systems timescale, for instance by demonstrating how real-time data play out stabilized interaction patterns that can be described as genres or Communicative Activity Types, e.g. doctor-patient interaction. Below these timescales, we find the bodily aspects of real-time interaction (gesturing, facial expressions, etc.)." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 47.
"From Bianka’s and Uryu’s statements [discourse examples], it is clear that intercultural interaction is channeled by pre-existing discourses that are very much out of our control. The feeling of disorientation and helplessness that Bianka describes upon being interpellated by the word Nazi, even though it was applied to the Pope and not to her, makes palpable the incommensurable gap between interlocutors from different linguistic and cultural backgrounds due to the condensed historicity of words.... One thing is certain: the use of a common language, here English, is no guarantee that the speakers’ words have the same value nor that the contexts evoked by these words are the same. As Judith Butler argues, speakers are responsible for the words they use but they are not necessarily the authors of these words:..." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 54. Reference: Butler, Judith. 1997. Excitable Speech: The Politics of the Performative. Routledge. "Both the German and the Japanese interlocutors were trapped in the ‘linguistic vulnerability’ that the word evoked. As Butler argued, language itself had acquired an ‘agency’ against which speakers felt ‘helpless’ or felt they had to perform a certain expected helplessness." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 55. Reference: Butler, Judith. 1997. Excitable Speech: The Politics of the Performative. Routledge.
"This body of work has taught us that personal identity is not determined by an essential core in the single individual, but rather negotiated in the course of the dialog: identity is an interactional phenomenon, not a discourse-external one. This is also at the core of an ecological understanding of identity: "However, an ecological approach takes the non-essentialist approach one step further than the various constructivist schools, as it considers the constructivist approach to be equally reductionist, because it restricts its scope to one particular timescale, i.e. that of the unfolding interaction." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. Pp. 55-6. Subquote: Kramsch, C. & S. Steffensen. 2008. "Ecological perspectives on second language acquisition and socialization." In: Hornberger, N. & P. Duff (Eds). Encyclopedia of Language and Education, Language and Socialization, vol. 8. Springer Verlag.
"In treating identity as, for instance, a matter of being Japanese, Russian or German, the former [essentialist position] has singled out a cultural timescale as the determining one, while the latter [constructivist position] has singled out the microsocial timescale by claiming that identity is solely interactionally constructed. "In an ecological approach, interaction is not merely unfolding on a microsocial timescale, and it does not constitute a situation that can be isolated from trans-situational characteristics. Accordingly, the participants do not find themselves ‘in’ a self-contained situation where the members ‘on the inside’ autonomously co-construct their identities. Rather, the interaction is an open system, where the participants depend on the dialogical system’s environment. The environment does not determine the identity of the participants, but it offers specific affordances that make certain identities more available than others. The implication of this view is that identity is neither stable nor constructed, but emergent. And the emergence of identity is determined by identity attractors on many timescales." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 56.
"In a sense, these data are a vivid illustration of Bakhtin’s statement that ‘Language is populated – overpopulated – with the intentions of others.’" Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 56. Subquote: Bakhtin, M. 1981. The Dialogic Imagination: Four Essays. U. of Texas Press. P. 294.
"If intercultural interaction attempts to open up the domain of the sayable across different discourse traditions, it also opens up speaking subjects to unpredictable selves." Uryu, Michiko, S. Steffensen & C. Kramsch. 2014. "The ecology of intercultural interaction: timescales, temporal ranges and identity dynamics." Language Sciences. 41: 41-59. P. 58.
"Halliday started off the discipline of ecolinguistics not by analysing the language of the environmental movement but instead by investigating aspects of grammar which he claims ‘conspire ... to construe reality in a certain way ... that is no longer good for our health as a species’. The first aspect he describes is that mass nouns like soil and water are unbounded and do not therefore reflect the limited supply of such essential resources; the second is that antonymic pairs have a positive (unmarked) pole which means that ‘bigger’ is aligned with ‘better’; the third is that humans tend to be given more agency in grammar than other species; the fourth is that pronoun use and mental processes divide the world falsely into conscious beings (humans and to some extent their pets) and non-conscious beings (other species). Chalwa likewise claims that ‘the language habits of fragmenting the mass, quantifying intangibles and imaginary nouns, and perceiving time in terms of past, present and future are factors in our inability to perceive the natural environment holistically’." Alexander, Richard & A. Stibbe. 2014. "From the analysis of ecological discourse to the ecological analysis of discourse." Language Sciences. 41: 104-10. P. 108. References: Halliday, M. 1990. "New ways of meaning. A challenge to applied linguistics." Journal of Applied Linguistics. 6: 7-36. Chalwa, S. 1991. "Linguistic and philosophical roots of our environmental crisis." Environmental Ethics. 13(3), 253-73.
"In that sense emotions are part of a human-environment system. They are part of our ecology as properties of whole situations, including individuals and environmental structures." Jensen, Thomas. 2014. "Emotion in languaging: languaging as affective, adaptive, and flexible behavior in social interaction." Frontiers in Psychology. Vol. 5. Art. 720. 1-14. P. 3.
"... one way to define languaging behavior more precisely is to see it as coordinated actions constrained by second order patterns." Jensen, Thomas. 2014. "Emotion in languaging: languaging as affective, adaptive, and flexible behavior in social interaction." Frontiers in Psychology. Vol. 5. Art. 720. 1-14. P. 12.
"Fifty years ago at the dawn of the molecular biology revolution, unprecedented enthusiasm was generated by the idea that biology was finally reduced to chemistry and consequently, the proposed way to understand organisms was to study them from the bottom up. Central to this view was genetic determinism, i.e. the perception that the organism was determined by a genetic program. The origin of systems biology, in contrast, attributed to von Bertalanffy, a biologist and philosopher, and Paul Alfred Weiss, a biologist, emphasized an organicist view where both bottom-up and top-down causation are considered. These two opposed views are represented by two discrete approaches in a new version of the systems biology discipline. O’Malley and Dupre call the genetic approach ‘pragmatic systems biology,’ which is centered around large-scale molecular interactions, such as gene networks, while the organicist approach, called ‘systems-theoretic biology’, is centered on system principles. The differences between both approaches are not technical but rather philosophical, given that both are committed to mathematical modeling." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 165. Reference: O’Malley, M. & J. Dupre. 2005. "Fundamental issues in systems biology." Bioessays. 27:1270-6.
"A main obstacle to the success of reductionism is the historicity of the organism, i.e. evolution and ontogeny." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 166.
"The upward causation assumption completely neglects the contribution of the environment and of the emergent structure itself (by downward causation)." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 168.
"Other network topologies emerge also naturally not showing small world properties. One prominent example is a road network connecting cities. In this case, each node is not only a point but has a certain size, cannot freely move and roads themselves (or edges) are restricted by the topographic and geological settings. This implies that having spatial constraints limiting the dynamic construction process can yield different network topologies. Therefore, it seems important to include spatial localization information when building gene regulatory networks or protein-protein interaction maps given that a substance can only react with another substance when both reside in the same spatial compartment." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 168.
"As physical laws rule the interactions between the parts in physical systems, we can exclude alternative explanations of pattern formation that require intervention from outside the system, such as (I) the presence of a leader, (ii) the existence of a blueprint, (iii) the execution of a recipe, or (iv) the use of a template. Although (i)-(iv) are relevant to biological systems, self-organization is certainly an option when it comes to explaining biological pattern formation where ‘the rules in self-organizing systems can be quite economical in the physiological and behavioral machinery needed to implement them’. This simplicity might give self-organization an evolutionary advantage over the alternative solutions (i)-(iv), making it more prevalent in biological systems. Having said this, it is certainly possible that a mixture of these mechanisms is present in the same system." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 168. Subquote from: Camazine, S., J. Deneubourg, N. Franks, J. Sneyd, G. Theraulaz & E. Bonabeau. 2001. Self-Organization in biological systems. Princeton University Press. P. 63.
"Since cells can only sense their local environment, the emergence of tissues can only be driven by rules governed by coordinated interactions with the local environment of each cell. This leads to the conclusion that the dynamic process of tissue formation must mainly be governed by self-organization." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 169.
"An example of a prominent parameter that causes quite controversial debates among biologists relates to cell proliferation. For a modeler, the default modus operandi of a cell can be both, proliferation or quiescence. To increase cell proliferation rates, a modeler either reduces the concentration of an inhibiting substance where proliferation is seen as the cell’s default or increases the concentration of a stimulating substance where quiescence is seen as default. Both models will yield the same qualitative behavior in their respective simulation, whereas the biological ‘truth’ is very likely to be reflected by only one of both scenarios. Unless such substance is directly found in the experiment itself, both modeling assumptions have to be seen as equivalent and undistinguishable as both models validate the same experimental observations (please note that indirect and intermediate processes might make it experimentally difficult to unequivocally discriminate between inhibitory and stimulating substances)." Saetzler, K., C. Sonnenshein & A. Soto. 2011. "Systems biology beyond networks: Generating order from disorder through self-organization." Seminars in Cancer Biology. 21: 165-174. P. 172.
"There is a general reason why Occam’s razor should be expected to fail as a paradigm for distinguishing between right and wrong theories: complexity is favored over simplicity by the second law of thermodynamics." Westerhoff, Hans, C. Winder, H. Messiha, E. Simeonidis, M. Adamczyk, M. Verma, F. Bruggerman & W. Dunn. 2009. "Systems Biology: The elements and principles of Life." FEBS Letters. 583: 3882-90. P. 3885.
"In a similar vein, just as much as there is a subliminal sentiment that solutions should be as simple as possible, there is a sentiment that if nature has a great many solutions to any particular problem, then it will try them all. Thereby multiplicity and diversity, which is one form of complexity and almost the opposite of Occam’s simplicity, is the rule." Westerhoff, Hans, C. Winder, H. Messiha, E. Simeonidis, M. Adamczyk, M. Verma, F. Bruggerman & W. Dunn. 2009. "Systems Biology: The elements and principles of Life." FEBS Letters. 583: 3882-90. P. 3885.
"Bottom-up Systems Biology is championing this hypothesis-driven part of biology, whereas top-down Systems Biology is engaging more in the empirical aspects.... "The aim of Systems Biology is to combine the two aspects in non-linear, synergistic ways. A spiral, inducing hypotheses from top-down Systems Biology, and testing them in a bottom-up fashion, followed by broader validation of more precise forms of the hypotheses in the top down arena, etc. should be an immensely powerful strategy." Westerhoff, Hans, C. Winder, H. Messiha, E. Simeonidis, M. Adamczyk, M. Verma, F. Bruggerman & W. Dunn. 2009. "Systems Biology: The elements and principles of Life." FEBS Letters. 583: 3882-90. P. 3887.
"The synergetic [synergistic] process accompanying molecular formation is thus accomplished through electron sharing among the constitutive atoms, thereby constraining some atomic properties together with a concurrent emergence of molecular properties. "Such constraints on properties have been recognized not only in molecules, but at all levels of complexity in nature, and they have been termed dissolvence to contrast this phenomenon with emergence." Testa, Bernard & A. Bojarski. 2000. "Molecules as complex adaptive systems: constrained molecular properties and their biochemical significance." European Journal of Pharmaceutical Sciences. 11 Supplement 2: S3-S14. P. S4.
"To this end, we consider molecular form (geometrical structure), molecular function (observable properties resulting from interaction with a probe) and molecular fluctuation (dynamics). Fluctuation is defined as the ensemble of all possible probabilistic changes a molecule can undergo in form and function. Here, it is important to explicate that fluctuation does not cover an almost unlimited time frame, but that each complex system has its own frequency range in which it fluctuates. From the hierarchy of dynamical time scales and the hierarchy of frequencies, there appears to be a consensus that an association exists between levels of complexity and the time scales in which complex systems operate. In other words, small systems at low levels of complexity have high frequencies of fluctuation, whereas large systems at high levels of complexity fluctuate over long periods." Testa, Bernard & A. Bojarski. 2000. "Molecules as complex adaptive systems: constrained molecular properties and their biochemical significance." European Journal of Pharmaceutical Sciences. 11 Supplement 2: S3-S14. Pp. S4-S5.
"... the three-dimensional interplay between cells and ECM [extracellular matrix] provides the environmental constraints shaping cells and tissue in their specific related ‘forms.’ Shape can therefore be considered the spatial geometric configuration acquired as a result of the integrated set of cellular and environmental cues participating in biological functions control. As a consequence, measurable parameters describing shape could be considered as ‘omics’ descriptors of the specific level of observation represented by the cell-stroma system." Dinicola, Simona, F. D’Anselmi, A. Pasqualato, S. Proietti, E. Lisi, A. Cucina & M. Bizzarri. 2011. "A Systems Biology Approach to Cancer: Fractals, Attractors, and Nonlinear Dynamics." OMICS A Journal of Integrative Biology. V. 15, No. 3. Pp. 93-104. P. 95.
"Indeed, shapes and structures of cells and tissues are as diverse as the functions ascribed to them. A long time ago, a clear-cut link between cell geometry and cell function was established by means of simple morphological observations. Numerous cellular behaviors in culture, including proliferation, apoptosis, lamellipodial extension, glucose metabolism, RNA processing, differentiation, epithelial-mesenchymal transition, and stem cell fate have been found to be determined by cellular geometry." Dinicola, Simona, F. D’Anselmi, A. Pasqualato, S. Proietti, E. Lisi, A. Cucina & M. Bizzarri. 2011. "A Systems Biology Approach to Cancer: Fractals, Attractors, and Nonlinear Dynamics." OMICS A Journal of Integrative Biology. V. 15, No. 3. Pp. 93-104. P. 96.
"In the case of protein structures, the number of folds is much lower than that expected when referring to the transfinite number of possible dispositions of N residues in space; different sequences may give rise to the same fold. This implies some sort of ‘energy minimization’ drastically constraining the number of allowable stable states, with the consequent onset of preferred stable states (attractors)." Dinicola, Simona, F. D’Anselmi, A. Pasqualato, S. Proietti, E. Lisi, A. Cucina & M. Bizzarri. 2011. "A Systems Biology Approach to Cancer: Fractals, Attractors, and Nonlinear Dynamics." OMICS A Journal of Integrative Biology. V. 15, No. 3. Pp. 93-104. P. 97.
"In nonequilibrium systems, the fractal attractor is a common feature because of the dissipative character of these systems. The information dimension can then be used to determine the number of undamped dynamical variables that are active in the motion of the system; this means that dimension is something related to the number of degrees of freedom of the system.... "The system is attracted to a lower dimensional phase space, and the dimension of this reduced phase space represents the number of active degrees of freedom in the self-organized system." Dinicola, Simona, F. D’Anselmi, A. Pasqualato, S. Proietti, E. Lisi, A. Cucina & M. Bizzarri. 2011. "A Systems Biology Approach to Cancer: Fractals, Attractors, and Nonlinear Dynamics." OMICS A Journal of Integrative Biology. V. 15, No. 3. Pp. 93-104. P. 98.
"Although these static representations [network theory] can provide some insight into general architectural principles, they lack two fundamental characteristics displayed by many complex systems. The first is the dynamical nature of the components and interactions that embody a particular function, and the second is evolution of the underlying network topology and form of component dynamics." Gorochowski, Thomas, M. Di Bernardo & C. Grierson. 2011. "Evolving Dynamical Networks: A Formalism for Describing Complex Systems." Complexity. V. 17, N. 3. Pp. 18-25. P. 18.
"In most cases dynamics and evolution are considered in isolation. Unfortunately for most systems this is not the case, with network topology, dynamics, and evolution all affecting one [an]other. For example, the network topology of a system will constrain any dynamics taking place over it, while evolution of this structure is influenced by these same dynamics." Gorochowski, Thomas, M. Di Bernardo & C. Grierson. 2011. "Evolving Dynamical Networks: A Formalism for Describing Complex Systems." Complexity. V. 17, N. 3. Pp. 18-25. P. 19.
"These [adaptive networks] are types of network where a local dynamical process taking place over the network structure is coupled to the evolutionary rules of the network itself; dynamics influence evolution and vice versa through the network topology." Gorochowski, Thomas, M. Di Bernardo & C. Grierson. 2011. "Evolving Dynamical Networks: A Formalism for Describing Complex Systems." Complexity. V. 17, N. 3. Pp. 18-25. P. 19.
"Formalizing network dynamics and evolution has seen some interest with examples including coupled cell networks, dynamic graphs, and complex adaptive systems." Gorochowski, Thomas, M. Di Bernardo & C. Grierson. 2011. "Evolving Dynamical Networks: A Formalism for Describing Complex Systems." Complexity. V. 17, N. 3. Pp. 18-25. P. 19.
"The previous sections described several attempts to formalize network dynamics and evolution, however, in all cases limitations were found. Here, we attempt to solve this problem by combining and generalizing several of these ideas to develop a new mathematical formalism called an evolving dynamical network (EDN). These networks provide a suitable framework to study complex systems, coherently incorporating network topology, dynamics, and evolution." Gorochowski, Thomas, M. Di Bernardo & C. Grierson. 2011. "Evolving Dynamical Networks: A Formalism for Describing Complex Systems." Complexity. V. 17, N. 3. Pp. 18-25. P. 21.
"Open questions from research in genetics, ecology, brain sciences, etc., have changed DST [dynamic systems theory] itself and lead to the discovery of a new dynamical phenomenon, i.e., reproducible and robust transients that are at the same time sensitive to informational signals." Rabinovich, Mikhail & P. Varona. 2011. "Robust transient dynamics and brain functions." Frontiers in Computational Neuroscience. June 2011. V. 5. Art. 24. Pp. 1-10. P. 1.
"Once the attractor (or its vicinity) is reached, the ‘dynamical’ nature of the brain becomes irrelevant. Furthermore, this scheme overlooks the informational qualities of the (transient) path from the initial condition to the attractor, an important phase where the brain could exploit its remarkable repertoire of behaviors. In this short review, we discuss an alternative/complementary paradigm, i.e., brain information processing based on robust transient dynamics which is observed in experiments as a sequential switching from one metastable state to another." Rabinovich, Mikhail & P. Varona. 2011. "Robust transient dynamics and brain functions." Frontiers in Computational Neuroscience. June 2011. V. 5. Art. 24. Pp. 1-10. P. 1.
"However, even the coupling detection is problematic in case of a ‘model-free’ inference under quite usual conditions. The problem of coupling quantification is more difficult." Smirnov, Dmitry. "2014. "Quantification of causal couplings via dynamical effects: A unifying perspective." Physical Review. E90. 062921. P. 062921-1.
"The suggested perspective also reveals that a completely model-free approach to causal coupling quantification universally applicable to compare ‘coupling strengths’ across pairs of different systems is not feasible.... In general, any causal coupling inference seems to be inevitably model based." Smirnov, Dmitry. "2014. "Quantification of causal couplings via dynamical effects: A unifying perspective." Physical Review. E90. 062921. P. 062921-10.
"It is argued that any attempt to develop a model-free approach to causal coupling quantification is, in essence, oriented to a certain class of systems and inevitably involves model assumptions to interpret the results." Smirnov, Dmitry. "2014. "Quantification of causal couplings via dynamical effects: A unifying perspective." Physical Review. E90. 062921. P. 062921-11.
"... one may recall that the alphabet and the first written records were invented for the sake of keeping track of economic transactions and fixing rules for sorting conflicts out. Along the same lines, one could argue that DNA was invented as a repository of information to keep a record of already existing metabolic phenomena as well as a sort of memory for re-enacting biochemical reactions when needed. This is the stance of the metabolism-first view of the Origin of Life, which rejects the idea of naked self-replicating molecules (e.g. RNA), and suggests instead a seminal metabolism centred on primitive and growingly complex metabolic reactions." De Lorenzo, Victor. 2014. "From the selfish gene to selfish metabolism: Revisiting the central dogma." Bioessays. 36: 226-235. P. 229.
"Most pairs of polymers will form a phase system if sufficiently concentrated, typically several weight percent of each polymer. Hence, Walter and Brooks in 1995 hypothesized that the cytoplasm of living cells, which contains on the order of 30 wt % total macromolecules, must consist of coexisting aqueous phases." Keating, Christine. 2012. "Aqueous Phase Separation as a Possible Route to Compartmentalization of Biological Molecules." Accounts of Chemical Research. V. 45, N. 12. Pp. 2114-24. P. 2116. Reference: Walter, H. & D. Brooks. 1995. "Phase separation, due to macromolecular crowding, is the basis for microcompartmentation." FEBS Letters. 361: 135-9.
"Phase separation has not been observed in most cell types, perhaps because the large number of different macromolecules, interaction types, and intracellular structures precludes its occurrence or its observation. A few examples of aqueous phase separation have been observed in biological cells. Phase separation is the cause of ‘cold cataracts’, a disease state in which the normally clear eye lens cytoplasm becomes cloudy, interfering with vision." Keating, Christine. 2012. "Aqueous Phase Separation as a Possible Route to Compartmentalization of Biological Molecules." Accounts of Chemical Research. V. 45, N. 12. Pp. 2114-24. P. 2122.
"The contemporary scientific usage of degeneracy thus refers to the variable pathways that can lead to the same outcome, or the ability of different structures to perform the same function. For example, different gestures can convey the same communicative message, different chemical pathways can be used to metabolise food, and different proteins can bind to the same molecules." Mason, P., J. Dominguez, B. Winter & A. Grignolio. 2015. "Hidden in plain view: degeneracy in complex systems." Biosystems. 128: 1-8. P. 2.
"In general, scientists have overlooked the concept of degeneracy not only because of the term’s dominant negative meaning but also, we would suggest, because degeneracy is predicated upon a view of causality as being manifold and distributed. Such a view underpins the idea of multiple arrangements yielding the same output. This view of causality clashes with a traditional scientific analytical approach that favors isolating single causes for a given outcome." Mason, P., J. Dominguez, B. Winter & A. Grignolio. 2015. "Hidden in plain view: degeneracy in complex systems." Biosystems. 128: 1-8. P. 2.
"A key corollary of degeneracy is that, because it entails diversity at the structural level, different circumstances may elicit different outputs from the same degenerate set. This one-to-many structure-function relationship has been dubbed pluripotentiality. The pluripotentiality of a degenerate set distinguishes it from a redundant set, which comprises identical structures that perform the same unique function." Mason, P., J. Dominguez, B. Winter & A. Grignolio. 2015. "Hidden in plain view: degeneracy in complex systems." Biosystems. 128: 1-8. P. 4.
"While a dependency between degeneracy and complexity has not been formally derived, current work has shown complexity emerges wherever there is selection for high degeneracy. This would suggest degeneracy is an essential ingredient of complex systems." Mason, P., J. Dominguez, B. Winter & A. Grignolio. 2015. "Hidden in plain view: degeneracy in complex systems." Biosystems. 128: 1-8. P. 4.
"What is molecular complementarity? Molecular complementarity is the stereopecific, reversible binding of two or more molecules achieved by a combination of hydrogen, ionic, and ð-ð overlap bonds augmented by van der Waals attraction and solvent exclusion. Molecular complementarity is therefore dependent on the fitness of the solvent to support reversible interactions (on Earth, water), as well as on solubility, concentration, and temperature." Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. Pp. 2170-1.
"One does not observe such ubiquitous molecular complementarity in random mixtures of compounds, so why in mixtures of cellular compounds?" Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. P. 2171.
"... we found that small molecules that functionally alter each other’s activity in biological systems almost always bind to each other and, conversely, small molecules that bind to each other will usually modify each other’s biological functions,..." Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. P. 2172.
"Dwyer proposed that self-complementary peptides might give rise to their own receptors. Insulin self-aggregates, so following Dwyer, I hypothesized that the insulin receptor should contain insulin-like regions at its binding sites. Homology searching verified this hypothesis, and experiments proved that insulin binds to these insulin-like receptor domains. Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. P. 2172. Reference: Dwyer, Donald. 1998. "Assembly of Exons from Unitary Transposable Genetic Elements: Implications for the Evolution of Protein-Protein Interactions." J. Theor. Biol. 194: 11-27.
"A molecular paleontology of small molecule complementarity adds significantly to our understanding of the evolution of chemical systems by providing several key components: a means of naturally selecting among molecules during evolution; a mechanism for stabilizing and buffering the resulting systems; ways of generating increased functional diversity; and perhaps most importantly, the ability to organize and replicate such systems." Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. Pp. 2173-4.
"Complementary modularity can increase the rate of evolution compared with purely random processes in two additional ways as well. First, complementarity stabilizes the components against hydrolysis, oxidation, photolysis, and other destructive effects, thereby acting as a form of chemical natural selection.... Second, complementarity-based modules can self-assemble and duplicate themselves so that our module-building, blind, clueless, watchmaker need to not randomly explore all of the possibilities every time she wants to make a new watch. Thus, both stabilization and replication lower the local entropy of the system." Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. P. 2175.
"Thus, we have summarized our novel integrative theory in two statements: (1) everything that could happen (in terms of chemical reactions) during the origins of life did happen; (2) life is adapted to its environment because it evolved in tandem with its chemical ecology." Root-Bernstein, Robert. 2012. "A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity." Accounts of Chemical Research. V. 45, No. 12. 2169-2177. P. 2176.
"The GARD [graded autocatalysis replication domain] model of the lipid world scenario for the origin of life is an embodiment of the metabolism-first approach. GARD is a systems-chemistry model which entails supra-molecular assembly of amphiphiles with intrinsic network of mutually catalytic interactions, which has been shown to portray a capacity to undergo replication mediated by homeostatic growth, as well as selection and evolution. Its species-like quasi-stationary states in compositional space are called composomes. GARD’s forte is in invoking a supramolecular structure that is on the one hand replicable and evolvable and on the other hand simple enough so that the molecular parameters may be directly and quantitatively related to resulting dynamics.... "GARD simulations are used here to quantitatively follow population dynamics of composmal species. In the foregoing analyses a multivariate logistic equation is used to relate systems chemical parameters of GARD assemblies, including chemical diversity, replication fidelity and compositional similarity to specific ecology-like measures such as the carrying capacity, the intrinsic growth rate and the competition parameters." Markovitch, Omer & D. Lancet. 2014. "Multispecies population dynamics of prebiotic compositional assemblies." Journal of Theoretical Biology. 357: 26-34. P. 27.
"... we posit that metabolic and replicative functions emerged hand-in-hand in networks of interactions best described as a pre-biotic ecology. Thus we consider life to have evolved as a diverse interacting community of molecules from the start, and not as a single replicating entity or as a unique primordial species, with divergent offspring." Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. P. 399.
