Topics in Cognitive Science, Volume 14, Issue 1, Page 163-188, January 2022.

Recently it has been argued that autocatalytic theory could be applied to the origin of culture. Here possible application to a theory of meaning in the philosophy of language, called radical interpretation, is commented upon and compared to previous applications.

This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We then argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets. We end with some speculation on how all this might lead to a generalized theory of autocatalytic sets, which could possibly be applied (...) to entire ecologies or even economies. (shrink)

Because of the important role which the ‘autocatalytic’ or ‘logistic’ equation has played in determining the direction of a good deal of research both in demography and in the study of individual growth phenomena, a critical and comparative evaluation of those leading ideas inRobertson's book which pertain to this equation and of some of the criticisms levelled against it seemed to be of interest. The present paper shows that, contrary to common belief,Robertson did not really assume that the (...) class='Hi'>autocatalytic reactions to which he compared growth processes, took place in closed systems . On the other hand, he does not seem to have found a satisfactory representation of how the growth phenomena of the individual cells in an organism might interact to yield the overall growth of the organism as a whole. Nor is the manner in which he made his equation account for the openness of the individual cells free from possible criticism. An alternative equation is here proposed, which will be discussed in another paper. The properties of the solutions of this equation are such that the autocatalytic theory might never have gained a foothold if this, more realistic, equation would have been the object of the initial studies. (shrink)

The origin of culture remains in the sphere of hypotheses. Although the hypotheses derive from two presumptions: first, how the structure of culture is envisaged, and secondly, how culture is thought to function. Juri Lotman dealt with both aspects of culture, initially the structural and typological and later the dynamic aspects. Thereby, he arrived at the culturalphilosophical hypothesis of the autocatalytic origin of culture. A catalyst is a component of a chemical reaction which itself doesn’t transform during the reaction, (...) but whose presence is needed to guarantee the reaction (or to stimulate it). Thus, autocatalysis is a paradoxical situation in which the genesis of something presumes the pre-existence of the final product. The paradox of the autocatalysis of culture lies in the fact that culture cannot emerge from anything other than from culture itself, from its own germination. In 1988, speaking about the autocatalysis of culture, Lotman refered tothe cultural historicist Nikolai I. Konrad (1891–1970), who undoubtedly borrowed this idea from Jacob Christopher Burckhardt (1818–1897). This undiscovered connection reminds us of the fact, that a model for autocatalysis (or an autopoiesis) was basic to Naturphilosophie of the 19th century. In the 20th century, this was represented by Vladimir I. Vernadsky (1863–1945), from whom Lotman in 1982 received the impetus to formulate the concept of semiosphere as well as of the autocatalysis of culture. The