"We propose an evolutionary process by which complexity can be boot-strapped from relatively simple organic molecules that self-assemble and interact with each other through non-covalent forces governed by the principles of molecular complementarity. These first compositionally diverse, non-homogeneous, non-covalent assemblies we call composomes." Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. P. 399.
"The result of such binding is to form complexes that are stabilized against oxidation, pH, heat denaturation and other degradative processes thereby conferring upon the constituents of such complexes an evolutionary survival advantage so that they may accumulate." Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. P. 400.
"In contrast to the elaborate covalent polymerization reactions necessary to transfer information to progeny by nucleic acid base pairing, non-covalent assemblies are proposed to transmit compositional, structural, network recognition and catalytic information by straightforward fission of the composome." Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. Pp. 401-2.
"The next problem that must be addressed is the evolution of function within networks of composomal aggregates. If composomes were merely stable associations (even self-reproducing ones) then they would have the non-evolutionary effect of locking up prebiotic material and removing it from the environment. In order to constitute a step towards living systems, composomes had to manifest secondary properties, such as catalytic activity, buffering capacity and metabolic control, which had to be encoded in their composition and functionally available to interact with the environment. In other words, composomes had to co-evolve with prebiotic ecologies." Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. P. 402.
"The fourth problem (the evolution of autocatalytic, controlled metabolism) is therefore one of population ecology. In general, we expect catalytic activity to lead to a growing, diverse and increasingly integrated population of composomes. In this context, the evolution of spatially diffuse or disseminated autocatalytic networks of ecologies of composomes might have evolved prior to the localization of a fully autocatalytic network within a single composome, or ‘proto-cell.’" Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. P. 403.
"The theme of this paper is that the co-evolution of populations of molecularly diverse aggregates (composomes) selected on the basis of molecular complementarity and the emergence of modular functionality forms a basis for addressing some of the issues raised by the origin of life and for recognizing some of the outstanding problems left unaddressed by other theories of the origins of life. In this picture, life emerged as a functioning ecological system through a process of integration from diverse components, not as a single entity that subsequently evolved by an as-yet-unknown process into an ecologically diverse system. In our model, there is no identifiable point at which life emerged. Rather, we have described a continuous process by which increasingly complex, integrated, self-replicating, autocatalytic, modular systems evolve new properties in tandem with their environments. We can summarize our theory by saying that it posits an ‘ecosystems-first- origin of life, rather than a metabolism or gene-first origin." Hunding, Axel, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram & R. Root-Bernstein. 2006. "Compositional complementarity and prebiotic ecology in the origin of life." BioEssays. 28.4: 399-412. Pp. 409-10.
"Resulting from complex interactions in space-time, the coordinative ‘acting in concert’ behavior of neural ensembles lies between the dual poles of segregation (tendencies for neural ensembles to diverge and function independently) and integration (tendencies for neural ensembles to converge and work together)." Tognoli, Emmanuelle & J. Scott Kelso. 2014. "The Metastable Brain." Neuron. 81. Pp. 35-48. P. 35.
"In its current form, the theory of Coordination Dynamics describes three qualitatively distinct collective behaviors in which integration and segregation come into play. The first two exist for components that are coupled, i.e., there is exchange of information and/or matter between the components, directly or indirectly, and irrespective of a (synchronized) collective outcome. The first scheme couples components whose intrinsic dynamics is similar. Attractors (dynamical structures in which the set of trajectories of a system converge to and persist in a given state) are created in the components’ coordination dynamics. As a result, neural oscillations may be trapped in states of phase and frequency locking. If more than one state exists in the latent dynamical structure of the system (a condition called bi- or multistability), brain dynamics may switch states under the effect of a perturbation, input, or fluctuations. Signature features of such phase transitions have been observed and modeled. In a second scheme, the components are also coupled. However, they differ enough in their intrinsic dynamics that they can no longer reconcile their behavior through the mechanism of phase locking. With the disappearance of the attractors, there is no longer any phase- and frequency-locking behavior. Since the components are coupled, however, they still influence each other, expressing their relationship in a temporally structured behavior in which lingering in quasisynchrony (integrative tendencies) and escaping from one another (segregation tendencies) coexist. This is called metastability. Integrative tendencies are strongest during moments of quasisynchrony or dwells: participating neural ensembles support a collective behavior. Segregative tendencies are observed as a kind of escape behavior: neural ensembles diverge and are removed from the collective effort. In the third and final scheme, the components do not exchange any information; they are completely autonomous and hence behave in total neglect of each other’s behavior. Any integrative or segregative tendency disappears, only independent behavior remains according to each component’s intrinsic dynamics. In nature, though symmetries are broken or lowered all the time, it is difficult for the parts to be perfectly isolated from one another: coupling tendencies may be vanishingly small and indirect, in effect approaching asymptotically the dynamics of uncoupled components." Tognoli, Emmanuelle & J. Scott Kelso. 2014. "The Metastable Brain." Neuron. 81. Pp. 35-48. P. 36.
"According to him [Gould], neutral and random mutations occur at the lowest level. At the highest level, massive extinctions are not due to adaptative struggles between individuals and/or species. Instead, massive extinctions result from accidental and catastrophic changes in environmental conditions. In contrast, the salient feature of life involves the stability of its bacterial mode, ‘physically constrained’ from the starting point due to the chemistry of life and self-organization. Gould calls this symmetry breaking between simple physics and biology ‘the left wall of complexity.’ Gould’s view emphasizes the tree of life with its maximum number of branches, and not the tiny right tail in the curve of evolution through a space of complexity. In other words, humans are just an accident and the bacterium the rule." Miquel, Paul-Antoine. 2011. "Extended physics as a theoretical framework for systems biology?" Progress in Biophysics and Molecular Biology. 106: 348-52. P. 349.
"Finally, the emeritus biologist Robert G.B. Reid, in his book Biological Emergences: Evolution by Natural Experiment (2007) claims that emergent complexity in evolution has been the result of an autonomous physiological experiment and that natural selection has played no significant role. In fact, Reid argues, it has often been a hindrance. He claims that freedom from ecological competition and natural selection has been an important facilitator of emergent evolution, and that the contribution of natural selection to the history of life on Earth has been confined at best to ‘fine-tuning’ and ‘stabilizing’ the innovations that arise from what he characterizes as an internally guided process. Once basic organismal integrity and homeostatic capabilities evolved, Reid says, evolution could go forward as an independent process subject only to the ‘obstructionism’ of natural selection. As Reid puts it, Darwin got it ‘fundamentally wrong.’" Corning, Peter & E. Szathmary. 2015. "‘Synergistic selection’: A Darwinian frame for the evolution of complexity." Journal of Theoretical Biology. 371: 45-58. P. 47.
"The synergism hypothesis represents an extension of this line of reasoning. The focus is on the selection of functional ‘wholes’ of different kinds, and the combinations of genes that produce those wholes. Simply stated, cooperative interactions of various kinds, however they may occur, can produce novel combined effects – synergies – that in turn become causes of differential selection. In effect, the parts (and their genes) that are responsible for producing the synergies may become interdependent ‘units’ of evolutionary change. "Thus, it is the ‘payoffs’ associated with various synergistic effects in a given context that constitute the underlying cause of cooperative relationships – and complex organization – in nature." Corning, Peter & E. Szathmary. 2015. "‘Synergistic selection’: A Darwinian frame for the evolution of complexity." Journal of Theoretical Biology. 371: 45-58. P. 48.
"Although the term [synergy] is sometimes treated as a synonym for cooperation, in fact it refers to the functional effects that are produced by cooperation." Corning, Peter & E. Szathmary. 2015. "‘Synergistic selection’: A Darwinian frame for the evolution of complexity." Journal of Theoretical Biology. 371: 45-58. P. 49.
"According to the RQH [Red Queen Hypothesis], each adaptation by a species is matched by counteracting adaptations in another interacting species, such that perpetual evolutionary change is required for existence." Brockhurst, Michael. T. Chapman, K. King, J. Mank, S. Paterson & G. Hurst. 2014. "Running with the Red Queen: the role of biotic conflicts in evolution." Proceedings of the Royal Society: B. 281: 20141382. Pp. 1-9. P. 1.
"West et al.’s emphasis on Hamilton’s model as the complete generalization of Darwinian theory allows us to identify a feature that all of the models undermined by the inclusive fitness maximization constraint have in common: They are led to hypothesize novel evolutionary mechanisms by supposing that cooperative behavior is harder for natural selection to support than is actually the case. This is closely related to the widespread view that humans are uniquely cooperative as a species, at least among noneusocial animals. West et al. challenge this second supposition directly. Humans, they observe, are less altruistic than a number of species scattered liberally around the tree of life, are by no means special in establishing cooperative relationships with nonrelatives, and are not unique in incentivizing cooperation by punishment of noncooperators. "This is immediately relevant to the individualism debate. Stories of human evolution that rest primary weight on overcoming obstacles to cooperation effectively presuppose individualism. They take the problem of the origin of human sociality to be: How do basically selfish individuals evolve commitment devices against their default Darwinian dispositions to defect against one another in prisoner’s dilemmas, public goods games, and similar strategic settings that preoccupy behavioral economists?" Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 23. Reference: West, S., C. El Mouden & A. Gardner. 2011. "Sixteen common misconceptions about the evolution of cooperation in humans." Evolution and Human Behavior. 32: 231-262.
"Individualism, I suggest, inflects many theorists’ entire views of human evolutionary history. "The demand for a specific explanation of how selfish, cognitively sophisticated individual hominids achieved cooperative dispositions is misplaced. All apes live in family groups. In such groups, inclusive fitness of individuals is typically best promoted by at least some level of resource-sharing and communal protection of young.... The most basic mechanism maintaining cooperativeness is a simple feedback loop. Animals that forage and nest in groups are likely to be more closely related to nearby conspecifics than they are to geographically distant ones." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. Pp. 23-4.
"It is important to distinguish between dispositions to cooperate in general and capacities to process information that facilitate specific forms of cooperation. That is to say, we must keep an eye on the difference between cooperation and coordination." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 24.
"It is every bit as compatible with the evidence to postulate that chimpanzee sociality has atrophied in their stable and food-rich forest environment as to speculate that human cooperative dispositions are exaggerated relative to such dispositions in early hominids." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 25.
"The economist Haim Ofek argues persuasively that specialization and exchange were a precondition rather than a consequence of the evolutionary trajectory from Homo erectus to modern Homo sapiens.... "Thus, Ofek argues, in company with Wrangham et al. and Wrangham, that mastery of fire was a specific precondition for at least the later and most rapid stage of human encephalization. He then marshals reasons to believe that fire-keeping was the first specialized occupation in the hominid social ecology. This involves interpretation of paleontological evidence in light of an economic analysis according to which, for Homo erectus and his immediate successors, it was much more efficient for specialists to maintain fires from which bands of local hunter-gatherers could draw in exchange for food and pelts than for each small band of hunter-gatherers to search for suitable kindling each day–which would have severely restricted their foraging ranges–and then endure the high-risk, failure-prone ordeal of starting a nightly fire without modern ignition technology. Caves, Ofek argues, were not primarily used as homes by early humans, as popular imagination supposes, but as fire service stations.... "Ofek’s project is not merely to explain the origins of markets. Rather, his thesis is that market exchange was the basic behavioral adaptation that allowed humans to construct a distinctive ecological niche, and the only such niche that tends by its own endogenous dynamic to expand indefinitely. Of central important to the present argument, this adaptation is primarily one of social organization, and only secondarily one of individual cognitive and preference dispositions." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. Pp. 28-9. References: Ofek, H. 2001. Second nature. Cambridge University Press. Wrangham, R., J. Jones, G. Laden, D. Pilbeam & N. Conklin-Brittain. 1999. "The raw and the stolen: Cooking and the ecology of human origins." Current Anthropology. 40: 567-594. Wrangham, R. 2009. Catching Fire. Basic Books. "Let us summarize. In an early human environment where most groups of relatives hunted and gathered, but some formed households that maintained fire services and general merchandise shops in caves, simple imitation could not tell a family what to do. If it sought to optimize, the family should in the first place have focused not on the special properties of its individual members, but on a social property: What were the local marginal costs and benefits of being respectively, the next foraging group in one’s area, the next foraging group in a new area, and going into retail? If the family opted for business, it then needed a basis for stable specialization among its members; who will cultivate the craft of hand-axe manufacture, who will concentrate on cave art, who will gather kindling for the fire? Basic principles of organizational psychology tell us that stability within the production unit is best served if people imaginatively identify themselves with their assigned roles. This gives all household members incentive to collaborate in reinforcing one another’s professional identifications.... "Specialization of labor thus promotes shared normative framing of individual differences. Such differences may sometimes have their basis in genetically produced variations in talent or temperament, but where they do, the members of a corporate entity have incentive to exaggerate these, and where they do not, to create them." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. Pp. 31-2.
"Based on game-theoretic logic, Ross has extensively characterized the processes by which people learn, over the course of childhood and adolescent development, to construct narrative selves that have the following properties: "(1) They are adapted to local cultural expectations, so that they facilitate location of equilibria in global games with others who share a similar cultural background. (2) The dimensions along which their variance is culturally salient form the basis for a prevailing typology of personalities and linked aptitude sets that are normatively and statistically associated with types of economic occupations and social roles. (3) They are attractive to others, and so encourage cooperative activities that exploit specialized, complementary roles, to the extent that they display creative uniqueness within the boundaries of local normative conventions. (4) They develop inconsistency, which tends in the limit to incoherence, if they are not reinforced by a person’s recurrent interactants; and inconsistent or incoherent narrative selves are regarded by others as diagnostic of unreliability at best and insanity at worst." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. Pp. 34-5. Reference is to five papers published by this author between 2004 and 2008.
"At three scales–that of the evolution of the modern human species, that of the cultural emergence of values adapted to giant industrial communities, and that of the etiology of distinctive personal characters–I have identified arcs of development from behavioral spaces with little individual variation to spaces characterized by emphasis on special capacities and characteristics of individuals. All of these developmental arcs are both driven and constrained by largely implicit and nondeliberative normative considerations. Specialization of labor was culturally promoted because it made people richer, and the promotion of such specialization in turn made people smarter." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 36.
"The history of attempts to base normative individualism on descriptive individualism, such as can be attributed to the Lockean tradition in political philosophy, appear profoundly confused from Darwinian and historical perspectives." Ross, Don. 2013. "The Evolution of Individualistic Norms." Pp. 17-43. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 37.
"These two distinctions–between past and present, and between mechanism and populations–are collapsed in the proximate-ultimate distinction. Mechanistic explanations tell us about the present, and population dynamics tell us about the past. This is a problem, because we might be led to believe that an interest in mechanism must focus on present behavior only, and any story about the history or origin of a trait is always about population dynamics." Calcott, Brett. 2013. "Why the Proximate-Ultimate Distinction is Misleading, and Why It Matters for Understanding the Evolution of Cooperation." Pp. 249-263. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 253.
"The proximate-ultimate distinction conflates two separate distinctions [mechanisms as proximate and population dynamics as ultimate], and obscures an important third option: Lineage explanation." Calcott, Brett. 2013. "Why the Proximate-Ultimate Distinction is Misleading, and Why It Matters for Understanding the Evolution of Cooperation." Pp. 249-263. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 253.
"Lineage explanations show how some prior mechanism capable of one task can, through only minor variations, be modified into a new mechanism capable of a different task." Calcott, Brett. 2013. "Why the Proximate-Ultimate Distinction is Misleading, and Why It Matters for Understanding the Evolution of Cooperation." Pp. 249-263. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 255.
"... plasticity is the primitive condition of biological processes–by default, things are sensitive to the context in which they occur. In general, it is adaptation that channels, controls, or prevents plasticity–it does not create it." Calcott, Brett. 2013. "Why the Proximate-Ultimate Distinction is Misleading, and Why It Matters for Understanding the Evolution of Cooperation." Pp. 249-263. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 259.
"Information transfers are achieved in bacterial systems through very different processes, such as quorum sensing, conjugation, and transformation, and these channels can be established even between bacteria of different species." Riboli-Sasco, Livio, F. Taddei & S. Brown. 2013. "Bacterial Social Life: Information Processing Characteristics and Cooperation Coevolve." Pp. 275-288. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 275.
"We propose an analysis along three main sets of characteristics: content-holding characteristics, interfacing, and transferring characteristics. Content-holding characteristics relate to the ability of systems to hold information within themselves. ‘Holding’ information thus goes along with structural identity. Information is enclosed within the system at stake.... The second main aspect of these systems is that there are interfaces between one layer of information and a resulting process. We call an interface a process that directly interacts with a piece of information to convert it into a subsequent information content or into an action. Encoding-decoding processes lie at the heart of any analysis of information processes. The last main dimension of our analysis is about transferring processes. The easiest approach is to consider the emission and reception characteristics separately, as these are not symmetrical. Types of emission vary depending on the network of agents involved. First of all we suggest analyzing emission in terms of frequency of emitted content. Two other key elements are whether the emission is targeted and whether this process is context-dependent." Riboli-Sasco, Livio, F. Taddei & S. Brown. 2013. "Bacterial Social Life: Information Processing Characteristics and Cooperation Coevolve." Pp. 275-288. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. Pp. 279-80.
"We define interoperability as [a] measure of the range of systems that are able to operate mobile information.... "Plasmids, and in particular ‘broad host range plasmids,’ are a paradigmatic example of interoperable information." Riboli-Sasco, Livio, F. Taddei & S. Brown. 2013. "Bacterial Social Life: Information Processing Characteristics and Cooperation Coevolve." Pp. 275-288. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 280.
"... interoperability allows large-scale sharing of action, as the information is not only shared but can also be operated. Thus, within the niche construction framework, higher levels of interoperability may correspond to, and coevolve with, important shared niche-construction abilities." Riboli-Sasco, Livio, F. Taddei & S. Brown. 2013. "Bacterial Social Life: Information Processing Characteristics and Cooperation Coevolve." Pp. 275-288. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 281.
"In the case of meerkats and ants, the environment offers resources that one individual cannot access on its own. In the case of ants, the individuals lack the knowledge about the location of food. If they were to search, alone and independently for food they may well starve before finding anything. Access to information about food location is thus easier and cheaper than accessing food directly. In the case of meerkats, accessing food is highly dangerous. The probability of getting killed is high. Accessing information about procedures to deal with dangerous food is thus easier and cheaper than trying to independently and naively access food. "In both examples, maintaining and sharing within the population information about resources can be viewed as a niche construction process." Riboli-Sasco, Livio, F. Taddei & S. Brown. 2013. "Bacterial Social Life: Information Processing Characteristics and Cooperation Coevolve." Pp. 275-288. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. Pp. 282-3.
"We argue that we can enhance our understanding of cooperation from an understanding of one of the core properties of life, namely that it is based on information processing. Information can potentially be interoperated between different agents or systems." Riboli-Sasco, Livio, F. Taddei & S. Brown. 2013. "Bacterial Social Life: Information Processing Characteristics and Cooperation Coevolve." Pp. 275-288. From: Sterelny, Kim, R. Joyce, B. Calcott & B. Fraser (Eds). Cooperation and Its Evolution. MIT Press. P. 286.
"At its most basic, evolutionary systems biology (ESB) is the synthesis of system-level approaches to biological function with evolutionary explanations of multilevel properties. ‘System’ in this context refers to dynamically interacting components that produce behavior not revealed by analyses of isolated components." Soyer, Orkun & M. O’Malley. 2013. "Evolutionary systems biology: What it is and why it matters." Bioessays. 35: 696-705. P. 696.
"This paper explains why replacement rather than extension is called for [for the Modern Synthesis]. The reason is that the existence of robust mechanisms of trans-generational inheritance independent of DNA sequences runs strongly counter to the spirit of the Modern Synthesis." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 7.
"GeneJ [a 1:1 relation between genetic factor (gene) and character; traditional concept named after Johannsen] referred to the cause of a specific inheritable phenotype characteristic (trait), such as eye-hair/skin colour, body shape and mass, number of legs/arms/wings, to which we could perhaps add more complex traits such as intelligence, personality and sexuality. "The molecular biological definition of a gene is very different. Following the discovery that DNA forms templates for proteins, the definition shifted to locatable DNA sequences with identifiable beginnings and endings.... I will call this definition of a ‘gene’ geneM." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 8.
"This diagram represents the interaction between DNA sequences, environment and phenotype as occurring through biological networks. The causation occurs in both directions between all three influences on the network." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 8.
"This difference between geneJ (which refers to indeterminate entities that are necessarily the cause) and geneM (whose causation is open to experimentation) is central.... The difference is in fact large as most changes in DNA do not necessarily cause a change in phenotype. Organisms are very good at buffering themselves against genomic change. Eighty per cent of knockouts in yeast, for example, are normally silent, while critical biological oscillators like the cardiac pacemaker or circadian rhythm are buffered against genomic change through extensive back-up mechanisms." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 9.
"Representing the direction of causality in biology the wrong way round is confusing and has far-reaching consequences. The causality is circular, acting both ways: passive causality by DNA sequences acting as otherwise inert templates, and active causality by the functional networks of interactions that determine how the genome is activated." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 9.
"The problem is that no complete algorithms can be found in the DNA sequences. What we find is better characterised as a mixture of templates and switches. The ‘templates’ are the triplet sequences that specify the amino acid sequences or the RNA sequences. The ‘switches’ are the locations on the DNA or histones where transcription factors, methylation and other controlling processes trigger their effects." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 10.
GenesM are best viewed therefore as causes in a passive sense. They do nothing until activated. Active causation lies with proteins, membranes, metabolites, organelles, etc., and the dynamic functional networks they form in interaction with the environment." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 11. "The alternative form of representation [to better describe genetics] depends on two fundamental concepts. The first one is the distinction between active and passive causes. GenesM are passive causes: they are templates used when the dynamic cell networks activate them. The second concept is that there is no privileged level of causation. In networks, that is necessarily true, and it is the central feature of what I have called theory of biological relativity...." Noble, Denis. 2015. "Evolution beyond neo-Darwinism: a new conceptual framework." The Journal of Experimental Biology. 218: 7-13. P. 11.
"Consider the situation where a thermodynamically open system (a cell) experiences an excess of free energy (nutrient) at its boundary with its environment. The principles of least action and least time, dictate that the system will strive to equalise the imbalance by diminishing free energy (consume the nutrient) as efficiently as possible. What Sharma and Annila point out is that if organised structures (the cell with its organelles etc.) can do this more efficiently than disordered structures, as is certainly the case, natural selection will favour ordered systems, albeit that the process has been erroneously assumed to entail increased internal entropy when entropy has been equated with disorder, rather than with bound energy." Baverstock, Keith. 2013. "Life as physics and chemistry: A system view of biology." Progress in Biophysics and Molecular Biology. 111: 108-115. P. 109. Reference: Sharma, V. & A. Annila. 2007. "Natural process-natural selection." Biophys. Chem. 127: 123-28.
"Thus, the genotype-phenotype relation cannot be understood outside a systems-physiology framework,..." Noble, Denis, E. Jablonka, M. Joyner, G. Mueller & S. Omholt. 2014. "Evolution evolves: physiology returns to centre stage." The Journal of Physiology. 11: 2237-2244. P. 2238.
"... it might be argued that the biomedical efforts informed by the Modern Synthesis have stalled or at least underperformed. In contrast, progress in epidemiology and public policy marches on, with ever more evidence showing the powerful effects of behaviour, environment and social circumstances on health." Noble, Denis, E. Jablonka, M. Joyner, G. Mueller & S. Omholt. 2014. "Evolution evolves: physiology returns to centre stage." The Journal of Physiology. 11: 2237-2244. P. 2240.
"The ubiquity and abundance of between-generation epigenetic inheritance has implications for assessing disease risk and the responses to ecological stresses. New methods for identifying and estimating the extent of heritable, epigenetic variation in populations are necessary.... The application of this or similar methods to epidemiological data can help to uncover the epigenetic correlates and causes of complex metabolic and environmental diseases and help in finding adequate treatments." Noble, Denis, E. Jablonka, M. Joyner, G. Mueller & S. Omholt. 2014. "Evolution evolves: physiology returns to centre stage." The Journal of Physiology. 11: 2237-2244. P. 2240. "Physiological science has an important role in this encompassing reform of evolutionary theory, because of three major contributions it can make, namely the reintroduction of function, the addition of higher order organizing principles and an account of organismal systems properties." Noble, Denis, E. Jablonka, M. Joyner, G. Mueller & S. Omholt. 2014. "Evolution evolves: physiology returns to centre stage." The Journal of Physiology. 11: 2237-2244. P. 2240.
"The hallmark of such a reform [of evolutionary theory] is a relinquishment of any privileged levels of causation in the evolutionary process and a replacement of gene reductionism by systems principles." Noble, Denis, E. Jablonka, M. Joyner, G. Mueller & S. Omholt. 2014. "Evolution evolves: physiology returns to centre stage." The Journal of Physiology. 11: 2237-2244. P. 2241.
"Systems biology is commonly regarded as the child of the 21st century, and of the human genome project. However, the term ‘systems biology’ is much older than is usually realized, being first used by Mesarovic (1968). It only occurred in a handful of publications before 2000, but in thousands since then. The ideas of systems biology, however, are much older again, and can be traced at least to the general system theory of Bertalanffy, developed in the 1930s, but summarized in English in von Bertalanffy (1969), .... Unfortunately much of the current enthusiasm for systems biology has led to the adoption of some of the terminology of systemic thinking while leaving its spirit largely ignored: systemic thinking means more than just accumulating huge amounts of data; the accent must be put on the organization more than on the details. In the Discussion we shall point out that the current theories of life reflect a spectrum from ones that concentrate mainly on details to ones that ignore details altogether." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 104. References: Mesarovic, M. 1968. "Systems theory and biology: view of a theoretician." Pp. 59-87. From Mesarovic, M. (Ed.) Systems Theory and Biology. Springer. Von Bertalanffy, L. 1969. General System Theory. George Braziller.
"... a consequence of closure to efficient cause is that it eliminates the whole idea of hierarchy from theoretical biology. If all components in a living system, whether enzymes, nucleic acids or conventional metabolites, are products of the system, then there is no hierarchy. This does not of course deny the practical usefulness of applying hierarchical ideas to parts of systems, but it does imply that the hierarchy disappears when the whole system is considered." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 105.
"In effect he [Humberto Maturana’s cognitive model as part of founding the concept of autopoiesis] proposed a new metaphor: instead of assuming that the nervous system is a device that decodes reality, he assumed that it is a system whose main property is to produce movements coherent with the current situation of the organism. Instead of focusing on perception, and the perfect decoding and internal representation of this perception, he assumed that the nervous system is always in a particular state of senso-motor coordination." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 106.
"Maynard Smith an Szathmary (1995) used the name Eigen’s paradox to refer to the puzzle that specifying the structures of enzymes requires a large genome, but producing and accurately replicating a large genome requires enzymes." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 107.
"Knowledge of chemistry and enzyme catalysis, however, suggests that some molecules should be completely ineffective for catalysing any reactions, with others capable of catalysing many similar reactions:..." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 108.
"... Barbieri lists more than 60 attempts to define life, from Lamarck until the 21st century. About 40 of these were written after Schroedinger,..." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 109. Reference: Barbieri, M. 2003. The Organic Codes: An Introduction to Semantic Biology. Cambridge University Press.
"As Hofmeyr has pointed out, the chemoton model contains no evident mechanism to avoid collapse due to parasitic reactions, because there is no explanation of the specificity that could prevent this. However, this problem is not unique to the chemoton, as all current theories of life, including (M,R) systems, autopoiesis, hypercycles, and autocatalytic sets require highly specific catalysts. Szathmary has recognized this problem, calling it the ‘paradox of specificity’, but adds that ‘nobody has yet provided a satisfactory solution.’.... "The importance of specificity is so great that the early organisms can hardly have become more complex without it. Its appearance must have been a powerful driving force for early evolution." Letelier, Juan-Carlos, M. Cardenas & A. Cornish-Bowden. 2011. "From L’Homme Machine to metabolic closure: Steps towards understanding life." Journal of Theoretical Biology. 286: 100-13. P. 111. Reference: Hofmeyr, J. 2007. "The biochemical factory that autonomously fabricates itself: a systems biological view of the living cell." From Boogerd, F., F. Bruggerman, J. Hofmeyr & H. Westerhoff (Eds). Systems Biology: Philosophical Foundations. Elsevier. Pp. 217-42. Szathmary, E. 2003. "The biological significance of Ganti’s work in 1971 and today." Pp. 157-68. From Ganti, T. The Principles of Life. Oxford University Press. "Robustness and function – originating as emergent property – are the two distinctive concepts in systems biology that characterize it in respect to traditional molecular biology investigations." Alberghina, Lilia, T. Hoefer & M. Vanoni. 2009. "Molecular networks and system-level properties." Journal of Biotechnology. 144: 224-33. P. 225.
"The structure of complex networks is typically characterized in terms of global properties, such as the average shortest path length between nodes, the clustering coefficient, the assortativity and degree distribution. However, these global quantities are truly informative only when one of two strict conditions is fulfilled: (1) the network lacks a modular structure, or (2) the network has a modular structure but (2.1) all modules were formed according to the same mechanisms, and therefore have similar properties, and (2.2) the interface between modules is statistically similar to the bulk of the modules, except for the density of links. If neither of these two conditions is fulfilled, then any theory proposed to explain,, for example, a scale-free degree distribution needs to take into account the modular structure of the network. "To our knowledge, no real-world network has been shown to fulfil either of the two conditions above; this implies that global properties may sometimes fail to provide insight into the mechanisms responsible for the formation or growth of these networks." Guimera, Roger, M. Sales-Pardo & L. Amaral. 2007. "Classes of complex networks defined by role-to-role connectivity profiles." Nature Physics. 3 (January): 63-69. P. 63.
"As an alternative to the average description approach, we determine the role of each node according to two properties: the relative within-module degree z, which quantifies how well connected a node is to other nodes in their module, and the participation coefficient P, which quantifies to what extent the node connects to different modules." Guimera, Roger, M. Sales-Pardo & L. Amaral. 2007. "Classes of complex networks defined by role-to-role connectivity profiles." Nature Physics. 3 (January): 63-69. P. 63.
"... tissues that are organized by physiological dynamics can undergo abrupt changes in pattern. In particular, oscillations and gradients could have existed in the embryos of unsegmented vertebrate ancestors for millions of years before a novel balance of rates resulting from mutational change, or a combination of mutation and environmental change, led to the relatively sudden and fortuitous appearance of a segmented body." Newman, Stuart. 2014. "Form and function remixed: developmental physiology in the evolution of vertebrate body plans." The Journal of Physiology. 592.11: 2403-12. P. 2406.
"But what is the whole ‘individual’ when one is dealing with a compound organism such as a hydroid, an aquatic invertebrate in which certain parts can live independently for part of their life cycle, but at other times form colonies? When is a unit a ‘part,’ and when should it be considered an autonomous ‘individual,’ as with the separate clumps of a creeping strawberry or the separate mouths of a colonial sea anemone? This problem has long faced students of compound organisms such as plants, jellyfish and corals; organisms with more obvious metamorphic stages, such as butterflies; and ‘colonial’ (eusocial) insects such as ants, termites, and bees that are morphologically autonomous but require individuals of different forms for the whole colony to survive. The problem also extended to parasites such as tapeworms, which have complex life cycles that can include both autonomous stages and stages in which the organism’s survival depends on its host." Nyhart, Lynn & S. Lidgard. 2011. "Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus der Individuen and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation." Journal of the History of Biology. 44: 373-443. Pp. 379-80.
"Leuckart showed how the division of labor was manifested among animals by leading his reader through a stepwise series. He categorized groups of organisms not simply along taxonomic lines, but by the degree to which their life histories, their parts (or members) and related behaviors partitioned the tasks of life. He began with isolated organisms that had separate sexes: the primary division of labor was a sexual one in which males differed from females only in their sexual organs and products (sperm and eggs). In the simplest case, those organisms had external fertilization, while organisms in the next step required a union for internal fertilization. This step then led to sexual pairs that divided labor in brood care, then polygamous unions in which brood care and other functions were separate. The next most complex form was the ‘animal state,’ represented by insect societies in which different individuals had strictly circumscribed tasks and both asexual and sexual individuals were common. In his description, the economy of the state was served by the organization of individual beings in the society, and the state was held together through communal interests and needs. In contrast, the last step comprised physiologically contiguous animal colones (‘animal stocks’), in which the colony developed by asexual multiplication of its members. Here the ‘individuals’ were integrated parts or members of the physically unified colony, which in turn grew by iterated budding (asexual multiplication) of these individuals.... "In fleshing out his argument, Leuckart concentrated on animal stocks. He focused primarily on two groups of colonial marine invertebrates, siphonophores and hydroids (both now placed in the Phylum Cnidaria)." Nyhart, Lynn & S. Lidgard. 2011. "Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus der Individuen and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation." Journal of the History of Biology. 44: 373-443. Pp. 386-7.
"‘Alternation of generations’ refers to a cycle of reproduction and development differing from both the simple vertebrate sequence from birth through development and sexual reproduction to death and the metamorphic sequence familiar in butterflies and moths. The term was introduced in 1819 by the French-born German voyager Adelbert von Chamisso to describe an odd cycle that connected two morphologically distinct forms of the salp, a free-living pelagic tunicate. A solitary form would bud asexually, producing a hermaphroditic chain-form, which in its turn would sexually produce the solitary form again. Thus the term ‘alternation of generations’ implied both that the different stages comprised different individuals and that the mode of generation (sexual or asexual) alternated as well." Nyhart, Lynn & S. Lidgard. 2011. "Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus der Individuen and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation." Journal of the History of Biology. 44: 373-443. P. 392.
"Tobias Cheung has argued that this term [organism] came to be associated with ‘individual’ only around 1830. Whereas in the seventeenth century, ‘organism’ referred to a principle of organization, the German Naturphilosophen redefined ‘organism’ into an entity." Nyhart, Lynn & S. Lidgard. 2011. "Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus der Individuen and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation." Journal of the History of Biology. 44: 373-443. P. 398. Reference: Cheung, Tobias. 2006. "From the organism of a Body to the Body of an Organism: Occurrence and Meaning of the Word ‘Organism’ from the Seventeenth to the Nineteenth Centuries." British Journal for the History of Science. 39(142): 319-39. P. 335.
"But Leuckart’s species was neither the same as the metaphysical ‘stem-types’ of Kant nor the ‘Urpflanze’ type of Goethe. Leuckart’s species was not an archetype, and he invoked no ‘formative force’ in the development of polymorphic individuals. His species, we suggest, was a higher-level union of individuals, and itself an individual." Nyhart, Lynn & S. Lidgard. 2011. "Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus der Individuen and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation." Journal of the History of Biology. 44: 373-443. P. 399.
"Researchers before 1859, he [Leuckart] wrote, had come to view the physiological dependency of organisms on each other as analogous to the dependency of the internal parts of an individual to the whole. But Darwin reinforced their belief in the analogy by demonstrating that “‘the animal world
is not simply physiologically but also genetically an interdependent
whole; its parts did not originate independently and from the beginning in
full possession of their characteristics, but emerged through the
transformation of [earlier] ones. Like the different states of the same
organism, so do the different animal species form a connected
developmental series, only one that stretches the time of development over
many hundred thousands of years.’” "Leuckart had earlier viewed the species as an idealized individual instantiated by lower-level material individuals. Here for a broad audience he took the analogy a step further; in presenting the animal species as ‘a connected developmental series,’ he compared the animal kingdom as a whole to an individual, as a way of showing his support for Darwinian evolution." Nyhart, Lynn & S. Lidgard. 2011. "Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus der Individuen and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation." Journal of the History of Biology. 44: 373-443. P. 403.
"The widespread occurrence of obligate symbioses and horizontal gene transfer also raise doubts about the nature or reality of ‘individuals’, in favour of viewing organisms as loci where life processes take place, rather than material objects, machines or ‘automata’. Dupré concludes that ‘biological entities are typically the sites of intersection of multiple processes, often on very different time scales’." Vane-Wright, R.I. 2014. "What is life? And what might be said of the role of behaviour in its evolution?" Biological Journal of the Linnean Society. 112: 219-241. P. 231. Reference: Dupré, J. 2014. Biological Journal of the Linnean Society. 112: 306-14.
"Metabolism of eukaryotes takes place primarily in organelles: chloroplasts, mitochondria, and ribosomes, which are, respectively, the sites of photosynthesis, respiration, and protein synthesis. These organelles are effectively invariant units; their structure and function are nearly identical across taxa and environments." Brown, James. J. Gillooly, A. Allen, V. Savage & G. West. 2004. "Toward a Metabolic Theory of Ecology." Ecology. 85(7): 1771-89. P. 1777.
"The fact that species diversity varies inversely with body size suggests that metabolism plays a central role." Brown, James. J. Gillooly, A. Allen, V. Savage & G. West. 2004. "Toward a Metabolic Theory of Ecology." Ecology. 85(7): 1771-89. P. 1781.
"It has long been known that diversity of most taxonomic and functional groups is highest in the tropics, but this has usually been attributed to higher productivity (resource availability) or reduced seasonality, rather than to the kinetic effect of higher temperatures. We have recently shown, however, that species richness in many groups of plants and animals has the same Boltzmann relationship to environmental temperature that metabolic rate does." Brown, James. J. Gillooly, A. Allen, V. Savage & G. West. 2004. "Toward a Metabolic Theory of Ecology." Ecology. 85(7): 1771-89. P. 1781.
"... metabolic theory suggests that energy and materials (or energy and stoichiometry) are not fundamentally different ecological currencies that operate independently or each other to affect the structure and dynamics of ecological systems. They are inextricably linked. The fluxes, stores, and transformations of energy and materials are stoichiometrically constrained by the biochemistry and physiology of metabolism.... At all levels, from individual organisms to ecosystems, the processing of energy and materials is linked due to metabolic constraints." Brown, James. J. Gillooly, A. Allen, V. Savage & G. West. 2004. "Toward a Metabolic Theory of Ecology." Ecology. 85(7): 1771-89. P. 1786. "Metabolism, like inheritance, is one of the great unifying processes in biology, making connections between all levels of organization, from molecules to ecosystems. Metabolic theory would by no means be the only ecological theory nor would it account for all important patterns and processes. It does, however, provide a conceptual framework for ecological energetics and stoichiometry." Brown, James. J. Gillooly, A. Allen, V. Savage & G. West. 2004. "Toward a Metabolic Theory of Ecology." Ecology. 85(7): 1771-89. P. 1786.
"In short, understanding the rates of growth and other biological processes requires knowledge not only of rates of energy use and how they may be physically constrained, but also of how biological information systems are used to manage the acquisition and allocation of energy in environmentally responsive and evolutionarily adaptive ways." Glazier, Douglas. 2015. "Is metabolic rate a universal ‘pacemaker’ for biological processes?" Biological Reviews. 90: 377-407. P. 379.
"... as well as the Darwinian random search ... there was and is a systematic larger-scale evolution dependent upon the opportunities which the large-scale evolving chemical element environment provided. It is, we believe, this strong and faster environmental development, in a given chemical direction, that guided the way to today’s organisms in a systematic, overall much slower, chemical evolution." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. Pp. 2-3.
"We shall observe later that as organisms evolved they became mutually dependent. This indicates that it is a total system that evolves, including the environment and organisms." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 3.
"The constraints on inorganic chemistry are frequently equilibria, thermodynamic relationships which are quantitatively well-defined by constants, solubility products, complex binding constants and redox potentials. The constraints on organic chemistry are quite differently, overwhelmingly, kinetics, rates of reaction, controlled by energy barriers. Hence many organic chemicals have to be constantly reproduced as they decay. They are energised molecules and react very slowly. They require catalysts and extra energy to change because they are in trapped forms behind energy barriers." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 7.
"Chemotypes, we will say, only arose as a consequence of systematic environmental changes, strongly implying that the dependent chemical evolution of groups of organisms has itself to be systematic, contrary to common belief." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 9. "The reactions of inorganic compounds are often fast so that they proceed to the most stable condition, quantitative equilibrium. By contrast organic compounds react very slowly because they are unstable but trapped in long lifetime energised states. Hence we consider first the principles of changes of much of inorganic equilibrium chemistry separately from any approach to organic chemistry. Because the organic chemistry is linked to the inorganic chemistry it follows that any changes in organic chemistry will be led by the fast inorganic changes, especially those producing catalysts of organic reactions." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 10.
"If we are to further our understanding of evolution we have to appreciate a further energisation of the original material present when Earth formed. This is the rate of weathering: the physical excitation of seawater to clouds and the consequential movement of material by rain. (The formation of raindrops can be catalysed by salt dust, compare biomineralisation.) The resultant weathering with oxidation by oxygen (from energisation of water) increases the amounts of catalytic chemical elements in the sea. Without much further consideration we see that the input of energy without direction is under gravity control and also leads to the irreversible degradation of minerals, giving rise to sediments which provide eventually novel regions, soils, with potential catalysis, for example, for plant growth on land. It is the subsequent role of catalysts to direct chemical and physical change both selecting synthesis and the concentrations of elements and compounds. This is the essence of the evolution of the living process in which weathering becomes central." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. Pp. 25-6.
"Remember that the chemical and physical changes are interactive in the total developing evolution of the environment/organism system." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 45.
“The basic settling
of Earth’s physical-chemical condition at 20° C from 3.5 to 0.75 Ga as
described in Section 2.2 was "These data [changes in element concentration in seawater resulting from geological processes] and the very use of equations (2.9) to (2.11) [three reversible chemical equations: the weathering of silicates with carbon dioxide; the biological process of carbon dioxide with water to produce carbon chains and oxygen; the weathering oxidation of pyrite by oxygen and water to give iron oxide and sulfate] show the very strong coupling of organism and geological chemistry in an ecosystem making it impossible for us to look upon evolution of organisms other than as strongly and systematically coupled to the environment. We stress that the environmental changes overall are unidirectional both in the effect of weathering and in the increase in the oxidation potential though fluctuations occur. They are coupled and inevitable." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. Pp. 62-3.
"The trilobites are an example of animal ‘shells’ of chitin but often include some calcium. Dating their appearance indicates that the hard plastic ‘shells’ evolved at about the same time as the composites. There is every grade of intermediate between highly mineralised and overwhelmingly plastic ‘shells’, but we shall treat their organic chemistry together." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 89.
"To explain the evolution of the ‘biominerals’ we see that we need knowledge of the origin of novel ways of handling certain inorganic elements, and of all trace elements needed in the catalysis of oxidative crosslinking of organic polymers for the matrix due to the variable oxidation states. The evolution of some novel proteins and other polymers could then be used to maintain ways of organising the inorganic materials to create fixed overall shapes or patterns." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 90.
"That is to say we seek systematic chemical change which led to circumstances advantageous to cell development and then organic-matrix and mineral formation particularly that with shape. There is one clear possibility, the rise in oxygen, and with it the changes in the chemical elements in the sea by weathering. It is then the environment which leads to the new possibilities and especially due to changes in oxidation state of inorganic elements and to changes of weathering. The fact that the overall chemical changes in the environment were certainly systematic, and that the fossil record has an obvious sequence which is parallel in many different groups of organisms, gives us strong reason to believe that there is a continuous system to the organic and inorganic chemistry in organisms and that this has led to a systematic evolution of life." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 97.
"The later release of oxygen inevitably changed the oxidation of the environment in stages of various simple chemicals, both the non-metals and the metal ions, in the order of their chemical redox potentials." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 101.
"Although the enzymes that utilise metal ions are no more than one-third of the total their role is frequently in energetically difficult but highly important reactions, including energy transduction, and they are directly connected to the evolving environment." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 104.
"While we showed that inorganic elements were essential for anaerobic life their use in micro-aerobes and aerobes is more extensive as oxygen and its environmental products can only be activated by inorganic chemicals." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. Pp. 126-7.
"A very surprising feature of evolution is that many of the genes lost by later complex organisms are those absolutely essential for life of all organisms. Remarkably the first things lost from the main DNA of the eukaryote cells was the need to produce chemical energy, ATP, and certain pathways such as the reverse Krebs cycle, fatty acid oxidation and nitrogen fixation. Their DNA is found only in the DNA from organelles, incorporated prokaryotes. What could be a more remarkable indication of one route to escape the difficulty of management of the chemical complexity introduced both by use of oxygen and of its environmental products? A possible rationale is that it is much easier to produce bioenergetic gradients in the smallest enclosed volume.... This is a clear indication that the genes which are lost (or not expressed) are those which provide essential products obtainable from the chemicals of the environment, that is from simpler organisms which must make them or from losses of environmental chemicals. But why do this? The losses are extensive and selective. The result is that symbiosis, internal or attached rather than the remote association of simpler with more complex organisms, became common, beginning with the arrival of eukaryotes some 2 or more billion years ago. Whatever the explanation it has to result from a feedback to a part of the DNA to make it redundant. The feedback has to be from the information that a synthesis is not required as the supply is adequate from its cellular environment. This is the same puzzle that arose in the creation of new genes for new chemicals. Clearly the DNA is sensitive in selective ways to its environment whether it is an external feature or a symbiont. The loss of redundant genes is of course an advantage in that it reduces complexity. A feature of it is that loss of certain genes is common across large groups of organisms ...." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. Pp. 281-2.
"The definition of a unique ‘DNA species’ as identifying an organism is less and less tenable as the developing organisms are seen to be dependent more and more on many different kinds of symbionts, both inside and outside organisms, from organelles to parasites inside the skin of multicellular organisms or attached externally to them." Williams, R. & R. Rickaby. 2012. Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life. The Royal Society of Chemistry. P. 289.
"A possible interpretation of the differences between deterministic and statistical law is that they imply a distinction between exact and historical sciences." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 4.
"In summary, the dichotomy between chance and determinism proposed by Laplace was radically inverted by contemporary science. Rather than exact expressions of pure and deterministic physical laws, simple interactions and particles of reality are intrinsically uncertain and probabilistic; and rather than the cause of ignorance, complexity or the statistical composition of entities and their interactions is the very reason for predictability and order that we observe around us." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 6.
"If the ultimate components of reality are intrinsically unpredictable, what is the appeal of the ‘simple’ in the natural sciences? In other words, why is reductionism so influential? The answer is that reductionism was never meant to be a tool against chance; it is a tool against history." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 7.
"Reductionism thus serves two main purposes. The first is the understanding of things composite or complex, such as tables or electromagnetic fields. The second purpose is the conquest of history. While statistical composition generates order from disorder as claimed by Schroedinger, it may also generate history or a record of past events when time is a relevant variable (i.e. when systems are not in equilibrium). This category of problem has come to the fore only recently in the physical sciences as the study of dynamical systems and shows that the concept of history can be extended well beyond its original use as a feature of human societies." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 8.
"The main problem with strictly genetic comparisons is that the information content of a genome (however defined) cannot be an intrinsic property of the sequences themselves; it depends on its effect on a target or receiver." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 26.
"The theory of major transitions has the merit of defining evolutionary increases in complexity both at the phenotypic-organizational (the newly evolved super-units) and genotypic-informational (the new methods of transmitting biological information) levels." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 29.
"The list of four fundamental levels of organisation described above (genetic, developmental, behavioural and cultural), although implicit in previous works, was explicitly proposed by Jablonka and Lamb as the ‘four dimensions’ of evolution." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 33.
"Thus, the evolutionary version of Schroedinger’s Principle proposes that a new biological code when entities that originally performed phenotypic functions gradually evolve into informational carriers themselves." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. Pp. 33-4.
"... Fisher’s argument for micromutations implied that the likelihood of a mutant phenotype being deleterious increases with the number of traits that it involves. Possible antagonistic pleiotropy may be also part of what Orr called the cost of complexity; in a more complex organism, it is more likely that a mutation increasing adaptation in one character may cause deleterious fitness effects on many other traits." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 90.
"... developmental modularity can neutralise one type of antagonistic pleiotropy, namely spatial pleiotropy. In simple terms, gene regulation may evolve so as to switch on or up-regulate a mutation in a module, organ or cell where its effects on fitness are positive, and at the same time switch off or down-regulate the gene in places where its effects are deleterious." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. Pp. 90-1.
"An important conclusion is that due to developmental modularity the origin, evolution and disappearance of countless effector genes, signalling cascades and metabolic pathways may have taken place in a single body segment or organ, or a single cell type.... This means that both genes and phenotypic traits in multicellular organisms are to a certain extent fragmented into a series of developmentally independent units; each of those units responds for a fraction of the phenotypic dimensions of the whole organisms, and for a fraction of the genome." Vinicius, Lucio. 2010. Modular Evolution: How Natural Selection Produces Biological Complexity. Cambridge University Press. P. 91.
"Underlying all information transfer is some form of positive feedback: one individual finds food, a second moves towards the first individual and then still a third moves towards the second and so on." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 44.
"The reason it is important to draw a distinction between cues and signals in information transfer is that signals incur an efficiency cost to the informed individual producing them." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 61.
"... I discuss three general settings under which co-operative signals can evolve in spite of the possibility that other individuals could cheat by following others’ signals while not producing their own. These are repeated interactions, synergisms, and inclusive fitness." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 62.
"The key idea in synergism is that although individuals pay a cost in signaling the location of food, the fact that all individuals in the group produce this signal provides a per capita benefit that outweighs the cost. In particular, provided per capita foraging success increases at least linearly with group size, synergies can evolve even if it would not pay an individual to start signaling in a group of non-signalers." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 62.
"... when confronted with the choice between ascending from one of two ends of a T-shaped structure, weaver ants build a chain down from only one side..." "In cases such as these, where individuals modify their environment, it is not entirely clear whether decisions arise because it is advantageous for individuals to be in a group, or because a choice made by one individual alters the environment in a way that makes it easier for other individuals to follow the same path. Thus, while U-shaped distributions are indicative of decision-making in response to the previous actions of others, they should not be necessarily interpreted as resulting from individuals acting in order to promote cohesion." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 83. "These empirical observations demonstrate a basic property of all collective decision-making and information transfer: positive feedback together with quorum responses lead to U-shaped choice distributions." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 83.
"The assumption that individuals are independent leads to a paradox in the theory of many wrongs [average choice of the group is more likely to be correct than that adopted by one randomly chosen individual – an application of the central limit theory]. On the one hand the theory says that the group is collectively wise, but on the other hand it requires individuals to be independent. If there is too much conferring among individuals before they reach a final decision then their decisions are no longer independent. Positive feedback can spread particular information quickly through the group, encouraging all individuals to make the same, possibly incorrect, choice. Alternatively, if there is too little conferring then each individual will act independently and fail to benefit from the input of others." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. Pp. 92-3 [Note from p. 89].
"Whether animals aggregate depends on their environmental context. Larger groups provide dilution from predator attack and individuals in smaller groups get a larger share of food discoveries... The distance at which a fish is attracted to another fish decreases in the presence of food and increases in the presence of a predator." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 108.
"An example of pairs or small groups of animals becoming anti-phase synchronized is sentinel behavior." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 149.
"Theraulaz et al. propose that local interactions between animals and their environment, a mechanism they call stigmergy, combined with interactions with large scale environmental features, which they call templates, provide two of the key mechanisms for nest construction by insect societies. Examples of templates include light, temperature, and humidity gradients that determine the point at which an individual picks up or drops building material. Templates may also be determined by a signal from individual insects. For example, the queen of the termite Macrotermes subhyalinus emits a diffusive pheromone, which decreases in concentration with distance from the queen." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. Pp. 151-2. Reference: Theraulaz, G., J. Gautrais, S. Camazine & J. Deneubourg. 2003. "The formation of spatial patterns in social insects: From simple behaviours to complex structures. Philosophical Transactions of the Royal Society of London: Series A–Mathematical Physical and Engineering Sciences. 361: 1263-82.
"Makse et al. proposed that cities were constructed according to the following two principles: (1) the probability of development decreases exponentially with distance from the center of the city; and (2) future development is correlated with past development, such that the probability of a particular site being developed increases with the existence of nearby, already developed sites." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 171. Reference: Makse, H. A., S. Havlin & H. Stanley. 1995. "Modeling Urban-Growth Patterns." Nature. 377: 608-612.
"The entrance to a honeybee colony, often referred to as the dancefloor, is a market place for information about the state of the colony and the environment outside the hive. Studying interactions on the dancefloor provides us with a number of illustrative examples of how individuals changing their own behavior in response to local information allow the colony to regulate its workforce. For example, upon returning to their hive honeybees that have collected water search out a receiver bee to unload their water to within the hive. If this search time is short then the returning bee is more likely to perform a waggle dance to recruit others to the water source. Conversely, if this search time is long then the bee is more likely to give up collecting water." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 175.
"Active regulatory feedback involves individuals producing a cue or a signal that in turn changes the probability of other individuals performing some action." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 177.
"... there are three factors that are required to produce over-compensation and chaos in regulatory feedback. The first is that feedback is active, if individuals simply retire from a food source when it becomes overcrowded and return independently from each other to assess whether it is exploitable then collectively they will not over- or under-shoot the equilibrium. The second factor is that information is local. Individuals that have sampled a single food unit cannot determine whether their experience reflects the overall state of the resource. If individuals were able to assess the entire resource then they would have a fuller picture of the effects of recruitment. The last factor is that there is a time delay between the observation and the regulatory response. The generation of instability and chaos depends on discrete time steps. If these are taken away, the oscillations are dampened out. "... Given that such over-compensation can lead to chaotic oscillations, why is active regulatory feedback so common in the interactions of social insects? A first answer to this question lies in the advantages of active feedback when a system is a long way from equilibrium.... In dynamically changing environments, positive feedback can communicate changes in the environment without requiring every individual to experience the change itself. "Even when positive feedback is used to actively up-regulate the number of individuals engaging in a particular task, under most natural conditions equilibrium is reached. Indeed, the three factors that are needed for over-compensation to occur are unlikely to be present simultaneously. In particular, positive feedback is not usually particularly strong within many insect societies." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. Pp. 177, 180.
"Some of the most interesting questions in understanding the organization of insect societies involve the interaction of self-organizing patterns with the behavior of individual workers." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 208.
"This chapter should thus provide a broad classification of many of the collective behaviors discussed in this book as arising from a combination of four distinct forms of cooperation (parasitism, mutualism, synergy, and repeated interactions) and altruism arising from inclusive fitness." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 224.
"In many ways, mutualisms provide a null hypothesis for co-operative behavior. If we see an animal performing a costly behavior that benefits another individual, the first question we can ask is what benefits it gains itself from the action. If it gains irrespective of the actions of its partner then the interaction is mutualistic. "Despite providing a somewhat obvious reason for individuals to cooperate, mutualisms are sometimes overlooked. This can be because the benefits are not immediately clear or the costs are overestimated." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 233.
"Although the members of insect societies are usually related, the relatedness within these groups is often lower than predicted by their supposed family structure. These observations have even led some to question whether relatedness has any importance at all in explaining co-operation." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 247.
"Most importantly, synergistic interactions and helping of relatives should not be viewed as distinct explanations of co-operation, but different parts of a common explanation." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 248.
"There is one last distinction that is worth drawing in the study fo collective animal behavior: that is between behaviors that are strictly co-operative and those that are co-ordinating. The distinction is based on whether the cost to the focal individual has evolved or is simply a by-product of the individual undertaking an activity that is otherwise beneficial to itself. This is the same distinction that is made between cues and signals." Sumpter, David. 2010. Collective Animal Behavior. Princeton University Press. P. 251. "Popper presents metaphysical determinism as being another type of determinism, which asserts that ‘all events in the world are fixed, or unalterable, or predetermined’, and whose determination does not require natural laws and is therefore unpredictable, unlike scientific determinism; in this sense it is not scientific." Nakajima, Toshiyuki. 2013. "Probability in biology: Overview of a comprehensive theory of probability in living systems." Progress in Biophysics and Molecular Biology. 113: 67-79. P. 71.
"Neither type of theory, whether subjective or objective, can comprehend the duality of probability. Subjective theories cannot deal with the objective world in terms of the relative frequency of events, and the objective theories cannot deal with the uncertainty of events that are experienced by subjects." Nakajima, Toshiyuki. 2013. "Probability in biology: Overview of a comprehensive theory of probability in living systems." Progress in Biophysics and Molecular Biology. 113: 67-79. P. 72.
"Knowing and movement have the same mathematical structure as a state change in their own state spaces.... "Unlike in the case of knowing by an external observer, the material entity causally affects the environment." Nakajima, Toshiyuki. 2013. "Probability in biology: Overview of a comprehensive theory of probability in living systems." Progress in Biophysics and Molecular Biology. 113: 67-79. P. 73.
"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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 242.
"... 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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 244.
"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 [sic] 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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 245.
"... the question of consistency between cell reproduction and molecule replication is raised. "First, we found universal statistics of the abundance of chemicals, for a cell that maintains reproduction and chemical compositions. We measured the rank-ordered number distributions of chemical species by plotting the number of molecules ni as a function of their rank determined by ni. The distribution exhibits a power law with an exponent of -1. In our model, this power law of gene expression is maintained by a hierarchical organization of catalytic reactions. 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 microarrary 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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 247.
"... we have recently proposed the following hypothesis: 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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 248.
"For simplicity we consider two types of mutually catalyzing molecules species (X and Y), each of which has catalytically active and inactive types. Here, most types are inactive, and only a specific pair of active types of X and Y mutually support the synthesis of the other. In other words, inactive types are synthesized by the active type of the other species, but they do not contribute to the others’ synthesis. In this sense, they are parasites in the replication system. Indeed, most mutant molecules are such parasites, and the removal of such parasitic molecules is an important question in the origin of life. Now, one of the species Y is assumed to have a much slower synthesis speed than X.... "Thus, through this growth-division process, the fraction of Y species is much lower than X. As the inactive types are more common, the protocell is expected to reach a state in which there exist no active Y molecules. Indeed, from the continuous rate equation, such a solution is expected. However, when there exist no active Y molecules, X molecules are no longer synthesized, and finally, active X molecules become extinct, so that the reproduction of the protocell would stop. 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 ... 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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. Pp. 248-9.
"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. 241-259. Meyer-Ortmanns, H. & S. Thurner (Eds). Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer. P. 251.
"Contrary to what was predicted, proteins lack specificity and this lack of specificity has been observed in all biological phenomena. By ‘lack of specificity’ I mean here that proteins can interact with multiple partners causing a great number of combinatorial interaction possibilities. Of course, this does not mean that they do not show any preference at all for binding with other molecules. It means that this is not absolute." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 47.
"Protein networks have a central hub where connection density is the strongest. This hub is composed of proteins that can bind to a hundred partners or more and constitute about 10% of the network. Their number is therefore in the order of 103. At the periphery of the networks the connectivity of proteins is much lower but, overall, the average connectivity is about 7 or 8. These data indicate that all the regulation pathways implicated in metabolism, signalling or gene expression are potentially interconnected with a great number of contact points because there are large combinatorial possibilities for molecular interactions. Therefore, contrary to what was predicted, a great number of proteins can interact with a great number of molecular partners." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 47.
"Another reason for the lack of molecular specificity is the binding of a single protein domain to different ligands.... This phenomenon causes the number of combinations of possible interactions to be multiplied and challenges the static view of stereospecificity. Indeed, for a single domain the possible ligands can be very different, in form, size and amino acid composition. There is a growing number of arguments indicating that this phenomenon is due to a protein interaction site not being a static entity, but a dynamic one. Its three-dimensional structure is not rigid but flexible. It constantly changes its configuration. A protein in solution would in reality be a population composed of a mixture of several conformations in dynamic equilibrium, each with a particular potential ‘specificity’.... Seen from this perspective, it is not the pre-existing structure of the protein which determines its future interactions but the ligand, which stabilizes one of these conformations and alters the equilibrium of the population." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 48.
"For example, HMGA is a nuclear protein which is intrinsically totally disordered. It has an important role in structuring chromosomes and chromatin, and in the transcription of at least 45 genes. To perform this role it interacts with the chromosomal structures, the nucleosomes, and with at least 18 different transcription factors. In each case, interaction with a different partner confers on it a particular functional structure." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 48.
"Their amino acid composition, hydrophobic nature and electrical charge give disordered proteins a characteristic signature which really differentiates them from structured proteins... They make up 36-63% of genomes in eukaryotes but only 7-33% in prokaryotes and archaebacteria. Protein disorder is therefore positively correlated with multicellularity. It is also significantly increased in signalling proteins and those implicated in cancer, in transcription factors, and in the ‘hub proteins’ of protein networks." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 48.
"How does the cell function in these conditions? To answer this question it is unanimously assumed that molecular networks are themselves subject to spatial and temporal dynamics.... "Signal transduction via a combination of pathways is another mechanism conferring specificity.... Finally, crossed-inhibition between two pathways and the intensity of pathways activation by signals have also been proposed to compensate for the lack of protein specificity." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 49.
"All the mechanisms that compensate for the lack of protein specificity are amply supported by data and they have been produced by researchers working in the frame of the genetic deterministic paradigm. However, it should be noticed that these mechanisms shake this paradigm to its roots. Indeed, they shift the explanation of biological specificity from the molecular to the cellular level. It is no longer the specificity of proteins at the molecular level that explains what happens at the cellular level but the reverse. All these mechanisms presuppose the existence of an organized cell structure expressing proteins in a very precise, spatially and temporally regulated manner, and sorting out non specific molecular interactions. The cell structure acts as a global constraint conferring specificity to molecular interactions." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 49.
"Protein interactions are subjected to macroscopic cell processes which sort them out and confer specificity on them. In this perspective, the chains of molecular interactions that we call networks are the result of these cellular processes, not their cause." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 50.
"Taking into account the intrinsically stochastic behaviour of proteins necessarily brings genetic determinism into question since it relies on the opposite idea that proteins are directed by their stereospecificity." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 50.
"In fact, if cell structure sorts and constrains molecular interactions in ontogenesis, this phenomenon and phylogenesis only form one and the same process and the classical evolutionary synthesis must be modified.... Molecular interactions are sorted by the cell structure which is itself sorted by natural selection, therefore, ultimately, natural selection sorts molecular interactions and the two processes of ontogenesis and phylogenesis are no longer separated, they form only one process that I suggest could be called ontophylogenesis." Kupiec, Jean-Jacques. 2010. "On the lack of specificity of proteins and its consequences for a theory of biological organization." Progress in Biophysics and Molecular Biology. 102: 45-52. P. 50.
"When described simply as a cellular aggregation, multicellular organisms are estimated conservatively to have evolved in at least 25 lineages, making it a ‘minor major’ evolutionary transformation. When more stringent criteria are applied, as for example a requirement for sustained cell-to-cell interconnection, communication, and cooperation, multicellularity has evolved multiple times in bacteria, but only once in the Animalia, three times in the Fungi, and six times among the algae." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 6.
"Nevertheless, the DPMs [dynamical patterning modules] identified by Newman and coworkers cannot be applied directly to plant or fungal development because of substantive differences among these three major eukaryotic clades. For example, during animal development, cells are typically free to migrate and slide past one another in ways that permit differential adhesion, cortical tension, and other processes that can facilitate the sorting and assembly of some tissues, e.g., differences in CAM and P-adherin promote cell sorting during in vitro (but not in vivo) Xenopus gastrulation. In contrast, plant cells are characterized as having rigid cell walls that are typically firmly fixed to one another. Plant signaling molecules can also act intercellularly as well as intracellularly as transcriptional modulators and determinants of tissue as well as cell fate, thereby blurring the functional separation of gene regulatory networks affecting multi- as opposed to single-cell differentiation. Although the intercellular transport of developmental transcription factors is not unknown in animal systems, it is very rare." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 10.
"In light of these and other issues, Hernandez-Hernandez et al. proposed a preliminary set of six DPMs associated particularly with critical embryophyte developmental processes: (1) the formation and orientation of a future cell wall (FCW), (2) the production of cell-to-cell adhesives (ADH), (3) the formation of intercellular lines of communication and spatial-dependent patterns of differentiation (DIFF), (4) the establishment of axial and lateral polarity (POL), (5) the creation of lateral protrusions or buds (BUD), and (6) the construction of appendicular leaf-like structures (LLS)." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 11. Reference: Hernandez-Hernandez, V., K. Niklas, S. Newman & M. Benitez. 2012. International Journal of Developmental Biology. 56:661-674.
"The roles of the FCW, ADH, DIFF, and POL modules played during the evolution of multicellularity are shown when their functionalities are mapped onto a morphospace identifying the major plant body plans and when this map is informed with a series of morphological transformations predicted by a simple multilevel selection model for the evolutionary appearance of multicellularity.... "Each intersection of two or more axes identifies a hypothetical phenotype with the character states specified by the variables or processes stipulated by the participating axes.... "A review of the secondary and primary literature treating the algae shows that all but two of the 14 theoretically possible phenotypes are represented by one or more species." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. Pp. 12-3.
"The ADH, FCW, DIFF, and POL modules also establish character polarities in the context of a multilevel selection theory for the evolution of multicellularity. This theory identifies the unicellular body plan as ancestral to the colonial body plan that in turn is ancestral to a truly multicellular body plan, i.e., it identifies a ‘unicellular => colonial => multicellular’ body plan transformation series that requires ADH to establish and maintain a colonial body plan and FCW, DIFF, and POL to coordinate and specify intercellular activities to achieve an integrated multicellular phenotype whose complexity exceeds simple dyatic interactions among individual cells." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. Pp. 13-4. "A morphospace for the four major plant body plans ...(unicellular, siphonous/coenocytic, colonial, and multicellular) resulting from the intersection of five developmental processes: (1) whether cytokinesis and karyokinesis are synchronous, (2) whether cells remain aggregated after they divide, (3) whether symplastic continuity or some other form of intercellular communication is maintained among neighboring cells, and (4) whether individual cells continue to grow indefinitely in size." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 14.
"Put differently, the evolution of a multicellular organism requires a means to guarantee the heritability of fitness at the emergent level of the multicellular entity. In some but not all multicellular organisms, this guarantee is accomplished by sequestering a ‘germline’, e.g., animals and embryophytes, respectively. A germ-soma separation may be an indirect consequence of the necessity to compensate for the increasing costs of evolving a progressively larger body size. Body size matters because the probability of compounding a genetic error or mutation increases as a function of the number of cell divisions required to achieve the size of a mature organism." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 16.
"Likewise, multicellularity is not required for cellular specialization. Unicellular bacteria, algae, yeast, and amoeba exhibit alternative stable states of gene expression patterns and manifest alternative cell morphologies during their life cycles, often as a result of competing processes, e.g., motility vs. mitosis. This feature is particularly intriguing in light of the studies showing that seemingly random fluctuations in cellular dynamics may provide a simple switch for changing cell fate. For example, Bacillus subtilis can exist in two stable forms, called vegetative and competent, under conditions of nutrient deficiency." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 16.
"Even a loose ‘colony’ of cells can have emergent biological properties that give it a collective edge in which every cell benefits. The origin of the cellular differentiation (DIFF) module therefore may reside in the inherent multistability of complex gene regulatory networks with somatic or reproductive functional roles for different cell-types possibly established by natural selection ad hoc." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 17.
"The conventional scenario for the evolution of multicellular organisms posits a unicellular (uninucleate) => colonial => multicellular body plan transformation series. However, an alternative series is equally plausible in the case of algae, embryophytes, fungi, and even animals–the direct developmental transition of a multinucleate cell into a multicellular life-form." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 17. "That this transformation series [unicellular(uninucleate) => siphonous => multicellular] is as rare as the evolution of very large siphonous/coenocytic organisms is not surprising. A siphonous organism is vulnerable to the rapid systemic spread of a pathogen if its cell membrane is breached. Likewise, although Caulerpa cells are among the largest cells, Einstein’s equation for random walks shows that, beyond a certain size, selection favors cellularization because the time a message takes to travel from one side of a cell to another increases dramatically as the volume of the cytosol increases." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. Pp. 17-8.
"As noted, regardless of an organisms’s body plan, every genome is capable of multiple gene expression patterns that can produce different cellular functionalities. This phenomenology is seen in unicellular bacteria as well as in unicellular algae, yeast, and amoebae exhibiting alternative stable states of gene activity during their life times. It therefore predates developmental transcription factors, such as MADS box and Hox gene products that regulate multistable regulatory networks whose alternative states determine cell type identity in multicellular organisms. Given this ubiquity, it is tempting to suppose that multicellularity might ‘simply happen’ if it conferred no disadvantage or if it provided even the slightest advantage as for example by allowing interconnected and related cells to use different resources simultaneously. Although a single cell cannot express multiple gene expression patterns simultaneously, a multicellular organism can." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 19.
"Nevertheless, there are undeniable advantages to a multicellular body plan and even to the colonial or siphonous body plan that theoretically prefigure its evolution. For example, even the most simple colonial body plan allows different cells to use different resources as a result of physiological specialization even in the absence of morphological differentiation. Likewise, the colonial body plan (and the siphonous body plan) can also reduce the risk of predation as a consequence of achieving larger sizes (that can ratchet body size upward as a result of an ‘arms war’).... The induction of colony formation in response to predation appears to be a widespread phenomenon in some lineages. Indeed, one explanation for the waves of multicellular experimentation occurring at ~1500 Mya in the fossil record is the expansion of predation resulting from the evolution of phagocytosis. Another benefit to aggregating cells into a collective is an increase in the acquisition and utilization of extracellular resources. For example, undifferentiated colonies resulting from incomplete cell separation of Saccharomyces cerevisiae appear spontaneously in cultures with low sucrose concentrations. The cells in these colonies cooperate in ways that reduce starvation and provide protection.... Further, growth experiments of organisms such as the coccolithophyte Phaeocystis show that the colonial phenotype has faster rates of cell division compared to the unicellular phenotype perhaps because the extracellular adhesive matrix can be used to store nutrients that can be used under conditions of environmental stress. These and other selective advantages are perpetuated in the multicellular body plan, which confers an additional benefit–the encapsulation of nuclei into separate but symplastically connected cells establishes discrete physiological boundaries that permit the isolation of different molecular regulators, trafficking routes, cytosolic recycling, transcytosis, exocytosis, and metabolite degradation. Intercellular communication within the multicellular body plan also permits the concerted coordination among these processes to establish, maintain, or switch supracellular physiological domains as well as a stratagem for segregating and isolating defective nuclei resulting from deleterious mutations, which are known to accumulate at cell- and tissue-specific rates." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. Pp. 19-20.
"Finally, it is worth noting that, across diverse animal and plant species, lifespans increase, albeit not one-to-one with increasing body size. For instance, Marba et al. analyzed published data and show that lifespan scales, on average, as the 1/4 power of body size across aquatic and terrestrial, unicellular and multicellular plant species.... If multicellularity confers even a marginal increase in longevity, it might evolve as a life-history strategy for finding an optimal window of opportunity for reproduction or a strategy for reducing transcription errors in cells sequestered for reproduction." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 20. Reference: Marba, N., C. Duarte & S. Agusti. 2007. "Allometric scaling of plant life history." Proceedings of the National Academy of Sciences USA. 104: 15777-15780.
"At least one theory for ageing predicts that, if the level of extrinsic mortality is low, selection can favor organisms with a greater investment in reproduction at the cost of somatic maintenance (and thus a decrease in the rate of survival of the individual). Conversely, under less optimal environmental conditions selection may favor larger organisms with a longer survival probability until conditions for reproduction become more favorable. It is therefore possible that the raison d’etre of multicellularity resides in the mathematics of a generic selection theory for reproductive success, although one must always entertain the possibility that increased lifespans are a consequence rather than a cause of multicellularity." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 20.
"The linkages among body size, life-history traits, and gene-expression patterns provide a logical extension of the previous line of speculation, viz., life cycles with a di- or polyphenic alternation of generations might evolve as a consequence of contentious maternal and paternal gene network expression patterns responding to unpredictable, stressful, or heterogeneous environmental conditions." Niklas, Karl. 2014. "The Evolutionary-Developmental Origins of Multicellularity." American Journal of Botany. 101(1): 6-25. P. 20.
"This view conceives the initial stages of the prebiotic earth as a huge flow reactor containing an amazingly complex set of small molecules of different types, eventually establishing a wide variety of possible interactions among each other. Provided that there is an overall flow of matter and energy across such a supersystem, therefore sustaining far-from-equilibrium dynamics, this complex set could explore an immensely large number of possible reaction pathways. In practice, that exploration would be geochemically and geophysically constrained (by limitations in resources and by the time required for different processes to actually take place), so kinetically driven pathways would have an advantage.... "Such a scenario implies that finding thermodynamically plausible chemical pathways toward life necessarily requires looking into at least moderately complex mixtures of various potential molecular components of life, and studying the chemical and physical interactions among them (e.g., interconversion processes, condensation and polymerization reactions, supramolecular aggregations processes, propagating chemical oscillations, surface and colloidal effects, etc.)." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. Pp. 287-8.
"In the complex prebiotic scenario we are envisaging, at the same time as more and more new molecules were formed by means of catalysis and the coupling of thermodynamically unfavorable reactions with favorable ones, the existing chemical space would have increased, and so would the number of possible catalysts and reactions that could interact with each other. This would certainly lead to a combinatorial explosion of molecular diversity. It has been shown, however, that such an explosion could be tamed by the presence of feedback loops and regulation mechanisms involving different intermediate species, redirecting synthetic processes in unexpected ways. Chemical autocatalysis, in all its forms, may have also funneled the prebiotic combinatorial explosion toward molecules currently recognized as relevant for life. As a result, protometabolic networks of different kinds could have emerged out of these hypothetical, complex molecular mixtures. This will be of crucial importance for our general conception of chemical evolution." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 297.
"Condensation reactions are among the most important processes in the pathway to life, since they contribute to the formation of biopolymers, including proteins and nucleic acids. The general problem regarding the condensation of small organic molecules to form macromolecules in an aqueous environment is the thermodynamically unfavorable process of water removal. In the current biosophere, these types of reactions are catalyzed by enzymes and energetically driven by pyrophosphate hydrolysis. Obviously, one cannot assume that biocatalysts and energy-rich inorganic phosphorus species were present on the Earth before life had actually originated. A number of proposals to overcome these difficulties have been made, taking into account possible scenarios where the abiotic polymerization of different biomonomers could have occurred. These proposed polymerization reactions can be divided into melting processes, hydration–dehydration cycles, heterogeneous systems involving other phases like lipid domains or mineral surfaces, and polymerizations induced by various coupling reagents in homogeneous solutions." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 297.
"Theories on the origin of homochirality in the living world can be classified into two major types: biotic and abiotic. The first ones suggest that selection and amplification of one of the enantiomers of chiral biomolecules took place at an early stage of biological evolution. This view is, however, not consistent with the notion that biopolymers need to be composed of chiral monomers in order to perform their functions. Proteins constituted by mixtures of L- and D-amino acids cannot form well-defined tertiary and quaternary structures.... An abiotic source of homochirality then seems more compatible with the principles of biology, but it implies the presumption of some kind of symmetry-breaking process leading to enantioenriched biomonomers. It is also plausible that enantioenrichment could have happened along the synthesis of biopolymers rather than at the monomeric molecular level. A compromise solution between both extremes would be that chiral monomers were only partially enantioenriched before they polymerized. The competition to build biopolymers would then be gradually won by the majoritarian enantiomer, leading to more efficient chiral selection as the complexity of biopolymers increased." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 303.
"In summary, given the large number of possible phenomena that have been described to generate chiral biomolecules from nonchiral matter, the assertion by Ball that we are ‘spoilt for choice’ among possible explanations for the origin of homochirality makes more sense every day." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 307. Subquote: Ball, P. 2007. Chem. World. 4:30.
"In fact, in chemistry nonlinearities abound, which may amplify microscopic fluctuations into long-range stable correlations, just as in physical systems. But the possibilities in terms of diversity of compounds and specific interactions among them (heterocatalysis, feedback loops, more indirect regulatory mechanisms, couplings between various autocatalytic cycles, etc.) are much wider and richer than in purely physical systems. In addition, other processes that involve many component parts but lead to quasi-equilibrium structures could be occurring locally at the same time. This second type of processes, when they happen spontaneously and are not dependent on the formation of covalent bonds but on weaker types of interaction (e.g., van der Waals, hydrophobic, medium-range ionic forces), are generally conceived as self-assembly and included within the area of supramolecular chemistry." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 308.
"Autocatalysis is a very common mechanism in chemistry and is considered crucial in all scenarios of the origins of life,...." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 310.
"... one should distinguish between network or cyclic autocatalysis, in which there is net production of (at least) one intermediate reactant within a closed cycle of chemical transformations, and molecular or replicative autocatalysis, where one of the products of a reaction serves as a catalyst for that very reaction." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 310.
"Strictly speaking, a protometabolic cycle could achieve self-sustenance simply by stoichiometric means. In cycles whose elementary reactions are stoichiometric, rather than catalytic, the cycle itself can act as a catalyst if some byproduct of the cycle is produced in excess. An example corresponding to the formose reaction, in which two molecules of glycoaldehyde are formed for each molecule entering the cycle, is depicted ..., but the same kind of behavior is observed in Calvin or citric acid cycles. The emergence of catalytic pathways for instance, by adjoining from the surrounding chemical milieu mineral catalysts, organocatalysts, or eventually ribozymes that catalyze one or various steps of the cycle obviously would offer a kinetic and, thereby, evolutionary advantage to the cycle. In fact, this represents the most logical and probable evolution from elementary autocatalytic cycles toward more intricate network topologies. "One of the main problems of this type of approach searching for protometabolic cycles is that, except for the already mentioned formose reaction, there are no other known examples of prebiotically plausible autocatalytic reaction cycles that could help to build a natural bridge between organic chemistry and biochemistry." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 311.
"... the term ‘replication’ will convey any reliable copying process, taking place at the molecular level, that gives as a result new molecules that conserve the specific sequence of a pre-existing one (commonly called the template); in turn, the term ‘reproduction’ will be used as a more general concept that involves the spatial multiplication or division of a whole system and is not necessarily reliable, in a statistically meaningful sense, as far as the production of identical copies is concerned." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 316. Based on idea put forward by Dyson, Freeman. 1985. Origins of Life. Cambridge University Press.
"As the number of components of the set increases, so do the possibilities of cross-catalytic and inhibitory or competitive pathways within the system, and ‘network behavior’ is more likely to appear; that is, situations in which the characterization of catalytic pathways in isolation and the expected relationships among them differ from the actual complete system dynamics." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 321.
"It is also important to mention that this kind of network behavior can be highly sensitive to experimental conditions... Ghadiri and co-workers designed a network of 81 peptide components, some of which were self-replicating and some cross-replicating. ... they employed nine different reactants plus a common substrate to give nine different template products. In principle, three of the templates behaved autocatalytically and 22 cross-catalytic interactions were identified (including two-, three- and four-member groups or cycles), but the most interesting feature was the fact that the topology of the network could substantially change depending on (i) which templates were initially present in the mixtures, (ii) whether the pH of the solution was lower than 5, and (iii) whether metal salts were introduced or not." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 322. Reference: Ashkenasy, G., R. Jagasia, M. Yadav & M. Ghadiri. 2004. Proc. Natl Acad. Sci. USA. 101: 10872.
"The latest achievement in the field of sugar-modified nucleic acid analogues has been reported by Holliger and co-workers, who showed that up to six artificial polymers can be used to store and propagate genetic information." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 325. Reference: Pinheiro, V., A. Taylor, C. Cozens, M. Abramov, M. Renders, S. Zhang, J. Chaput, J. Wengel, S. Peak-Chew, S. McLaughlin, P. Herdewign & P. Holliger. Science. 2012. 336: 341.
"The chemical basis of such versatility [roles of RNA in cells] relies on the fact that RNA is usually a single-stranded molecule, thus being able to promote intramolecular base-pairing and adopt a much greater variety of three-dimensional structural/functional motifs than double-stranded DNA. RNA secondary structure (the planar depiction of the intramolecular nucleotide pairing) offers a simplified yet appropriate representation of the genotype (sequence, object of mutations) to phenotype (shape and function, object of selection) map, useful for addressing relevant evolutionary questions." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 327.
"Indeed, the RNA world hypothesis posits that as metabolic requirements became more sophisticated, increasing demand on different kinds of catalysis was a selective pressure leading to the transition to protein enzymes." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 328.
"The emergence of dynamic combinatorial chemistry (DCC) was probably the most important event toward the development of systems chemistry,... "DCC is defined as combinatorial chemistry under thermodynamic control. A dynamic combinatorial library (DCL) is formed by a set of interconvertible molecules through reversible bond formation. This definition implies that the distribution of library members is governed by their relative free energies. Moreover, any external stimulus, either a chemical or a physical process able to change the free energy of one or more of the DCL members, can ultimately alter the whole energy landscape as well as the products distribution of the library." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 338.
"Combining DCLs with irreversible chemistries (e.g., catalysis, self-replication, or self-assembly events) is another way to make them kinetically driven, normally implying a significant increase in the amplification of target-selected library members." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 339.
"As has been summarized in the sections above, the problem of the origins of life is related to the characterization of plausible synthetic pathways to biological monomers and their subsequent nonenzymatic polymerization." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 342.
"In vitro evolution of nucleic acids allows the screening of large combinatorial libraries of RNA or DNA molecules for a specific function, such as catalysis or target-binding. These cell-free evolution experiments have led to the selection of novel ribozymes, artificial DNA enzymes, and target-binding nucleic acid molecules (i.e., aptamers). The iterative in vitro process involves serial cycles of amplification and selection of the functional nucleic acid until the desired activity is reached." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 346.
"In vitro evolution is distinguished from in vitro selection in that the former includes continuous introduction of genetic variation in the molecular population, through mutation and/or recombination. A further step in experimental directed evolution was the development of a system for continuous in vitro evolution of nucleic acids, which, in contrast to the stepwise protocol, combines the processes of selection, amplification, and genetic diversification within the same reaction mixture." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 347.
"It has been demonstrated that polymerization of amino acids and nucleotides can be assisted by mineral (e.g., montmorillonite clay) or metal surfaces, lipid membranes, eutectic phases in water–ice, and small cofactor molecules." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 349.
"One of these versions [of the role of autocatalysis in different origin of life scenarios] is cyclic autocatalysis, in which there is net production of at least one intermediate species within a closed cycle of chemical transformations (e.g., in the formose reaction or in metabolic pathways).... Most probably, autocatalytic networks of this kind may have been assisted, at the very begining, by mineral or organic catalysts.... "Besides mechanical extrusion, this process generally occurs through growth and subsequent division, when vesicles reach sizes at which they become unstable. Vesicle growth can be induced by the addition of more amphiphilic molecules, in the form of micelles, or by generating the amphiphile in situ from a precursor. Interestingly, this type of vesicle growth has been shown to be autocatalytic under certain conditions, when the incorporation of new amphiphile molecules is accelerated by the presence of preformed vesicles.... "The third type of autocatalysis relevant to the origins of life is template-directed molecular autocatalysis, ..." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 350.
"Although the RNA world hypothesis, mainly based on the capacity of RNA to play both roles of information storage and catalysis, is supported by much theoretical and experimental data, it is unlikely that the first self-replicating ribozymes could have survived and evolved in bulk solution, given the heterogeneous chemical map of the prebiotic Earth. That is why the role of mineral surfaces, membrane compartments, small cofactor molecules, and metabolic networks is being considered as a new, key element of this hypothesis." Ruiz-Mirazo, Kepa, C. Briones & A. De la Escosura. 2014. "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life." Chemical Reviews. 114: 285-366. P. 350.
"...competitive coherence. This process is a particular way of selecting a subset of elements from a much larger set. This subset is an active subset insofar as it determines the behaviour of the system. Such a subset is selected by a competition between (1) those elements that have a relationship with the elements in the previous subset and (2) those elements that have a relationship with the elements already selected to be part of the new, emerging subset." Norris, Vic. 2014. "What Properties of Life Are Universal? Substance-Free, Scale-free Life." Orig Life Evol Biosph. 44: 363-367. Pp. 363-4.
"The second universal property of life is differentiation. Differentiation is almost inescapable in systems where negative feedback operates globally and positive feedback operates locally. During the cell cycle of E. Coli, the two daughter chromosomes (that for my purposes here are essentially identical) compete for limiting factors like RNA polymerases, which constitutes a global negative feedback; at the same time, a region of one chromosome that is being expressed by polmerases is pulled by these polymerases out of the nucleoid (where it could be buried and relatively inaccessible) thereby increasing the region’s accessibility to more polyermases, which constitutes a local positive feedback. Therefore these chromosomes have different patterns of expression and confer different phenotypes on the daughter cells that inherit them." Norris, Vic. 2014. "What Properties of Life Are Universal? Substance-Free, Scale-free Life." Orig Life Evol Biosph. 44: 363-367. P. 364.
"The third universal property of life is dualism. Living systems are often forced to choose between apparently incompatible strategies: either (1) to interact, take risks and grow of (2) to minimise interactions, avoid risks, shut themselves down and survive. An organism that tries to grow exponentially will run out of resources and be forced to abandon this strategy if it is to survive. An organism that never grows whilst others manage to do so successfully will be forced to abandon this strategy if it is not to be out-competed. In the limit, living systems at different evolutionary times and in different places in the cosmos have to navigate in phenotype space between the two basins of growth and survival.... The population solution to this problem is evident in modern bacteria, which display a significant phenotypic heterogeneity such that some bacteria are growing rapidly whilst others are ready for stresses." Norris, Vic. 2014. "What Properties of Life Are Universal? Substance-Free, Scale-free Life." Orig Life Evol Biosph. 44: 363-367. P. 364.
"The sixth universal property is the maintenance of connectivity.... A physical object might be said to exist if there is a topologically closed (or nearly closed) discontinuity in the connectivity of the elements in an environment; this discontinuity constitutes a frontier of connectivity that makes an object different from its environment. The exact nature of this object is defined by the pattern of connectivity of its constituent elements.... One of the fundamental characteristics of living systems is that either they grow now or they (or their ancestors) once grew or both. Growth entails the addition of new bits or constituents. Such addition does not necessarily change the number of [sic] nature of the connections between the constituents so the average connectivity of the constituents in the growing system stays the same." Norris, Vic. 2014. "What Properties of Life Are Universal? Substance-Free, Scale-free Life." Orig Life Evol Biosph. 44: 363-367. P. 365.
"The seventh universal property is the combination of intensity sensing and quantity sensing. The intensity problem confronting living systems during growth is that the non-equilibrium constituents that do the work – like the enzymes in a cell – eventually reach a point at which they are working with such intensity that they can do no more; the cell can then do no better than grow linearly. The quantity problem that also confronts living systems during growth is that the quantity of unused, quasi-equilibrium material – such as some of the macromolecules in a cell – accumulates; this material risks being a waste of resources. By sensing both intensity and quantity, a living system like a cell can decide when it is time to increase the number of enzymes and to convert its unused macromolecules into another form." Norris, Vic. 2014. "What Properties of Life Are Universal? Substance-Free, Scale-free Life." Orig Life Evol Biosph. 44: 363-367. P. 366.
"... biology of the 20th century has been overtaken by an ‘autonomy of biology’ philosophy, one openly endorsed by Ernst Mayr, one of the leading evolutionary biologists of the 20th century, whereby biology is treated as a disparate science governed by a separate philosophy to the one underpinning the physical sciences. There are two kinds of matter, inanimate and animate, the physical sciences deal with the former; the biological sciences deal with the latter, and that’s that!" Pascal, Robert & A. Pross. 2014. "The nature and mathematical basis for material stability in the chemical and biological worlds." Journal of Systems Chemistry. 5:3. P. 1. Reference: Mayr, Ernst. 1988. Toward a New Philosophy of Biology. Harvard University Press.
"Though energetic stability necessarily leads to time stability, the reverse does not necessarily apply. A system may well be stable in a time sense (persistent) without being stable in an energy sense. The familiar concept of kinetic stability characterizes that other stability kinds, as exemplified by a hydrogen and oxygen gas mixture. Such a mixture is highly unstable in an energetic sense, but can be highly stable in a time sense – a mixture of the two gases may well persist over long periods of time. "But, as noted earlier, within the biological world as well as parts of the chemical world, an alternative kinetic stability kind exists and governs the nature of transformations with that world – DKS, a stability kind associated solely with the replicative world, and distinct to the more familiar static kinetic stability mentioned above.... They [replicating systems] are stable, not because they do not react, but because they do – to make more of themselves – thereby opening a door to a distinctly different organizational form of matter." Pascal, Robert & A. Pross. 2014. "The nature and mathematical basis for material stability in the chemical and biological worlds." Journal of Systems Chemistry. 5:3. P. 4.
"Nowadays the central question posed by ‘the environment’ is not what it can teach us about ourselves and our place in the larger cosmic order, as it was in ancient times, but rather how we can understand its workings so as to make better decisions about our own conduct regarding it." McShane, Katie. 2012. "The Environment: How to Understand It and What to Do about it." Pp. 1-18. Kabasenche, William, M. O’Rourke, and M. Slater, Eds. 2012. The Environment: Philosophy, Science, and Ethics. MIT Press. P. 2.
"The last universal ancestor is envisaged as a gene-swapping community of thermotolerant organisms that were genetically redundant, metabolically diverse, and structurally complex." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 58. "LUCA was neither simple nor rough-hewn; she was not a eukaryote in the modern sense but may have been a protoeukaryotic communal organism whose rich and dispersed genome threw offshoots both up the scale of cellular organization and down. Eukaryotes arose by the accretion of greater complexity, larger size, superior autonomy, and more efficient use of energy; these laid the foundations for their subsequent spectacular advances in physiology and morphology. Prokaryotes, by contrast, are products of reductive evolution. Selection for rapid reproduction and the quick utilization of resources whenever they happened to become available favored small size, specialization, and streamlined genomes. Archaea in particular appear specialized for life at high temperatures and other stressful circumstances." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. Pp. 59-60.
"By hypothesis, she [LUCA] was not a particular organism at all but an eco-system, a community of quasi-cellular entities that exchanged genes and evolved collectively, and from which the progenitors of the three domains crystallized. Mobile genes probably rode on the ubiquitous viruses, themselves members of a parallel virus universe, as ancient as that of cells." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 75.
"How is spatial organization carried from one generation to the next? Genes are part of the answer but not all: genes specify molecular structures but not cell organization. Instead, a growing and dividing cell constructs the new generation upon its predecessor. The existing cell structure guides the placement of newly produced molecules in their proper position. Offspring resemble their parents because they share the latter’s genes, but also because they were built upon the same template. The new cell is physically and architecturally continuous with its progenitor; and the chief agents of structural continuity are the cytoskeleton and cellular membranes." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 93.
"He [Guenter Blobel] realized that a functional membrane studded with a particular set of enzymes, transport-carriers, and receptors can never be generated de novo; it must arise from a preexisting membrane either by modification, or else by growth and division, or by budding. Moreover, since proteins can only be inserted after interactions with a complementary receptor, a growing ‘genetic’ membrane propagates its own kind. Just as every cell comes from a cell, so does every membrane come from a membrane." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 94. Reference: Blobel, G. 1980. "Intracellular membrane topogenesis." PNAS USA. 77:1496-500.
"The central function of eukaryotic endomembranes is not bioenergetics but transport: they mediate both secretion and the uptake of particulate matter, and communicate (usually) by means of cargo-carrying vesicles that bud off one compartment and fuse with another." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 120.
"The origin of life ... is also the black hole at the root of biological organization,..." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 165.
"... a protozoan cell has much more power at its command than a bacterial cell:... Eukaryotes made use of that surplus energy to expand their genomes by orders of magnitude:..." Harold, Franklin. 2014. In Search of Cell History: The Evolution of Life’s Building Blocks. University of Chicago Press. P. 206.
"Recently I showed that a simpler physical effect [than membrane separation] can lead to evolution in a chemical system; namely, the thermodynamic fluctuations of concentration of the polymers.... Local differences in molecule concentration play the role of the volumes delimited by membranes, leading to the increase of the concentration of the superior mutants. Anyhow, no individual living entities are present–evolution involves the whole solution.... In other, more dramatic words, there has been no ‘first living cell,’ but a ‘living ocean,’ which later split into protocells.... "Summarizing the above concepts, thermodynamic fluctuations can provide a mechanism for evolution, alternative to the presence of membranes, in marginally stable chemical systems." Brogioli, Doriano. 2011. "Marginal stability in chemical systems and its relevance in the origin of life." Physical Review E. 84, 031931. P. 2.
"In mechanics, an example of marginally stable system is a marble on a horizontal track. The marble can remain at any point of the track, since any point is a marginally stable equilibrium state. On the other hand, a disturbance will result in a displacement of the marble along the track. The marble will not return to the original position, but it will reach a different stationary point since there is no restoring force. By analogy, the presence of the stationary state curve of Fig. 3 allows the chemical system to move smoothly under the effect of spontaneous concentration fluctuations, passing from a stationary state to one of the surrounding, without being called back. This is not possible in a system that presents a single stable stationary state, because the system eventually comes back to the stationary attractive state, after having been displaced." Brogioli, Doriano. 2011. "Marginal stability in chemical systems and its relevance in the origin of life." Physical Review E. 84, 031931. P. 6.
"Marginal stability allows drift along the stationary-state curve under the effect of concentration fluctuations.... The drift can be interpreted as the evolution toward a more efficiently replicating system." Brogioli, Doriano. 2011. "Marginal stability in chemical systems and its relevance in the origin of life." Physical Review E. 84, 031931. P. 12.
"In general terms, complexity C may be considered to result from a combination of three features: Multiplicity, interconnection, and integration.... "... the multiplicity M represents chemical diversity in constitution and function, I1 stands for the interconnections–interactional (noncovalent), reactional (covalent), as well as their dynamics–and the third term, I2 indicates the full integration of all features (constitutional, functional, motional) through networks with feedback and regulation; ..." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2838.
"Chemistry, [is] the bridge between the laws of the universe and their expression in a highly complex feature (life), thereby unraveling the generation of complex matter by self-organization, the driving force of the evolution of the universe." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2838.
"Increasing complexity leads to the emergence of higher level features in chemistry and biology. Such chemical evolution rests on selection, operating on structural and functional diversity generated by the action of intra- and intermolecular electromagnetic forces on the components of matter. It is clear that, before Darwinian evolution of living organisms, there must have been a purely chemical evolution that progressively led to the threshold of life. Indeed, prebiotic self-organization needs to be understood to establish the basis for biotic self-organization." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2838.
"Thus, beyond self-organization by design, which relies on programming, self-organization may take place with selection, by virtue of a basic feature inherent in supramolecular chemistry, the dynamic character residing in its ability to undergo constitutional dynamics.... "Thus, in addition to reactional dynamics and motional dynamics, there is a third type of dynamic processes to be considered: constitutional dynamics." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2840.
"Molecular motions in biological entities occur in a viscous medium, that is, at low Reynolds number R, which represents the ratio of inertial momentum to viscous forces. Thus, life occurs at low Reynolds number." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2840.
"CDC [constitutional dynamic chemistry] has been operational in the implementation of selection in chemistry. Selection in a DCL [dynamic combinatorial library] is performed by interaction of its constituents with a target or an effector. It depends on the information stored in the constituents and its processing through the interaction patterns. Thus, DCLs and their behavior lead to a paradigm shift from the notion of ‘pure compounds’ towards an ‘instructed mixture’, which involves the spontaneous but controlled build-up of structurally organized supramolecular entities from a mixture of instructed components, following well-defined programs and interactional algorithms." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2842.
"The three basic types of dynamic chemistry processes–reactional/interactional, motional, and constitutional dynamics–may be combined in an orthogonal fashion to provide features of higher complexity to the system. "Reactional/interactional dynamics concern the making and breaking of chemical bonds on the molecular level and of intermolecular interactions on the supramolecular level, respectively.... "Motional dynamics cover molecular motions, reversible changes in shape (morphological exchange, including conformational and configurational changes), molecular motors, and ‘machines’. "Constitutional dynamics involve reversible changes in the constitution of molecular and supramolecular entities by component exchange." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. Pp. 2842-3.
"Adaptive chemistry explores the response of a system to physical or chemical agents, such as environmental/medium influences, phase exchange, physical stimuli (temperature, light, pressure), chemical effectors (protons, ions), morphological switching." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2843.
"Co-evolution processes allow for fast optimization and provide a strong driving force in adaptive chemical systems through simultaneous selection of the mutually ‘fittest’ partners." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2844.
"In the long range perspective, the development of chemical science is toward complex systems, spanning the broadest outlook from divided to condensed matter then to organized and adaptive matter, on to living matter and thinking matter, up the ladder of complexity." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2847.
"... maybe chemistry is in charge of the biggest question of all, and that is: How does and did matter become complex?... It is the task of chemistry to decipher what lies behind this word [self-organization], to fill in the steps that progressively led to matter of increasing complexity, to find out how new properties emerged at each level, to look beyond at what higher forms of complex matter are there to be evolved, to be created in the minds and hands of the scientists. Thus, chemistry builds the bridge between the laws of the universe and their specific expressions in life and thought." Lehn, Jean-Marie. 2013. "Perspectives in Chemistry–steps towards Complex Matter." Angewandte Chemie International Edition. 52; 2836-2850. P. 2848.
"Although its impact on the activity of chemists has not been comparable, so far, with the impact of systems biology within biology, systems chemistry has managed to bring together scientists from various areas, like supramolecular chemistry, far-from-equilibrium chemistry and prebiotic chemistry. And, in fact, it constitutes a similar shift in focus towards complex dynamic behavior, supported by a novel suite of methodologies (including dynamic combinatorial chemistry, high-throughput techniques applied to populations of macromolecules, as well as micro- and nano-fluidics...)." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381:11-22. P. 12.
"Thus, chemists have also contributed to the shift by abandoning, in the last decades, the ‘security zones’ of solution-phase and solid-state chemistry, addressing processes that take place in soft matter, on surfaces and at interfaces." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 14.
"More generally speaking, such a ‘prebiotic systems chemistry’ view would be based on the assumption that heterogeneous aqueous solutions of different monomers and oligomers coexisted in the pre-cellular world, and that different catalytic species might have been present, including metals, mineral surfaces, and reactive interfaces with water-based media. Thus, it seems that the traditional gene-first vs. metabolism-first controversy will be progressively substituted by a scenario in which all the basic molecules co-evolved from the beginning in different (though sooner than later interconnected) environments, forming heterogeneous, pre-biochemical interaction networks. This more integrative approach, all the way from the very beginning could help to explain the transition from complex (but still just thermodynamically driven) chemical systems into proto-biological ones and eventually, into mature living organisms (where kinetic and spatial control of reactions take over...)." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 15.
"... thanks, as well, to the presence of other biomolecules (the genes or, rather, the whole cell DNA, the genome) that stay there, practically unaltered–in characteristic metabolic time scales–as a reference for the rest, so that the system does not lose its complexity and eventually decays." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 17. "The question under focus here would be how to generate chemical microenvironments that distinguish themselves from the surrounding milieu and have, therefore, chances to become progressively more complex than the latter." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 18.
"... the key point to be highlighted here is that, even for the earliest steps of prebiotic chemistry, a diverse combination of molecular ingredients and processes might well be required. The intuition behind this conceptual change is that a certain number of different ‘chemical tasks’ (not just catalysis, but also transduction mechanisms, spatial confinement, mediated diffusion or template activity) may need to be jointly performed in order to ensure a minimal level of dynamic stability or robustness, even in the simplest infrabiological systems." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 18.
"... the option ... would entail the functional engagement of four main types of ingredients (membranes, catalysts, energy currencies and templates) that become increasingly complex and interdependent as protocells develop ...." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 19.
"The main goal of systems chemistry is to ascertain the roots of biological complexity, ..." De la Escosura, Andres, C. Briones & K. Ruiz-Mirazo. 2015. "The systems perspective at the crossroads between chemistry and biology." Journal of Theoretical Biology. 381: 11-22. P. 20.
"The involvement of processes in which a flux of energy (or matter in an activated state) is irreversibly transformed through a dissipative process, producing entropy in the environment in a way that is coupled to a local decrease within the self-organizing system, is then crucial for living organisms. With regard to the origin of life, the formation of an organized system coupling the use of this irreversible energy flux with self-organization must have required the spontaneous decay of chemical species involved in the process to be slow enough so that features of organization can develop." Pascal, Robert. 2012. "Suitable energetic conditions for dynamic chemical complexity and the living state." Journal of Systems Chemistry. 3:3. Pp. 1-2.
"... chemical self-organization cannot emerge when species decay with fast rates toward the equilibrium state." Pascal, Robert. 2012. "Suitable energetic conditions for dynamic chemical complexity and the living state." Journal of Systems Chemistry. 3:3. P. 2.
"Considering that the practical lifetime of an energy carrier or a metabolite that accumulates significantly in a metabolic or proto-metabolic pathway must be comprised between 1 s to 100 yr (more than 9 orders of magnitude) an assessment of the kinetic barriers needed for a system capable of self-organization at moderate temperature (300K) can be given as a range of free energy of 74 to 129 kJ mol-1." Pascal, Robert. 2012. "Suitable energetic conditions for dynamic chemical complexity and the living state." Journal of Systems Chemistry. 3:3. P. 3.
"... the kinetic barrier of the reverse of the activation reaction must be high enough so that the proto-metabolism works as a one-way chemical system." Pascal, Robert. 2012. "Suitable energetic conditions for dynamic chemical complexity and the living state." Journal of Systems Chemistry. 3:3. P. 4.
"Most importantly, the cancer attractor model naturally unites genetic and non-genetic aspects of cancer development, as well as offers a systems framework for tumour reversion and other non-cell-autonomous aspects of cancer." Plankar, Matej, I. Jerman & R. Krasovec. 2011. "On the origin of cancer: Can we ignore coherence?" Progress in Biophysics and Molecular Biology. 106: 380-390. P. 384.
"Engel et al. have for the first time directly measured quantum coherent energy transfer through the entire bacteriochlorophyll complex of green sulphur bacteria, which is composed of several protein monomers and light pigments. According to the authors, the measured coherence time (660 fs) is long enough to guide the dynamics of the biochemical reactions of the complex. Specifically, the coherence allows the complex to sample vast areas of the energy phase space simultaneously (by exploiting the quantum phenomenon of superposition), to find the most efficient path for light energy transfer to the reaction centre. This mechanism contrasts with a semi-classical ‘hopping’ mechanism through which the electron excitation would move stepwise between different excited states, dissipating energy at each step, where only one state could be occupied at any one time. Since 2007, several subsequent studies have confirmed this result with almost identical conclusions." Plankar, Matej, I. Jerman & R. Krasovec. 2011. "On the origin of cancer: Can we ignore coherence?" Progress in Biophysics and Molecular Biology. 106: 380-390. P. 384. Reference: Engel, G., T. Calhoun, E. Read, T. Ahn, T. Mancal, Y. Cheng, R. Blankenship & G. Fleming. 2007. "Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems." Nature. 446: 782-6.
"On the other hand, much indirect evidence indicates the generic presence of coherent endogenous electromagnetic fields in living organisms, behaving classically compared to quantum entangled states in the photosystems. These include, for example, a strong frequency-dependent growth rate of bacteria, indicating resonant electromagnetic interactions, coherent nanomechanical vibrations in the yeast cell wall, strong dielectrophoretic behaviour of particles in the vicinity of cells (indicating the presence of endogenous electromagnetic fields), and direct measurement of electromagnetic fields around different cells." Plankar, Matej, I. Jerman & R. Krasovec. 2011. "On the origin of cancer: Can we ignore coherence?" Progress in Biophysics and Molecular Biology. 106: 380-390. P. 384.
"We will broadly define biological coherence as a synchronized behaviour of coupled elements within a biological system, either of quantum or electromagnetic origin, able to influence biological processes in a biologically meaningful way." Plankar, Matej, I. Jerman & R. Krasovec. 2011. "On the origin of cancer: Can we ignore coherence?" Progress in Biophysics and Molecular Biology. 106: 380-390. P. 384.
"The physical milieu integrating through long-range correlations different chemical as well as physical components is recognized as the ‘morphogenetic field’. Morphogenesis and phenotypic differentiation are therefore time and space-dependent processes." Bizzarri, Mariano, A. Palombo & A. Cucina. 2013. "Theoretical aspects of Systems Biology." Progress in Biophysics and Molecular Biology. 112: 33-43. P. 36.
"Indeed, it could be envisaged that a relevant role for ‘genes’, emerges only when the systems is experiencing a phase-transition, like those occurring during differentiation and/or when cells acquire a new phenotype." Bizzarri, Mariano, A. Palombo & A. Cucina. 2013. "Theoretical aspects of Systems Biology." Progress in Biophysics and Molecular Biology. 112: 33-43. P. 39.
"Several reports have later confirmed that the microenvironmental field can revert the neoplastic phenotype in both in vitro and in vivo experiments." Bizzarri, Mariano, A. Palombo & A. Cucina. 2013. "Theoretical aspects of Systems Biology." Progress in Biophysics and Molecular Biology. 112: 33-43. P. 39.
"Thereby, cell shape should be considered a critical determinant of cell function, given that it appears to govern how individual cells will respond to physico-chemical cues in their local microenvironment." Bizzarri, Mariano, A. Palombo & A. Cucina. 2013. "Theoretical aspects of Systems Biology." Progress in Biophysics and Molecular Biology. 112: 33-43. P.40.
"Compatibilism is the most complex and the most interesting position, both in moral thought, where it involves recognising a degree of determinism while also arguing that we have what Dennett called some ‘elbow room’ within a deterministic universe.... What is the analogue to compatibilism in the biological sphere? Precisely, the anti-essentialist privileging of chance, which recognises the existence of causality without defending causal fundamentalism ( a pluralism of causes, then)." Wolfe, Charles. 2012. "Chance between holism and reductionism: Tensions in the conceptualisation of Life." Progress in Biophysics and Molecular Biology. 110: 113-120. P. 115.
"An alternative to SMT [somatic mutation theory of carcinogenesis] is tissue organization field theory (TOFT), which posits that cancer arises from the deregulated interplay among cells (cells/stroma) and their microenvironment. According to TOFT, the microenvironment represents the physical-biochemical support of the morphogenetic field which drives epithelial cells towards differentiation and phenotype transformation, according to rules understandable only by means of a systems approach." Bizzarri, Mariano & A. Cucina. 2014. "Tumor and the Microenvironment: A Chance to Reframe the Paradigm of Carcinogenesis?" BioMed Research International. 934038. P. 2.
"The switching between different stable states (representing differentiated or pathological phenotypes) requires that the activity/expression of several ‘signaling’ molecules change in concert. Indeed, phenotype reversions are linked to the simultaneous coexpression of hundreds of different transcription factors and multiple downstream genes." Bizzarri, Mariano & A. Cucina. 2014. "Tumor and the Microenvironment: A Chance to Reframe the Paradigm of Carcinogenesis?" BioMed Research International. 934038. P. 4.
"The balance between tensional forces and the cytoskeleton architecture modulates thereupon several complex cell functions like apoptosis, differentiation, proliferation, and ECM [extracellular matrix] remodeling among others. That model can help in understanding the ‘dual’ role displayed by a lot of ‘signaling molecules,’ selective sensitivity to drugs, and why cancer cell behavior may proceed regardless of their ‘mutated’ genes..... To date, an overwhelming body of data has revealed that mechanical tension generated through molecular interactions within the cytoskeleton is indeed critical for modulating molecular activity and to dramatically influence cell form and function." Bizzarri, Mariano & A. Cucina. 2014. "Tumor and the Microenvironment: A Chance to Reframe the Paradigm of Carcinogenesis?" BioMed Research International. 934038. P. 4.
"The term ‘microenvironment’ encompasses discrete, interacting elements, such as extracellular matrix (ECM), stromal cells, molecular diffusible factors, configuration of the cell-stroma architecture, nonlocal control through field’s forces, and topologic geometry of the emerging tissue.... In other words, to understand tissue level phenomena, it is necessary to study the tissue and not single pathway [sic] in cells isolated from their tissue environment. The radical change in theoretical perspective requires a shift from the gene-centric paradigm to the cell-microenvironment system, ...." Bizzarri, Mariano & A. Cucina. 2014. "Tumor and the Microenvironment: A Chance to Reframe the Paradigm of Carcinogenesis?" BioMed Research International. 934038. P. 5.
"As the surfaces of proteins are more mobile and more extensive than those of substrates there are many possible very similar states. There is then the possibility that an assembly of proteins can fluctuate or can be adjusted in shape, energised, as in muscles, or that one protein can travel on another as in transport on tubules, linear diffusion." Williams, R. J. P. 2011. "Chemical advances in evolution by and changes in use of space during time." Journal of Theoretical Biology. 268: 146-159. P. 150.
"Since the building blocks are from C, N, O and H atoms and the environment could only provide them in a very few small molecules, mostly chemically inert, CO2, CH4, CO, N2, H2O with more reactive H2S and NH3, there had to be, as well as ways of capturing energy, ways of increasing reactivity." Williams, R. J. P. 2011. "Chemical advances in evolution by and changes in use of space during time." Journal of Theoretical Biology. 268: 146-159. P. 151.
"In the cytoplasm the only way it could exist [retention of necessary metallic catalysts in early life] was to expel Ca2+ ions, which would have precipitated too many organic and inorganic anions, and much of the Na+ and Cl- ions as they, at the levels in the sea, would have caused osmotic rupture due to the presence in the cell of organic molecules of living processes. Removal of Ca2+, Na+ and Cl- is a major, essential, very early required, energised chemical step before the contents of the isolated space became active in organic synthesis." Williams, R. J. P. 2011. "Chemical advances in evolution by and changes in use of space during time." Journal of Theoretical Biology. 268: 146-159. P. 151.
"Plants depend on bacteria for nitrogen and on fungi for minerals. Plants and animals depend on vitamins, including the many essential coenzymes, and recent animals require additionally essential amino acids and sugars from many sources. They are obtained by feeding. The ensemble of organisms became a large cooperative network in an environment/organism system in which the definition of species becomes difficult. However, speciation is not important in main line chemical evolution." Williams, R. J. P. 2011. "Chemical advances in evolution by and changes in use of space during time." Journal of Theoretical Biology. 268: 146-159. P. 156.
"The proof of the steady state applicable to all cells’ vesicles lies in their different ion concentration and the observed universal concentration of ions in the cytoplasm." Williams, R. J. P. 2011. "Chemical advances in evolution by and changes in use of space during time." Journal of Theoretical Biology. 268: 146-159. P. 158.
"What are the conditions for open-ended evolvabiity? A necessary but not sufficient condition is a very rich combinatorial generative mechanism. For biology that mechanism is ultimately organic chemistry. It is this chemical combinatorics that to large extent underlies the ‘evolvability’ of niches also. A second condition is unlimited heredity; namely, that the number of possible heritable types should more than astronomically exceed the number of individuals in the population. A third condition is an inexhaustible fitness landscape. By this we mean that as evolution proceeds, there should be newer and newer possibilities for empty niches. For this a rich, dynamical environment is needed. Of course, a good part of the environment includes other evolving populations with which the local population can potentially interact." Vasas, Vera, C. Fernando, A. Szilagyi, I. Zachar, M. Santos & E. Szathmary. 2015. "Primordial evolvability: Impasses and challenges." Journal of Theoretical Biology. 381: 29-38. P. 37.
"The most exciting form of evolvability is indefinite, open-ended ongoing evolution, possibly leading to an increase in complexity, at least in certain lineages. We think that for this to occur there are a few necessary conditions: (1) a rich chemical combinatorics, (2) digital inheritance based on template replication, (3) an environment made more complex by evolution itself, and (4) the fact that we cannot pre-state in general the possible preadaptations." Vasas, Vera, C. Fernando, A. Szilagyi, I. Zachar, M. Santos & E. Szathmary. 2015. "Primordial evolvability: Impasses and challenges." Journal of Theoretical Biology. 381: 29-38. P. 38.
"From the results of our experiment, we argue that there are at least two notions of biological information: the first involves a notion where information is generally understood as a set of attributes pertaining to an object, typically the genetic sequence, which can be analyzed by means of information theory. The second notion deals with the ways in which certain attributes acquire meaning. We have called these kinds object-information and process-information, respectively. We suggest that the controversy surrounding the notion of information is in part the result of conflating two related but independent notions of information." Mercado-Reyes, Agustin, P. Padilla-Longoria & A. Arroyo-Santos. 2015. "Objects and processes: Two notions for understanding biological information." Journal of Theoretical Biology. 380: 115-122. P. 116.
"In our account, information is not something, but rather some relationship. Both process- and object-information are powerful concepts because of the richness and diversity of the situations and objects that fit the network of relations they posit." Mercado-Reyes, Agustin, P. Padilla-Longoria & A. Arroyo-Santos. 2015. "Objects and processes: Two notions for understanding biological information." Journal of Theoretical Biology. 380: 115-122. P. 121.
"... if a sequence, which fits the object-information theoretical framework, is treated like process-information, it is automatically endowed with more attributes than it can possibly have. We can extract useful data from the sequences, such as informational entropy or algorithmic complexity; but this kind of quantitative analyses will never reveal the network of relationships that an information-carrying object has in a biological system. This is precisely the usefulness of process-information; it treats information as this network of relationships, which eventually elicit changes in the dynamics of the system." Mercado-Reyes, Agustin, P. Padilla-Longoria & A. Arroyo-Santos. 2015. "Objects and processes: Two notions for understanding biological information." Journal of Theoretical Biology. 380: 115-122. P. 121.
"Physicists do excellent science without a definition for time, space or energy; biologists do excellent science without a definition for life!" Bruylants, Gilles, K. Bartik & J. Reisse. 2011. "Prebiotic chemistry: A fuzzy field." Comptes Rendus Chimie. 14: 388-91. P. 389.
"For evolutionists like Lamarck and Darwin, the definition of biological species was conventional. Interestingly enough, scientists involved in prebiotic chemistry are exactly in the same situation: the barrier between the ‘non living’ and the ‘living’ world is conventional and when it is introduced, it is only ‘for the sake of convenience’." Bruylants, Gilles, K. Bartik & J. Reisse. 2011. "Prebiotic chemistry: A fuzzy field." Comptes Rendus Chimie. 14: 388-91. Pp. 389-90.
"Initial studies of complex and poorly understood phenomena often make use of simplified laboratory models; however, as our understanding increases and our technical abilities improve, it becomes both possible and necessary to investigate increasingly realistic models of the phenomenon in question. Just such changes are occurring in diverse aspects of studies of the origin of life, such as the prebiotic chemistry of nucleotide synthesis, the growth and division of model protocell membranes and the replication of primitive genetic polymers. In the first two cases, moderate increases in initial chemical or physical complexity led to solutions to problems that previously seemed intractable, and in the third case, an analogous approach looks promising." Szostak, Jack. 2011. "An optimal degree of physical and chemical heterogeneity for the origin of life?" Philosophical Transactions of the Royal Society: B. 366: 2894-2901. P. 2900.
"Scenarios involving moderate chemical and physical complexity are, in general, more geochemically sensible, and thus more prebiotically plausible than over-simplified laboratory models. It would, therefore, be very satisfying indeed if such scenarios turned out to be not only compatible with but also necessary for the key steps in the chemical origins of life." Szostak, Jack. 2011. "An optimal degree of physical and chemical heterogeneity for the origin of life?" Philosophical Transactions of the Royal Society: B. 366: 2894-2901. P. 2900.
"The English word ‘environment’ was coined in the late 1820s by the Scottish essayist Thomas Carlyle and popularized in the second half of the century by the philosopher Herbert Spencer. But what is so important about a word? It is not as if earlier thinkers had any trouble discussing the influence of external factors on organisms. For example, Buffon wrote the following in his multi-volume Natural History: ‘The temperature of the climate, the quality of food, and the evils of slavery [i.e., domestication]–these are the three causes of change, alteration, and degeneration in animals’. Soon after, French naturalists began to employ umbrella terms for these and other factors, the most influential of which were Jean-Baptiste Lamarck’s ‘circumstances’ and Georges Cuvier’s ‘conditions of existence.’" Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. P. 14. Subquotes: Buffon, G-L L. 1766. "De la degeneration des animaux." Histoire naturalle, generale et particuliere, avec la description du cabinet du roi, vol 14. Lamarck, Jean-Baptiste. 1801. Systeme des animaux sans vertebres, ou tableau general des classes, des ordres et des genres de ces animaux.
"Thus naturalists in the early nineteenth century were investigating the influence of external factors–physical and biological–on plants and animals, and employing terms such as ‘conditions’ and ‘circumstances’ to refer collectively to such factors." Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. P. 15.
"In the French tradition, the term ‘milieu’ (medium) as the counterpart of ‘organisme’ was an innovation of the 1830s, although Lamarck had earlier employed the plural ‘milieux’ to refer to environing media such as water or air." Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. P. 15.
"Comte ... insisted that ‘the idea of life constantly supposes the necessary correlation of two indispensable elements, an appropriate organism and a suitable medium.’" Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. P. 16.
"... life evolves by improving organism-environment correspondence... said Spencer ... "But Spencer talked mostly about just one causal direction: environments modifying organisms." Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. Pp. 17-8.
"Thus, the followers of Lamarck could take the environment as the primary source of variation, but had difficulty explaining how such variation was inherited, whereas the neo-Darwinians had difficulty accounting for the origin of variation, but no problem explaining how existing variation was passed on...." "The Baldwin Effect was thus a compromise position between Lamarck and Weismann: it emphasized the role of environment-induced variation in evolution without depending on the inheritance of acquired characters." Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. Pp. 21-2.
"The idea that progress in the organic world involves an increase in the number, range, and complexity of organism-environment adjustments is right out of Spencer’s Principles of Psychology, as Dewey’s citation indicates." Pearce, Trevor. 2014. "The Origins and Development of the Idea of Organism-Environment Interaction." Pp. 13-32. Barker, Gillian, E. Desjaardins & T. Pearce, Eds. Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer. P. 25.
"Metaphorically speaking, the tree of life appears rootless." Mann, Stephen. 2013. "The Origins of Life: Old Problems, New Chemistries" Angewandte Chemie: International Edition. 52: 155-162. P. 155.
"In essence, such an endeavor [the transition from non-living to living matter as a chemistry problem]–we might call it ‘protolife science’–represents the search for the minimal organizational logic that is sufficient for the emergence of matter with a basic level of systems autonomy, ultimately capable of undergoing evolutionary change." Mann, Stephen. 2013. "The Origins of Life: Old Problems, New Chemistries." Angewandte Chemie: International Edition. 52: 155-162. P. 159.
"Synthesis and design is per se a chemical endeavor – but the goal of synthesis in chemistry is usually a chemical structure. On the other hand, the design and synthesis of complex dynamic behavior in chemical systems is as much in its infant shoes as the reduction and reconstruction approach of synthetic biology. It is a challenge for the chemistry of the 21st century. Let us now try to generalize the challenges that face Systems Chemistry in the near future. Systems chemistry seeks to combine the ‘classical’ knowledge of chemistry, viz. the language of molecules, their structures, their reactions and interactions, together with the ‘classical’ knowledge derived from existing forms of life. One component of this approach, acting both as a translator and abstractor between these languages comes from the fields of theoretical biology and complex systems research; the other key component comes from a chemistry that is the offspring of both supramolecular and prebiotic chemistry, and adds a new dimension that has not been sufficiently addressed so far. Over the past decades more and more chemists have learned to design and implement chemical systems showing emergent behavior, such as simple self-replicating and self-reproducing systems, chiral symmetry breaking reactions, as well as far-from-equilibrium self-organizing systems (i.e. oscillating reactions, Turing patterns) and today we even have the first examples of systems chemistry making molecular motors." Von Kiedrowski, Guenter, S. Otto & P. Herdewign. 2010. "Welcome Home, Systems Chemists!" Journal of Systems Chemistry. 1: 1. P. 4.
"It is to be concluded that nature did not choose RNA according to the criterion of maximizing base-pairing strength; since oligomer systems with much stronger pairing exist among the nucleic acid alternatives taken from RNA’s structural neighborhood." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. P. 12825.
"What is called for in this situation [looking for RNA emergence from ‘informational forerunner systems’] is a radical step: we should experimentally map the landscape of potentially primordial informational oligomer systems without any structural constraints, oligomers of any type of backbone, of any type of recognition elements, as long as structures remain chemically functional and fulfill the generational imperative of prebiotic chemistry. Only when we know the lowest level of structural complexity that still allows an oligomer system to function as an informational system, and only when we know the kind and degree of generational simplicity that prebiotic chemistry has in store for such a system, only then shall we be in a position to assess the chances of such a system to have assembled itself." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. P. 12826.
"The reasoning behind these elaborations on a hypothetical chemistry of the three mono-carbon materials HCN, CO, and CO2 is not to argue in any way in favor of any of them as being the most probable primordial carbon source, but to look at these schemes from a purely chemical point of view and take serious what is obvious, namely, that in principle each of these carbon sources could have the capacity of generating glyoxylic acid and dihydroxyfumaric acid as the result of appropriate hydrolytic intervention in their oligomerization. In the case of HCN, the oligomerization is known to be spontaneous, in the case of CO it would require (unknown) catalysis under non-reductive conditions, and the case of CO2 it would have to be brought about by a strong electron source.... "... if biomolecules could derive from a single carbonaceous starting material that would not necessarily depend from just one geochemical source, but could come from any of the three major carbon sources HCN, CO and CO2 (or its heteroatom-isomers), such a scenario would have a degree of independence from the contingencies of the geochemical environment." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. Pp. 12834-5.
"First, the question behind all those schemes is of course as to whether or not, or under what conditions, these hypothetical reactions are part of chemical reality. From the etiological point of view, the question is not primarily of interest because the proposed chemistry may provide alternative pathways to biomolecules, but rather because it might be a chemistry that may have the potential to mediate, or to be part of, a process in which a library of chemical reactions moves toward becoming a network of metabolic reactions. Only with regard to such a perspective is it the case that a proposal of such highly non-robust reactions requiring subtle reaction conditions can possibly make sense." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. P. 12837. "Second, since the outset of prebiotic chemistry, it has been taken for granted that sugars were primordially formed by way of the formose reaction. Convincing as this presumption may appear, it could be a mistake to conclude that there is neither room nor the need for looking out for alternatives.... The glyoxalate scenario offers alternative pathways to both á-amino acids and carbohydrates; each of them happens to be closely related to those [other alternative pathways] just referred to." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. P. 12837.
"Yet, there is no reason to a priori exclude the possibility of constitutionally much simpler ‘genetic’ cycles, simpler with regard to ‘sequence length’, that could involve constituents capable of acting as organo-catalysts to evolutionary relevant reactions steps of either their own cycle or other cycles." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. P. 12838.
"It seems that, by looking at the problem of biogenesis closer and closer to the molecular level, the difference between the geneticist’s and the metabolist’s point of view may become more and more blurred." Eschenmoser, Albert. 2007. "The search for the chemistry of life’s origin." Tetrahedron. 63: 12821-44. P. 12838.
"By bringing chaos and irreversibility together it [complexity science] showed that deterministic and probabilistic views, causality and chance, stability and evolution were different facets of a same reality when addressing certain classes of systems." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. vii.
"... complexity research is today both one of the most active and fastest growing fields of science and a forum for the exchange of sometimes conflicting ideas and views cutting across scientific disciplines." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. viii.
"The basic thesis of this book is that a system perceived as complex induces a characteristic phenomenology the principal signature of which is multiplicity. Contrary to elementary physical phenomena like the free fall of an object under the effect of gravity where a well-defined, single action follows an initial cause at any time, several outcomes appear to be possible. As a result the system is endowed with the capacity to choose between them, and hence to explore and to adapt or, more generally, to evolve." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 3.
"Another interesting class of control parameters are those associated to a constraint keeping the system away of a state of equilibrium of some sort. The most clearcut situation is that of the state of thermodynamic equilibrium which, in the absence of phase transitions, is known to be unique and lack any form of dynamical activity on a large scale. One may then choose this state as a reference, switch on constraints driving the system out of equilibrium for instance in the form of fluxes of matter or energy across the interface between the system and the external world, and see to what extent the new states generated as a response to the constraint could exhibit qualitatively new properties that are part of the phenomenology of complexity." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 5.
"All elements at our disposal from the research in nonlinear science and chaos theory lead to the conclusion that one cannot anticipate the full list of the number or the type of the evolutionary scenarios that may lead a system to complex behavior." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 8.
"There is a widely spread feeling in some parts of the literature that complexity is in fact mainly concerned with the class of systems giving rise to criticalities, scale free states and power laws. We see no reason to subscribe to this rather limited view. For one thing an important manifestation of complexity in living matter – arguably, the prototype of complexity – is coherence, reflected by the total or partial synchronization of the activities of individual units (cells or otherwise) to a dominant temporal or spatial mode." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 12.
"... therefore, differentiated ‘complex’ matter as we observe it today can be viewed as the ‘fossil’ outcome of a global primordial nonequilibrium [Big Bang] and of local short-ranged interactions." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 295.
"Technically, causes may be associated to the initial conditions on the variables describing a system, or to the constraints (more generally, the control parameters) imposed on it. In a deterministic setting this fixes a particular trajectory (more generally, a particular behavior), and it is this unique ‘cause to effect’ relationship that constitutes the expression of causality and is ordinarily interpreted as a dynamical law. But suppose that one is dealing with a complex system displaying sensitivity to the initial conditions as it occurs in deterministic chaos, or sensitivity to the parameters as it occurs in the vicinity of a bifurcation. Minute changes in the causes produce now effects that look completely different from a deterministic standpoint, thereby raising the question of predictability of the system at hand. Clearly, under these circumstances the causes acquire a new status. Without putting causality in question, one is led to recognition that its usefulness in view of making predictions needs to be reconsidered. Statistical laws impose then themselves as a natural alternative. While being formally related to the concept of chance, the point stressed throughout this book is that they need not require extra statistical hypotheses: when appropriate conditions on the dynamics are fulfilled statistical laws are emergent properties, that not only constitute an exact mapping of the underlying (deterministic) dynamics but also reveal key features of it that would be blurred in a traditional description in terms of trajectories. In a sense one is dealing here with a ‘deterministic randomness’ of some sort." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. Pp. 297-8.
"In a different vein to the extent that initial conditions may be arbitrary, chance – here in its traditional interpretation – may be regarded as a probe of the different potentialities of a system: by switching on pathways that would remain dormant in the absence of variability chance is a prerequisite of diversification, evolution and complexity ..." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 298.
"In addition to the arrow of time a minimal dynamical complexity is thus needed, before the historicity of a process acquires a meaning." Nicolis, Gregoire & Catherine Nicolis. 2012. Foundations of Complex Systems. World Scientific. P. 300.
"At the very least, six different catalytic activities would have been needed to complete the reverse citric acid cycle. It could be argued, but with questionable plausibility, that different sites on the primitive Earth offered an enormous combinatorial library of mineral assemblies, and that among them a collection of the six or more required catalysts could have coexisted." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. Pp. 0007-8.
"While enzymes discriminate readily between very similar substrates, such discrimination is rare, but not impossible, in reactions catalyzed by small molecules or mineral surfaces. There are a few places where a catalyst would need to be specific with respect to the components of the reverse citric acid cycle in the sense that it facilitated the transformation of one component of the cycle while failing to transform another component of the same chemical class.... "Two highly specific catalysts would clearly be needed to overcome this difficulty." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. P. 0008.
"Enzymes that use transition metal ions or iron-sulfur clusters play an important role in the reverse citric acid cycle, but are absent from the Calvin cycle, which uses Mg2+ and occasionally Zn2+ cofactors in its enzymes. It seems plausible, therefore, that the enzymes of the reverse citric acid pathway evolved in a region rich in transition metal ions and sulfur, whereas those of the Calvin cycle evolved where phosphate and magnesium were abundant." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. Pp. 0008-9. "The catalytic properties of enzymes are remarkable. They not only accelerate reaction rates by many orders of magnitude, but they also discriminate between potential substrates that differ very slightly in structure. Would one expect similar discrimination in the catalytic potential of peptides of length ten or less? The answer is clearly ‘no,’ and it is this conclusion that ultimately undermines the peptide cycle theory." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. P. 0011.
"Peptides as short as tetramers, for example the peptide Asn-Asn-Gln-Gln, form long fibrils. These stable structures are formed by the very close packing of pairs of identical â sheets. The sheets associate together along the fiber axis by hydrogen bonding." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. P. 0012.
"The most serious challenge to proponents of metabolic cycle theories–the problems presented by the lack of specificity of most nonenzymatic catalysts–has, in general, not been appreciated." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. P. 0012.
"The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed." Orgel, Leslie. 2008. "The Implausibility of Metabolic Cycles on the Prebiotic Earth." PLOS Biology. Vol 6. Issue 1. E18. P. 0012.
"Philosopher and physicist Paul Davies has succinctly outlined ‘three philosophical positions concerning the origin of life: (I) it was a miracle; (ii) it was a stupendously improbable accident; and (iii) it was an inevitable consequence of the outworking of the laws of chemistry and physics, given the right conditions.’" Shapiro, Robert. 2006. ""Small molecule interactions were central to the origin of life." The Quarterly Review of Biology. Vol. 81. No. 2. P. 105. Subquote: Davies, Paul. 1995. Are We Alone?: Philosophical Implications of the Discovery of Extraterrestrial Life. BasicBooks. P. 21.
"The redox energy [at a hydrothermal vent in prebiotic conditions] is derived primarily from encounters between the effluents of a reduced mantle and the more oxidized atmosphere and lithosphere produced by the loss of hydrogen to space, after the photochemical decomposition of water." Shapiro, Robert. 2006. ""Small molecule interactions were central to the origin of life." The Quarterly Review of Biology. Vol. 81. No. 2. P. 118. "These assumptions have been challenged, however. Orgel has pointed out that ‘each step of a proposed cycle must proceed at a reasonable rate, and that this will often depend on the availability of a suitable catalyst.’ He questions why, fortuitously, a participant in a particular metabolic cycle should catalyze other reactions in that cycle, or why a particular mineral should catalyze the suite of reactions in a cycle rather than other processes that would disrupt the cycle... Pross has noted that no experimental evidence exists to support the spontaneous formation of such a metabolic cycle." Shapiro, Robert. 2006. ""Small molecule interactions were central to the origin of life." The Quarterly Review of Biology. Vol. 81. No. 2. P. 119. References: Orgel, Leslie. 2000. "Self-organizing biochemical cycles." PNAS. 97: 12503-7. P. 12504. Pross, A. 2004. "Causation and the origin of life: metabolism or replication first? Origins of Life and Evolution of the Biosphere. 34:307-21.
"I will argue that these objections [against chemical self-organization by small molecules or a primitive metabolic cycle] can be met in principle by the introduction of a limited number of assumptions: (1) A thermodynamically favorable, irreversible ‘driver’ reaction that is directly coupled to an external source of available free energy can occur in a plausible abiotic setting. (2) A multistep reversible pathway is possible that converts the product of the driver reaction back to the starting material, completing a cycle. (3) The cycle functions at a ‘profit’ within its environment; the gain of carbon by the cycle exceeds its loss by all mechanisms." Shapiro, Robert. 2006. ""Small molecule interactions were central to the origin of life." The Quarterly Review of Biology. Vol. 81. No. 2. P. 119.
"Coupled reactions are quite common in the biochemistry of modern cells, where they allow a thermodynamically favorable reaction to drive an unfavorable one. For example, if the reaction of A to B has an unfavorable free energy, it will not occur spontaneously. The coupling of this reaction to the highly favorable process of X r Y allows the combined reaction A + X r B + Y to take place; the conversion of X to Y drives the A to B conversion.... "If B could revert directly to A, then the A-B system would simply be acting as a catalyst for energy release. If the system is to be capable of growth and chemical evolution, however, an indirect and reversible pathway for the return of B to A must exist to complete a cycle.... The continual energy-driven depletion of A, however, would pull material from the side branches into the central cycle. The concentrations of the cycle participants should therefore increase at the expense of those other substances." Shapiro, Robert. 2006. ""Small molecule interactions were central to the origin of life." The Quarterly Review of Biology. Vol. 81. No. 2. Pp. 120-1.
"An interesting property that can emerge from DCLs consisting of building blocks of different hydrophobicity is their ability to reversibly form supramolecular assemblies composed of amphiphilic library members. Such processes can trigger drastic changes in physicochemical properties of the system on the macroscopic scale. Necessary shifts in the DCL composition can be induced by various external stimuli,..." Li, Jianwei, P. Nowak & S. Otto. 2013. "Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry." Journal of the American Chemical Society. 135: 9222-39. Pp. 9232-3.
"Watson-Crick DNA base pairing constitutes a reliable way of templated information transfer into a complementary strand, which in turn can be used for building cross-catalytic systems. In nature however, a polymerase enzyme is required to synthesize a complementary copy, and the reaction itself is irreversible. On the other hand, the DCC methodology has allowed for enzyme-free functionalization of an oligomer, based on nucleobase pairing. Reversible thioester bond formation between thioester-functionalized nucleobases and oligocystein provides a possibility to keep the system at the thermodynamic equilibrium and influence its composition by introduction of an oligonucleotide template. In contrast to enzymatic DNA polymerization, this process is reversible, allowing for error correction and relatively high fidelity, conmpared to other enzyme-free polymerizations." Li, Jianwei, P. Nowak & S. Otto. 2013. "Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry." Journal of the American Chemical Society. 135: 9222-39. P. 9234.
"Early definitions of DCC considered only systems at equilibrium. However, the functional properties exhibited by equilibrium systems are dwarfed by those of far-from-equilibrium systems. An exciting new area is now being uncovered based on DCLs that combine equilibration processes with kinetically controlled chemical or physical steps, including catalysis and autocatalysis. Particularly rich are dissipative systems, in which a sustained supply of energy yields behavior such as (directional) movement, transport, and adaptive self-replication. This trend toward increasing the complexity of not just DCLs but assemblies of their members and experimental conditions has guided the field into the area of systems chemistry, which focuses on emergent properties of complex (but not necessarily covalently dynamic) mixtures. In this way DCC together with systems chemistry is establishing new connections between chemistry, biology, and nanotechnology. This has been a natural development of the field as it increases its focus on complexity and emergence, complementing a more traditional approach to chemistry where the emphasis is on single and pure compounds." Li, Jianwei, P. Nowak & S. Otto. 2013. "Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry." Journal of the American Chemical Society. 135: 9222-39. P. 9236.
"The term self-sorting describes the ability of mixtures of different molecules to recognize their mutual counterparts selectively so that specific pairs are formed rather than a library of all possible non-covalent complexes of the compounds present in the mixture. Self-sorting is related to systems chemistry as it is the result of a network of competing recognition events defined by the binding constants between all the possible pairs. Self-sorting systems thus have higher information content and are more organized than an unspecific mixture, because only one or very few complexes are selected out of a larger number of potentially possible assemblies based on the delicate balance of all the competing interactions between the molecules in the mixture." He, Zhenfeng, W. Jiang & C. Schalley. 2015. "Integrative self-sorting: a versatile strategy for the construction of complex supramolecular architecture." Chem. Soc. Rev. 44: 779-89. Pp. 780-1. "First of all, self-sorting can be thermodynamically or kinetically controlled. Self-sorting can be also classified into narcissistic – all compounds only recognize identical copies of them and form homomeric complexes – and social self-sorting – pairs of compounds mutually recognize each other and form heteromers." He, Zhenfeng, W. Jiang & C. Schalley. 2015. "Integrative self-sorting: a versatile strategy for the construction of complex supramolecular architecture." Chem. Soc. Rev. 44: 779-89. P. 781.
"If one aims at making use of self-sorting to construct larger, programmed assemblies from a number of different building blocks that are all correctly positioned in the final complex, it is useful to synthesize one or more components integrating binding sites from different motifs. Accordingly, we distinguish non-integrative, from integrative self-sorting." He, Zhenfeng, W. Jiang & C. Schalley. 2015. "Integrative self-sorting: a versatile strategy for the construction of complex supramolecular architecture." Chem. Soc. Rev. 44: 779-89. P. 781.
"From this four-component social self-sorting system [an example], an integrative self-sorting complex can be obtained by joining at least one binding site from each motif covalently into one integrative component, which acts as a molecular ‘hub’ bringing the other units together into one well-defined assembly." He, Zhenfeng, W. Jiang & C. Schalley. 2015. "Integrative self-sorting: a versatile strategy for the construction of complex supramolecular architecture." Chem. Soc. Rev. 44: 779-89. P. 781.
"Also, mismatched complexes that are disfavored by thermodynamics may well play a role in the assembly process. Kinetic path selection is therefore likely to occur and is probably rather the rule than the exception. The importance of this aspect becomes immediately clear when considering protein folding as a natural analogue. Here, path selection is not only of major importance, but is actively supported in the living cells by chaperone proteins." He, Zhenfeng, W. Jiang & C. Schalley. 2015. "Integrative self-sorting: a versatile strategy for the construction of complex supramolecular architecture." Chem. Soc. Rev. 44: 779-89. P. 784.
"... we can almost always detect antifragility (and fragility) using a simple test of asymmetry: anything that has more upside than downside from random events (or certain shocks) is antifragile; the reverse is fragile." Taleb, Nassim. 2012. Antifragile: Things that Gain from Disorder. Random House. P. 5.
"Recently proteins have been synthesized by constructing random sequences of amino acids, and despite this randomness, these proteins possess some functions found in the proteins occurring naturally." Kaneko, Kunihiko. 2006. Life: An Introduction to Complex Systems Biology. Springer. P. 33. "However, neither the methodology of enumerationism itself nor the field of systems biology in its present form provides the grounds to judge what molecules are ‘important.’ To make such a determination, some other theory is needed." Kaneko, Kunihiko. 2006. Life: An Introduction to Complex Systems Biology. Springer. P. 33.
"... the rate equations of chemical reaction can be considered accurate descriptions of actual processes only if the number of molecules participating is very large. In the case of the reactions taking place within cells, the actual numbers of molecules are not large, and for this reason, fluctuations in molecule number play an important role." Kaneko, Kunihiko. 2006. Life: An Introduction to Complex Systems Biology. Springer. Pp. 33-4.
"Present living systems are extremely complicated products of history, and for this reason, it is probably not possible to judge what is essential by considering only these. In other words, studying these organisms alone, we cannot determine what properties [of life] are simply the accidental results of evolution and what properties are indeed inevitable." Kaneko, Kunihiko. 2006. Life: An Introduction to Complex Systems Biology. Springer. P. 38.
"In the study of high-dimensional chaos, there is often a state that switches back and forth between fully disordered state and several ordered states. Here fully disordered state can be approximated partly by ‘random motion’ which may be described as the motion consisting of many degrees of freedom. The ordered states are given by effectively low degrees of freedom and located in a low-dimensional region in the phase space. There are several such ordered states. The itinerant motion among varieties of ordered states through high-dimensional chaotic motion is commonly observed. The term for this is chaotic itinerancy." Kaneko, Kunihiko. 2006. Life: An Introduction to Complex Systems Biology. Springer. Pp. 74-5.
"We do not propose to understand life in terms of the ‘rigid,’ precisely determined behavior of logical systems. Rather, the picture we present is based on complex, ‘loose’ dynamics from which recursive ‘types’ are formed." Kaneko, Kunihiko. 2006. Life: An Introduction to Complex Systems Biology. Springer. P. 316.
"Confinement, especially on a crystalline mineral surface, might limit the number of different sugars formed, reduce the amount of branching in sugar polymers, and prevent the formation of complex tarry products. "Proteins in confined spaces are stabilized against denaturation. Confinement by pressure induces polymerization of actin and glycine." Hansma, Helen. 2014. "The Power of Crowding for the Origins of Life." Orig Life Evol Biosph. 44:307-311. Pp. 307-8.
"There are two overriding factors which control the ways in which elements as atoms come together in a preferred ordered manner in the absence of motion: (1) the strength of bonding, i.e. the extent the potential energy becomes more negative as the units (atomic elements) combine in simple small molecules to give low molecular weight compounds; and (2) the co-operative modes of interaction between these molecules (or ions, or atoms themselves), related to the extra strength with which they attract one another; and sometimes rearrange, in a condensed, continuous solid state." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 89.
"The simplest way to describe metallic states then is to consider that their most stable condition is one in which the lattice of atoms is really a lattice of positive ions buried in a freely mobile, shared sea of some negative electrons. The electrons are not associated with particular atoms or localised, as in covalent or ionic solids, but fill space around the positive ions, without structural implications." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 94.
"All aspects of structure [for molecules] are then characterisable by variation in composition and potential energy." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 97.
"It is solubility that determines the availability (not the abundance) of elements. Availability is then a heavy environmental constraint on the composition variable for all of life, just as there is a decided limitation on the temperature variable due to the use of liquid water with its narrow liquid range." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 169.
"We shall refer to all association reactions between ions (or between ions and molecules) as acid-base reactions, where the acid is the group accepting pairs of electrons, partially, and the base (usually called the ‘ligand’ in complex species) is donating them." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 173.
"Elements that tend to form ions (negative redox potentials) are called electropositive, relative to H+." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 184.
"... environmental equilibria impose strong limitations upon the possible chemistry and biochemistry on the Earth’s surface." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 189. "Now, in itself, a protein in water can still be treated both as a molecule in solution and as a separate phase which has a melting point." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 201.
"Since each compartment can be changed independently, the number of variables increases dramatically once equilibrium between them is lost (remember that the equilibrium conditions restrict the number of degrees of freedom) so that only a very descriptive account of the nature of the whole can be given." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 212.
"These polymers [protein, DNA or RNA] have considerable internal mobility which varies greatly from one to another. Many physical responses of the molecules are then due to cooperative global reorganization from one set of mobile states to another. The processes may well resemble (second order) phase transitions. One such possibility could involve small adjustments of many H-bonds, as well as of side-chains, as the energy of a transition distributes itself cooperatively. Here a protein would behave as a very small phase or system." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 213.
"At this level of description a molecule as large as DNA may never visit the same conformation twice during a cell’s life cycle." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 213.
"... there are four kinds of changes to be considered, all of them involving flow: (1) downhill change towards stable states; (2) uphill change, which requires energy to generate stationary states; (3) steady conditions in a system with unchanging flow, where the condition does not move of necessity towards a stable state over a long period of time although it can move to another steady state; and (4) developing systems such as living organisms." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 216.
"The limitations, kinetic traps, on changes of chemical elements on Earth can be treated in two theoretical ways. The first, so-called collision theory, states that, generally, in order to change, particles (atoms or molecules) must come together and collide with one another, i.e. reactions are of the kind, "A + B –> AB –> products "A and B may both be atoms or molecules, or A can be an atom or molecule while B can be a barrier to diffusion. The collision can result in activation of A alone, for a unimolecular reaction, or of AB, for a bimolecular reaction, or of A with the barrier for physical transfer, depending upon the nature of the reaction. Change can only occur if the collision is of sufficient energy to overcome the barrier.... "A second treatment of reaction rates is the ‘transition state theory’ (or ‘activated complex theory’) of chemical kinetics, based on concepts of statistical thermodynamics. In this theory we may characterise the probability of the equilibrium concentration of a required activated complex, AB* relative to the probability of absence of association, by the equilibrium constant of the activated complex, K*." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. Pp. 220-1.
"Clearly, control over change is exerted by two factors: (1) by the physical barriers to motion in bulk space to be overcome by energy, generating diffusion in a direction; and (2) by chemical bond barriers in a complex to be overcome by energy to give directed local motion of atoms or groups. Catalysts... are substances, metals or compounds, that help to overcome one or all of the barriers to chemical change in local bond space, while pumps (transfer catalysts), which transport units without chemical change, create modes of movement, if necessary with applied energy, across physical barriers in bulk space, e.g membranes." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. Pp. 222-3.
"A different type of reaction of water exchange involves the attack of water (here in water) on an organic molecule; this is called hydrolysis, and its reversal is called condensation. Here, there occurs the rearrangement of covalently bonded atoms in space, which is normally slow "X-Y + H2O –> X-OH + HY (hydrolysis) X-OH + HY –> XY + H2O (condensation) "Many organic molecules undergo such transformations, but while reaction (1) is going to a more stable condition, reaction (2) goes to a more unstable one and requires a source of energy. Nevertheless, reaction (2) is the main route to the formation of biological polymers such as DNA, polysaccharides and proteins." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 233
"This leads us to quite a new question which is: ‘Is it a feature of these organisations [self-sustained systems such as organisms or human industry] that only certain values of the rates of the different transformations and transport paths are mutually supportive? This would imply that the variables of change (of flow) have optimal values for survival in a particular system. We can then consider plots of survival value against the variables, ... much as we plotted stability, -ÄG, against several variables for non-living systems .... Where such plots are not smoothly continuous there should be found separate regions of the variable where survival value is high and others where it is low. This is observed. Unfortunately, to date, study of such systems has not generated an assessment of survival value to parallel ÄG, where the survival value would be related to effective collective terms (compare with maximum entropy) to ensure quantitative success." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. Pp. 245-6.
"Biological chemical pathways are frequently shown as linear lists of substances connected by enforced changes due to enzymes. They are pathways in the sense that barriers to particular local directional re-arrangement of atoms within molecules are lowered, so that atoms in space are moved locally along a given route. They are not pathways in bulk space unless: (1) enzymes are physically coupled in bulk space and substrates are handed on physically from one catalyst centre to another; (2) the enzyme is a device that acts while also moving a substrate through bulk space, e.g. through a membrane in a direction. Such an enzyme is simultaneously a pump. Gross patterns of chemicals in space are set up by the controlled movements in bulk space. The more usual situation of many enzymes is that they do not lend any directed bulk motion to substrates since the enzymes rotate and diffuse relatively freely in solution. The two senses of a pathway must be clearly separated. Since energy is distributed in changes in local bondings, e.g. in pathways or in bulk space.... Movement in bulk space is obviously more simple and we observe it everywhere around us. At the present time we are not fully aware of the way chemical reaction pathways and bulk movements are integrated in cells, but we know that they are." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 248.
"... their [organisms’] chemicals are selected for functional purpose, not stability." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 291.
"The intriguing feature [of the chemistry of organisms] is that the incorporation of elements from some 14 groups in the periodic table implies an almost complete involvement in organisms of the full variety of chemistry that can possibly be generated by the nature of the periodic table. The chemistry of elements within groups is, of course, similar (but not identical). This suggests that living systems have found the best of all possible uses for the available elements, employing their particular properties as expected from the position they occupy in the periodic table, for the diversity of functional tasks organisms need to undertake. Note that the fundamental units of composition are now restricted to some 20-30 rather than to the full list of 90 stable elements on Earth." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 293.
"While many of the molecules of C, H, N, O, P and S contain easily ionisable groups, e.g. -COOH, -SH, -OPO3H2, and become negatively charged, this charge must be largely neutralized.... "In most cells, therefore, the electroneutrality and the osmotic pressure are managed by exporting Na+Cl- (Na+ and Cl- ions), the most concentrated salt of the sea, and taking in K+ ions, which are relatively dilute in the sea.... Since the internal content of C, H, N, O, P and S molecules is closely fixed, generating a given osmotic concentration and negative charge, so must the final content of K+, Na+ and Cl- be fixed." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. Pp. 299-300.
"In summary, there is an analytical content of about 20 elements, all required in fixed ratios in every cell we know of, but the exact contents in cells of each species, and within a species in each differentiated cell, can be different." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 300.
"An illustrative and strange example is that virtually no nitrogen, from N2 or NO3, can be fixed by life without molybdenum. We could well say molybdenum is the essential element of life since without it no proteins or DNA would exist." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 301.
"As far as is known, calcium was rejected by all cells, at least to around 10-5 M in primitive organisms.... Since calcium binds easily and relatively strongly to negatively charged groups, aggregation of organic anions inside cells was and is avoided in this way." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 301.
"... there were three major sources of energy [for life]: (1) chemical reactions of components in stationary states, i.e. energy stored in chemical bonds; (2) compartments out of equilibrium with respect to temperature or fields due to mass or charge; (3) chemicals out of physical exchange equilibrium in gradients of pressure or concentration between compartments." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 304.
"A sugar is a better, more kinetically stable, long-term energy store than ATP, which is more useful in energy transfer." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 311.
"Thus, the elements of the periodic table can also be described by functional value,... Put simply, for organisms, of the available elements only C, H, N, O polymers can make the machinery, only Na+, K+, Cl- can be fast current carriers, only Mg2+, Ca2+ and HPO42- can assist relatively quick mechanical change and only transition metals and sulphur and selenium can be used in electronic conduction or oxidation-reduction catalysts, while ions such as Zn2+ are the most effective acid catalysts, free from the complication of redox reactions." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. Pp. 314-5.
"Now the study of living organisms shows us that, over very considerable periods of time, while in steady state, all H, C, O, N atoms of the vast majority of the molecular constructs present in cells, probably all except DNA, are exchanging between different molecules, at particular rates, through controlled pathways of degradation and synthesis. Leaving aside DNA, the fact that these molecules are in such fixed exchange means that all their relative concentrations are not variables in this steady state but are fixed, much though they may fluctuate slightly. Thus, a living steady state does not have components as variables. (Note again that the fixed relative concentrations of such molecules are not now related to the free energy differences, ÄG, corresponding to the transformation of them to other forms, and are not, therefore, related to any equilibrium consideration. Furthermore, they are not restrained by barriers which keep chemicals in stationary states, i.e. as true components. In fact, the concentrations have evolved in an overall network of flow to optimise overall cellular function, using energy and material input from outside to generate this chemical flow.) Since all the elements in these molecular ‘components’ of life exchange, it would appear that the variable of composition in organisms, which could dominate speciation in biology, is reduced to the number of elements involved. "Thus the ratios of concentrations are decided by the co-operative functional use of elements (not molecular components), including catalysts, in the whole machinery of the cell, while energy passes through it. Hence, one and the same element composition may give rise to several different chemical combinations, that is, different steady states exist due to energy flow differences. For example, it could be that CH3-CHO, together with HO-CH=CH2, could be found in different steady-state ratios due to different energy flow, while, through metabolic activity, the molecules exchange C, H, and O between themselves and even with the contents of the whole system at particular rates. This contrasts directly with the use of these two chemicals as components of a non-exchanging mixture,... Note again that the ratios that develop are not equilibrium values: they are decided by energy input and catalysts. If we look upon a cell as such an holistic steady state and co-operative dynamic activity, then there could also be a discontinuous variety of compositional flow systems of elements plus energy throughput, which could have given rise to successful machines where rate of energy input together with selected element input dominate. Such an approach allows us to consider survival of steady states in terms of these two variables, element composition and energy throughput." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. Pp. 325-7.
"Clearly, the value of the internal potential energy of interaction between units of the components is greatest (more negative) in the solid and least in the gaseous state, while the liquid state is intermediate in nature." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 488.
"We evaluated, therefore, a statistical measure of the disorder called the entropy (S) which is a useful variable, related quantitatively but not linearly to temperature and pressure and connected to the probability of a given physical state of a bulk material, independent from its internal energies due to binding between atoms. From the entropy of states we could calculate an entropy bias in energy terms in favour of change from an ordered to a disordered state, TÄS, which competes with the binding in the ordered condensed state expressed by the heat content or enthalpy change, ÄH, at constant pressure.... At certain temperatures and pressures, those corresponding to the melting and boiling points, the different physical states come into balance, whence disorder and order are in equilibrium, and new physical states form. "This formation of phases is then an emergent property resulting from the balance of variables." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 488.
"... two different levels of static systems are: (1) the fundamental variables composition and spatial distribution; (2) the derived statistical thermodynamic variables ÄG, ÄH, p, v, T and ÄS." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 493.
"DNA represents then a time sequence, as well as a structure sequence in the conventional sense, and codes for sequences in other polymers and their properties and for the whole timed sequence of activities of cells." Williams, R. & J. Frausto da Silva. 1999. Bringing Chemistry to Life from Matter to Man. Oxford University Press. P. 508.
"... we need a critical analysis of the concept ‘complexity’. Complex systems (CS) are systems requiring highly nontrivial auxiliary conditions (e.g., initial and boundary conditions) to emerge, called ‘fundamental requisites (FR), which cannot be prepared readily without devoting a great deal of resources in terms of time and information." Aono, Masashi, N. Kitadai & Y. Oono. 2015. "A Principled Approach to the Origin Problem." Orig Life Evol Biosph 45:327-38. P. 328.
"Most metabolic pathways are kinetically hard without enzymes. No spontaneous reactions as unruly as the HCN polymerization appear. This suggests that even prebiotically the precursor reactions do not proceed without catalysts, and that no spontaneously feasible reactions are crucial. The lack of spontaneity may be a key feature of biological systems. Even at the earliest stages of biological evolution, and possibly before, spontaneity should have been restricted. "Reactions with high activation energy barriers, are potentially regulated and controlled more easily, so they can be exploited to make organized systems. On the other hand, very spontaneous reactions are too uncontrollable to be used as a part of an organization, if they could stand by themselves without help, from enzymes." Aono, Masashi, N. Kitadai & Y. Oono. 2015. "A Principled Approach to the Origin Problem." Orig Life Evol Biosph 45:327-38. Pp. 329-30.
"Since the added chemical [to an existing metabolic network] is not a product of the network, if it is not amply supplied, then the reaction with the network component(s) consumes it. Only when the added chemical is steadily supplied or a part of another running network, it can be qualified to be incorporated into the joined network. Thus, unless the unconnected chemical is amply supplied, it is irrelevant to the network (except perhaps as a cofactor). This should be called the principle of ‘chemical qualification,’ so to speak. In other words, the compounds not intrinsic to a given chemical network are irrelevant to it." Aono, Masashi, N. Kitadai & Y. Oono. 2015. "A Principled Approach to the Origin Problem." Orig Life Evol Biosph 45:327-38. P. 330.
"The principle of chemical qualification implies that if no polymerization mechanism is invented as a part of the evolving chemical network, polymers are useless as reactants. Perhaps polymers might have been produced abiotically, but the resultant polymers are, especially if stable, nothing but organic compounds just as woody materials of the Carboniferous without lignicolous fungi." Aono, Masashi, N. Kitadai & Y. Oono. 2015. "A Principled Approach to the Origin Problem." Orig Life Evol Biosph 45:327-38. P. 334.
"At the level of our argument, we assume that each genotype (or network structure) is in turn associated with a particular geometry of phase space – a specific phase portrait. The phase portrait links genotype to phenotype, and thus represents the characteristics of the genotype-phenotype map ...." Jaeger, Johannes & N. Monk. 2014. "Bioattractors: dynamical systems theory and the evolution of regulatory processes." The Journal of Physiology. 592.11 Pp. 2267-81. P. 2270.
"Thus genotype networks conveying robustness correspond to large basins of attraction, which are spread across phase space, and persist across large regions of the parameter space of the underlying dynamical system." Jaeger, Johannes & N. Monk. 2014. "Bioattractors: dynamical systems theory and the evolution of regulatory processes." The Journal of Physiology. 592.11 Pp. 2267-81. P. 2274.
"... I showed that molecular environments display several processes and interactions characteristic of ecological communities, such as competition, predation, mutualism, and metabolic cooperation." Nathan, Marco. 2014. "Molecular ecosystems." Biol Philos 29:101-122. P. 120.
"(The Weak Arrow of Complexity [AOC]) Evolutionary systems have a robust tendency to produce ever more complex organisms (species).... "(The Strong Arrow of Complexity). Evolutionary systems have a robust tendency to become ever more complex. "Strong AOC is not a minor variant of Weak AOC: they are altogether different beasts. We emphasize the distinction between these two forms of complexity–that is, organismic complexity and biosystemic complexity–because it has been either widely confused or widely ignored in the debate on the evolution of complexity." Korb, Kevin & A. Dorin. 2011. "Evolution unbound: releasing the arrow of complexity." Biol Philos. 26:317-338. P. 322.
"MML [Minimum Message Length theory] specifically applies information measures to the job of statistical inference. It does this by dividing messages describing an observed state of a system into two components, one (call it h) which describes the hypothesis under consideration and another (call it e) which describes the sample statistics available (evidence)." Korb, Kevin & A. Dorin. 2011. "Evolution unbound: releasing the arrow of complexity." Biol Philos. 26:317-338. P. 331.
"Entropy measures merge all varieties of diversity together, those that contribute to biological complexity along with physical forms of complexity that are usually either orthogonal or contrary to sustaining biological complexity. By contrast, two-part messages such as MML, allow us to separate the separable." Korb, Kevin & A. Dorin. 2011. "Evolution unbound: releasing the arrow of complexity." Biol Philos. 26:317-338. P. 332.
"(The Arrow of Niche Complexity (Niche AOC)) The Arrow of Niche Complexity has an exponential trajectory. "With complexity interpreted simply as the number of niches, this means that any ecosystem not limited by capacity constraints will robustly tend to produce new niches at an exponential growth rate." Korb, Kevin & A. Dorin. 2011. "Evolution unbound: releasing the arrow of complexity." Biol Philos. 26:317-338. P. 335.
"... the self-assembly of lipidic amphiphiles into freely floating vesicles, requires a minimal concentration of the amphiphiles (the critical vesiculation concentration, CVC) that is relatively high for prebiotically plausible molecules." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1241.
"Thus, solid surfaces and those of soft-matter structures, as well as heterogeneous phases in aqueous solutions, could have also played the roles of ‘pseudo-comparments’ by fostering the formation of molecular concentration gradients needed to initiate catalysis." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1243. "Such dispersed systems [proto compartments of longer organic molecules] may have encompassed various types of molecular assemblies, for example: ‘self-organized entities of congealed organic matter’; organic hydrogels; coacervates (gelling mixtures of macromolecules and other organic ingredients); thermal proteinoids (microspheres); micellar and related self-assembled aggregates of lipidic amphiphiles (including oil-in-water emulsions); aggregates of amphiphilic peptides or mixtures of lipidic and peptidic amphiphiles; or atmospheric aerosoles. It is likely that such a comparmentalization promoted prebiotic chemical reactions via compartment-confined and surface-confined chemical reactions." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1244.
"Every type of building block self-assembles once its overall concentration reaches a threshold value: in the case of plausible prebiotic amphiphiles, this concentration (so called critical aggregation concentration, CAC; CVC in the specific case of the formation of vesicles,...) was found to be dependent on both the molecular properties (types of hydrophilic headgroups, length of the hydrophobic chains), as well as on the medium conditions." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1246.
"In general, for a given headgroup, e.g., the COOH-group of fatty acids, the likely molecular abundance on the early Earth decreases with the increase of the hydrocarbon chain length. This is simply because the formation of molecules with many C-C bonds is more difficult than the synthesis of molecules with only a few C-C bonds. Thus, plausible molecules that were present on the early Earth were most likely short fatty acids with high CACs, a fact that must have rendered the formation of protocellular structures from a pure compound more difficult." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1246.
"... potential roles of prebiological compartments ..." "Ensure some form of integrity by co-localization and encapsulation...." "Define the system compositional identity and heritable traits...." "Promote catalytic reactions...." "Stabilize reaction intermediates through incorporation into compartment boundaries ...." "Regulate exchanges of molecules with the environment by association and simple permeability...." "Support energy uptake and conversion...." "Trigger self-reproduction...." "Impart evolutionary advantages due to its composition...." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. Pp. 1249-50.
"Nonetheless, the potential for a co-localization on a surface of a relatively complex reaction network is plausible because essential functions on or within amphiphile compartment boundary cores have been observed; systems catalyzing transformation of precursor molecules into amphiphiles, or energy uptake. An evolution towards encapsulation in the aqueous lumina could then have taken place as the compartment boundary composition evolved towards more stable systems composed of mixtures of amphiphiles." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1250.
"... several reports exist that underline the importance of the compartment molecular make-up, but in conjunction with other aspects of the chemical systems. For example, Chen et al reported that osmotically swollen vesicular compartments, i.e., compartments under osmotic stresses due to high solute concentrations in their aqueous lumina, will grow at the expense of other ones that are isotonic with the external medium. That is, an inherent link between an increase of internal solute concentration, e.g., due to a very efficient internal catalytic activity, and boundary growth could be achieved by simply relying on physical processes, provided the amphiphile structures can maintain molecular gradients long enough. This hypothesis is supported by recent observations made during the synthesis of small hydrophobic dipeptides within fatty acid vesicles, which led to the preferential growth of vesicles with a functional internal catalytic system. Moreover, the composition of compartment boundaries, themselves, can also ensure a better access to resources by increasing their stability, thus prolonging the time an internal catalytic network is preserved in a functional state. Therefore, a chemical evolution by the transmission of molecule composition and their resulting catalytic properties could have already started for chemical systems (prebiological compartments) before an evolved biological information apparatus existed." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1253. Reference: Chen, I.A., R. Roberts & J. Szostak. 2004. "The emergence of competition between model protocells." Science. 305:1474-76.
"First, the multiplicity of the proposed diverse protocell make-ups can be considered advantageous for the field in general. Indeed, it is likely that various chemical systems must have co-existed during the chemical evolution leading to the first cells." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. P. 1253. "Second, while investigations of individual compartment-forming molecules is useful, it seems that multi-component chemical systems, i.e., complex mixtures of chemicals that together form prebiological compartments and simultaneously catalytic networks, will probably more accurately model prebiological systems. Thus, research on protocell models should emphasize its ‘systems chemistry’ nature, which comes at an experimental cost: an increase of the system complexity. This idea is supported by recent developments in the fields that show the enhancement of basic functions in chemical systems that are composed of a multitude of specialized molecules." Monnard, Pierre-Alain & P. Walde. 2015. "Current Ideas about Prebiological Compartmentalization." Life. 5:1239-1263. Pp. 1253-4.
“These [hydrothermal
fields] are characterized by fluctuating environments in which cycles of
hydration and dehydration occur in small ponds undergoing evaporation and
replenishment by variable hot springs and precipitation. "Selection begins during the hydrated phase when some vesicles are lost to the bulk or disrupted while others survive. Survival is promoted by the encapsulated contents of the vesicles. For instance, if a vesicle happens to contain a polymer that stabilizes the membrane, analogous to cytoskeletal proteins of cells today, it will resist disruptive forces such as mechanical shear caused by turbulence." Damer, Bruce & D. Deamer. 2015. "Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life." Life. 5:872-887. P. 877.
"In the next dehydration cycle, the surviving protocells aggregate on the mineral surface and fuse again with the multilamellar matrix. During this process, the encapsulated contents mix and distribute stabilizing polymers into the next generation of protocells. We term this a coupling of the contents of the protocells between the two phases. In other words, two phases of a naturally recurring process–hydration and dehydration–lead to an initial synthesis of a polymer in an anhydrous phase followed by selection of encapsulated polymers in a hydrated phase. The coupled cycles occur indefinitely, thereby allowing accumulation of increasingly complex systems of polymers." Damer, Bruce & D. Deamer. 2015. "Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life." Life. 5:872-887. P. 878.
"What are the properties of successful protocells? In a sense, the scenario is a version of the ‘compositional genome’ explored by Segre et al in which certain properties of lipid vesicles can be inherited according to their composition rather than information in a polymer sequence. The properties emerge from a synergy between the components of the system, which are the polymers and the surrounding membrane. All of the processes up to this point have been driven by self-assembly and a very simple source of energy–the chemical potential of dehydration that drives ester and peptide bond synthesis so that monomers can form polymers." Damer, Bruce & D. Deamer. 2015. "Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life." Life. 5:872-887. P. 880. Reference: Segre, D., D. Ben-Eli, D. Deamer & D. Lancet. 2001. "The lipid world." Orig Life Evol Biosph. 31:119-45.
"We are not specifying the nature of the polymers, but if the solutes include monomers like nucleotides and amino acids, the polymers would resemble RNA and peptides, as well as possible complexes of RNA and peptides. If so, we can make a list of the functional properties of the polymers, and the list defines the steps required for stepwise evolution of protocells toward living systems. "S-polymers have the simplest function, which [is] to bind to and stabilize a membrane-bounded compartment so that its contents are less likely to disperse into the environment. Examples in cells today are cytoskeletal polymers like spectrin that stabilize erythrocyte membranes. "P-polymers also have one of the simplest functions, which is to form pores in the bilayer membrane that allow access of potential nutrients to the interior volume.... "M-polymers catalyze the steps of a primitive metabolism involving chemical reactions among potential nutrients from the external medium after they enter the protocell. The reactions are a source of energy, and the products can be used for polymerization reactions. "R-polymers are able to undergo a primitive version of replication. It may be possible that the monomers not only form polymers under hydrothermal field conditions, but, once formed, can undergo non-enzymatic replication. The reason is that after the first cycle, any newly synthesized polymer can then act as a template.... "C-polymers are a subset of R polymers that happen to be able to catalyze their own replication.... "F-polymers are able to provide feedback control for the processes listed above. "D-polymers initiate and control the division of a protocell following the duplication of its distinct sets of functional polymers. The first D-polymer may have been a primitive version of FtsZ protein that forms a contractile ring in today’s bacteria and is required for cell division." Damer, Bruce & D. Deamer. 2015. "Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life." Life. 5:872-887. Pp. 880-1.
"Among the six CO2 fixation pathways known, the acetyl-CoA pathway, or Wood-Ljungdahl pathway, is the only one known that occurs in both archaea and bacteria." Sousa, Filipa & W. Martin. 2014. "Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism." Biochimica et Biophysica Acta. 1837: 964-981. P. 965.
"The parallel origin of enzymes that are i) ancestral for archaea and bacteria respectively, but ii) different in the two groups suggests that when the enzymes arose, they were selected to accelerate preexisting, similar and spontaneous reactions that predate the enzymes themselves. That is, it suggests that the basic underlying chemistry of the pathway is older than the enzymes that catalyze it." Sousa, Filipa & W. Martin. 2014. "Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism." Biochimica et Biophysica Acta. 1837: 964-981. P. 968.
"... enzymes do not create new reactions, they optimize existing ones." Sousa, Filipa & W. Martin. 2014. "Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism." Biochimica et Biophysica Acta. 1837: 964-981. P. 976.
"Conserved acetyl thioester synthesis in the acetyl-CoA pathway, together with independently invented methyl synthesis pathways using independently invented pterin C1 carriers, appear to hold clues about the energetic and chemical environment within which the progenote and its descendant stem lineages arose. The prevalence of methyl groups in the chemically modified bases in the ribosome and tRNAs also, in our view, points to the environment in which the progenote navigated the transition from geoenergetics and geosynthesis to bioenergetics and biosynthesis, within the confines of naturally forming inorganic microcompartments at a Hadean hydrothermal vent, one that was rich in reactive methyl groups, a world of one carbon compounds, or a ‘C1 world’, were one so inclined." Sousa, Filipa & W. Martin. 2014. "Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism." Biochimica et Biophysica Acta. 1837: 964-981. P. 977.
"We recently demonstrated a prebiotically plausible systems chemistry route to pyrimidine ribonucleotides... Accordingly, we are investigating other subsystems to synthesize lipids, peptides and metabolites. Should we find that the conditions under which these other subsystems are synthetically productive match any of the conditions of ribonucleotide synthesis, it will strengthen the case for the occurrence of the common conditions on the early Earth, and further support the prebiotic plausibility of the syntheses." Powner, Matthew & J. Sutherland. 2011. "Prebiotic chemistry: a new modus operandi." Philosophical Transactions of the Royal Society: B. 366:2870-7. P. 2871.
"The slow reversibility means that chemoselectivity can result from thermodynamic and kinetic effects." Powner, Matthew & J. Sutherland. 2011. "Prebiotic chemistry: a new modus operandi." Philosophical Transactions of the Royal Society: B. 366:2870-7. P. 2873.
"Exponentially increasing effectiveness of nutrient extraction by weathering, erosion and transportation into the ocean is critical. A rough estimate of effectiveness, as compared to hydrothermal fracturing system, is 1 million times more effective extraction of nutrients, particularly well balanced nutrient concentration in the case of the surface of the Earth, because granite is the major rock component of continental crust." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. P. 146.
"Plate tectonics functioned as a geochemical cleaner, transporting the metallic ores generated at the ride to the trench, and dumping them into the mantle by subduction. The growing TTG [tonalite-trondhjemite-granodiorite] crust promoted the geochemical filtering of the Hadean ocean." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. P. 149.
"About 700-600 Ma ago, the ocean thickness started to decrease, and about 600 m has been reduced until now through the fluctuations in the balance between output vs input of water into the mantle." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. P. 151.
"We envisage the following processes for the dawn of Phanerozoic. First, initiation of return-flow of seawater into mantle caused hydration of mantle wedge, leading to the lowering of sea-level. Subsequently, the coast line moved oceanward to increase the size of landmass, with the resultant birth of huge rivers to transport large volumes of sediments leading to the burial of organic matter synthesized by photosynthesis by algae and cyanobacteria. The burial of organic matter kept the high oxygen content in [the] atmosphere by preventing from back reaction to consume the stock of free oxygen. The increased oxygen in [the] atmosphere finally diffused upwards to create the ozone layer. The birth of ozone layer shielded the ultraviolet radiation from Sun, thereby enabling plants and animals to invade the land. Firstly, cyanobacteria invaded in the swamp along the river[s] to lake[s]. It gradually evolved to algae, bryophytes and to tracheophytes by late Devonian." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. Pp. 154-5.
"If the ocean was even only 1 km thicker than today, the metazoans could not have appeared yet. If the thickness of primordial ocean was 2 km thinner than today, plate tectonics would not have operated because of mid-oceanic ridge rising above sea-level. The lack of hydration of oceanic slabs at mid-oceanic ridge prevents plate tectonics, hence no ways to clean-up ocean, and no accumulation of TTG materials through time." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. P. 155.
"... various kinds of nutrients such as P, K, Ca, Fe and other trace metals were more essential factors to be prepared for life to evolve. For example, Mo is a key element to fix N by Prokaryotes to make protein. Mo is hyper-enriched in granite and nearly absent in peridotite and basalts. Even if oxygen pressure turned to be high, metazoans cannot be synthesized if the above elements that make up the metazoans were not supplied." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. P. 155.
"The paleontological evidence of appearance of Ediacaran fossils after 580 Ma, SSFs (small shelly fossils), and first fish coincide with increased oxygen level in the crude sense. The volume of animals increased to 1 million times larger than that of Eukaryotes. Thus, the increased amount of landmass, supply of large amount of nutrients in the platform, and high oxygen level in atmosphere all coincide in time, and hence must be related in process among one another." Maruyama, S, M. Ikoma, H. Genda, K. Hirose, T. Yokoyama & M. Santosh. 2013. "The naked planet Earth: Most essential pre-requisite for the origin and evolution of life." Geoscience Frontiers. 4: 141-65. P. 155.
"Hence, ‘energy rate density’ (also termed power density), symbolized by Öm, is a useful operational term whose expressed intent and plain units are easily understood, indeed, whose definition is clear, the amount of energy passing through a system per unit time and per unit mass." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. Pp. 4-5.
"Although of lesser complexity and longer duration, the Milky Way is nearly as metabolic and adaptive as any lifeform–transacting energy while forming new stars, cannibalizing dwarf galaxies, and dissolving older components, all the while adjusting its limited structure and function for greater preservation in response to environmental changes." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 9.
"Photosynthesis is limited by a wide range of variables, including light intensity, CO2 abundance, H2O availability, environmental temperature (Te), and leaf morphology, all of which interact in complicated ways; the process also has optimal ranges for each of these variables, such as a minimum Te above which photosynthesis will not operate." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 16.
"Amongst the rarest of plants, the more advanced and complex C4-type plants (that initially fix CO2 around the key enzyme RuBisCO to make 4-carbon sugars, such as for maize, sorghum, millet, amaranth, and sugarcane, but also including some of the worst weeds such as crabgrass) have photosynthetic efficiencies about twice (i.e., 2-3.5%) that of the simpler, more widespread C3-type plants (such as rice, wheat, barley, beans, potatoes, tomatoes, and sugar beets that have 3-carbon sugars). This is probably so because the specialized C4 pathway–nonetheless practiced by ~7,500 species of plants today, mostly grasses–uses less H2O and CO2, employs greater nutrient uptake, and displays longer growth cycles, although both use the Calvin-cycle to facilitate CO2 assimilation. "Empirical records imply that C4 plants evolved from their C3 ancestors only as recently as ~20 Mya or ~30 Mya, in any case well after the Cretaceous-Tertiary geological boundary and even long after the appearance of the first C3 grasses ~60 Mya." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 16.
"Angiosperms have higher growth rates and nutrient needs than gymnosperms; they sequester more N and P in their leaves, which then decompose quicker and thus, by positive feedback, create richer soil conditions for their own growth." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. Pp. 16-7.
"... the origin, maintenance, evolution, and fate of all systems are infused with energy." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 30.
"Life seems to function optimally within certain boundary conditions and not surprisingly also has an optimal range of normalized energy flow; so do all other complex systems." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 31.
"Environmental conditions per se are not an underlying reason for complexifications; energy flows through systems likely are; energy is the cause, complexity is the effect." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 31.
"The word ‘evolution’ should not be restricted to biology alone; a broad interpretation of this term generally applies to all complex systems, living or not; thus the subject of cosmic evolution includes physical, biological, and cultural evolution." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 32.
"... prebiological molecules bathed in energy were selected in soupy seas to become the building blocks of life; certain kinds of amino-acid bonding were favored while others were excluded, implying that the evolutionary steps toward life yielded new states more thermodynamically stable than their precursor molecules. Crystal growth among many other nonliving systems (such as clays) also displays simplified selection; ice crystals grow and slightly complexify when water molecules collide and stick, and although the initial molecular encounters are entirely random, the resulting electromagnetic forces that guide them into favorable surface positions are not." Chaisson, Eric. 2014. "The Natural Science Underlying Big History." The Scientific World Journal. Art. No. 384912. P. 33.
"Beyond assemblies that are kinetically trapped, there are those that persist far from equilibrium, provided that they are sustained by a continuous supply of energy, be it from a chemical, electrochemical or photochemical source." Stoddart, J. Fraser. 2015. "A Platform for Change." Supramolecular Chemistry. Vol. 27. No. 9. Pp. 567-70. P. 568.
"In origins of life research one is interested in the transition from non-living to living chemical systems. Our results suggest that the addition of a cycle is a necessary condition. Furthermore the evolution from one autopoietic system to another one then includes the additons, changes and/or deletions of cycles." Kreyssig, Peter, G. Escuela, B. Reynaert, T. Veloz, B. Ibrahim & P. Dittrich. 2012. "Cycles and the Qualitative Evolution of Chemical Systems." PLOS One. V. 7. Issue 10. E45772. P. 10.
"The results presented here provide a framework to study how the inner and outer perturbations lead to qualitative changes in the composition of a chemical system. We emphasize, that this is not only a change of state going from stable state to another one, but a change in the molecular species present at the stable state." Kreyssig, Peter, G. Escuela, B. Reynaert, T. Veloz, B. Ibrahim & P. Dittrich. 2012. "Cycles and the Qualitative Evolution of Chemical Systems." PLOS One. V. 7. Issue 10. E45772. P. 10.
"In a dynamic combinatorial library (DCL) building blocks react with each other reversibly to yield multiple library members that are at equilibrium. Self-assembly of one of these library members will shift this equilibrium in favor of the assembling molecule, resulting in a material that is therefore not only self-assembling but also self-synthesizing. "While self-synthesis can, in principle, create materials starting from the inactive subcomponent, there is one significant obstacle: the formation of the replicator (nucleation) is normally spontaneous and thus gives little room to make the process controllable. However, in Nature materials do not emerge spontaneously; their nucleation is usually triggered by separate entities or processes. Microtubule self-assembly is a representative example. The constituting proteins (á- and â-tubulin) assemble into microtubules spontaneously, but the nucleation barrier is high. To trigger the formation of microtubules, cells use the ã-tubulin ring complex, which templates the assembly." Nowak, Piotr, M. Colomb-Delsuc, S. Otto & J. Li. 2015. "Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library." Journal of the American Chemical Society. 137: 10965-69. P. 10965.
"According to the anabolist theory reproduction and evolution are induced by the reductive formation of low-molecular-weight organic compounds from volcanic C1-compounds by transition metal catalysis. For these redox reactions liquid water is a benefit rather than a detriment. Key to understanding the possibility of reproduction and evolution at this simple molecular level is the recognition that some of the produced organic compounds have functional groups, by which they may become ligands of transition metal centers, increasing their catalytic activity. There are two effects of an organic product B: Feedback effect on catalyst for producing the same organic product B (metabolic reproduction); or feed forward effect on catalyst for producing another organic product C (metabolic evolution). New ligands improve catalysts, which then elicit new metabolic reactions with new products that become further new ligands and so forth. In this manner the metabolism evolves by terminal extension of lateral branching of its pathways, by closing reaction cycles, by recruiting new nutrients or new catalytic metals, or by conquering new environments. By these effects the metabolism self-expands at an accelerating pace, resulting in an avalanche breakthrough." Waechtershaeuser, Guenter. 2012. "Origin of Life: RNA World Versus Autocatalytic Anabolist." The Prokaryotes – Prokaryotic Biology and Symbiotic Associations. Pp. 81-8. Rosenberg, Eugene, E. DeLong, E. Stackebrandt, S. Lory & F. Thompson (Eds.) Springer. P. 82.
"By the anabolist theory life began with a direct mechanism of evolution, organic products, e.g., peptides, feeding directly as ligands into metallocatalysts. Originally, the components of nucleic acids (ribose, bases, nucleosides, nucleotides) earned their keep also as ligands;..." Waechtershaeuser, Guenter. 2012. "Origin of Life: RNA World Versus Autocatalytic Anabolist." The Prokaryotes – Prokaryotic Biology and Symbiotic Associations. Pp. 81-8. Rosenberg, Eugene, E. DeLong, E. Stackebrandt, S. Lory & F. Thompson (Eds.) Springer. P. 82.
"If a new pathway branches from a preestablished metabolism and a product of said new pathway feeds back into its own synthesis, we speak of an egotistic or parasitic catalyst. It may be seen as the earliest form of a virus. A dramatically different situation arises, if a product of a branch pathway exhibits a ‘dual feedback’ effect: an ‘egotistic feedback’ effect directly promoting its own synthesis and a compensatory ‘altruistic feedback’ effect promoting the preexisting metabolism (vitalizer effect). It may persist by virtue of its egotistic feedback component even though the chemical conditions for its de novo synthesis may have vanished. Therefore, with every new dual feedback, the metabolism switches into a new, relatively stable expanded state. This constitutes a stabilizing memory effect. Extant cellular organisms are replete with vitalizers, e.g., DNA, ribosomes, translocases, coenzymes." Waechtershaeuser, Guenter. 2012. "Origin of Life: RNA World Versus Autocatalytic Anabolist." The Prokaryotes – Prokaryotic Biology and Symbiotic Associations. Pp. 81-8. Rosenberg, Eugene, E. DeLong, E. Stackebrandt, S. Lory & F. Thompson (Eds.) Springer. P. 84. "By the anabolist theory the racemic state of organic products is a benefit, because it broadens the space of feedback possibilities. Homochirality is a later ‘invention’ of life,..." Waechtershaeuser, Guenter. 2012. "Origin of Life: RNA World Versus Autocatalytic Anabolist." The Prokaryotes – Prokaryotic Biology and Symbiotic Associations. Pp. 81-8. Rosenberg, Eugene, E. DeLong, E. Stackebrandt, S. Lory & F. Thompson (Eds.) Springer. P. 85.
"The oldest microfossils with remains of cell walls of uniform thickness, carbon content with 13C-depletion and pyrite deposits have been dated to 3.4 billion years ago, more than a billion years after the origin of the Solar System (4.567 billion years ago)." Waechtershaeuser, Guenter. 2012. "Origin of Life: RNA World Versus Autocatalytic Anabolist." The Prokaryotes – Prokaryotic Biology and Symbiotic Associations. Pp. 81-8. Rosenberg, Eugene, E. DeLong, E. Stackebrandt, S. Lory & F. Thompson (Eds.) Springer. P. 86.
"Racemic lipids are able to form stable membranes with a patchwork of chirally segregated lipid domains and with cellular structures undergoing frequent fusions and fissions as in rapidly growing Thermococcus coalescens, thereby generating a first subset of pre-cells with a predominance of one lipid enantiomer and a second subset of pre-cells with a predominance of the other lipid enantiomer. Between these two subsets fusions would have been less probable than within each subset. They would have served as placeholders for the later independent emergence of the phylogenetic domains of the Bacteria and Archaea by the appearance of enantioselective enzymes for lipid synthesis–origin of speciation preordained in the universal laws of physical chemistry." Waechtershaeuser, Guenter. 2012. "Origin of Life: RNA World Versus Autocatalytic Anabolist." The Prokaryotes – Prokaryotic Biology and Symbiotic Associations. Pp. 81-8. Rosenberg, Eugene, E. DeLong, E. Stackebrandt, S. Lory & F. Thompson (Eds.) Springer. P. 86.
"Domain structures necessary for ‘information’ functions appear later than metabolic functions, with ‘translation’ being the first minor functional informational category to appear in evolution." Caetano-Anolles, Gustavo & M. Seufferheld. 2013. "The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm." Journal of Molecular Microbiology and Biotechnology. 23:152-177. P. 165.
"... a major transition in evolution ~3.1 billion years ago brought independently evolving ribosomal subunits together by unfolding inter-subunit (bridge) contacts and interactions with tRNA structures;... a second evolutionary transition occurred almost concurrently with the ‘great oxidation event’ of our planet (~2.4 Gy) and involved the appearance of the L7/L12 protein complex that stimulates the GTPase activity of elongation factor G. This second transition must have notably enhanced ribosomal efficiency." Caetano-Anolles, Gustavo & M. Seufferheld. 2013. "The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm." Journal of Molecular Microbiology and Biotechnology. 23:152-177. P. 165.
"We have proposed a detailed model [of origin of life] describing how ‘adaptive’ peptides enriched these vesicle compartments stabilizing and extending their life. The model also describes ancient vesicles as ‘bioreactors’ capable of retaining cellular components that were beneficial (amphiphiles, peptides, polyphosphate, polyhydroxi-butirate) and discarding through vesicle rupture those that were not. Flaccid vesicles with enhanced protoplasmic content and complexity increase chances to entrap components such as peptides with catalytic and transport abilities. These primordial cellular environments would have enhanced dipeptidase and peptide ligation activities and the length of proteins and their structure-function potential. The model proposes a chain of events that explains the most basal placement of áâá-layered structures in our ToDs [Tree of Domains] as these gain energy interconversion, chaperone and enzymatic activities, and the crucial ability to actively control transmembrane protein content and function." Caetano-Anolles, Gustavo & M. Seufferheld. 2013. "The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm." Journal of Molecular Microbiology and Biotechnology. 23:152-177. P. 170.
"Other important cellular structures appeared very early in evolution. Cells control their shape and stabilize themselves using ‘tensegrity’, geodesic architectures that provide mechanical stability through continuous tension and local compression. This physical ‘ying-yang’occurs in hierarchical self-assembly processes at all size scales, adding an additional design principle to processes such as energy minimization, topological constraints, autocatalytic sets and structural hierarchies.... This suggests primordial networks of scaffolding molecules were already operational in protocells prior to the establishment of the genetic code and the ribosome, providing tensegrity mechanisms of cellular stability." Caetano-Anolles, Gustavo & M. Seufferheld. 2013. "The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm." Journal of Molecular Microbiology and Biotechnology. 23:152-177. P. 173.
"Our phylogenomic results change the perception we have of the rise of modern biology, prompting the abandonment of ‘world’ paradigms with limited explanatory power. Instead, results suggest we focus on the emergence of biological complexity in an ever-expanding coevolving world of macromolecules." Caetano-Anolles, Gustavo & M. Seufferheld. 2013. "The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm." Journal of Molecular Microbiology and Biotechnology. 23:152-177. P. 174. |
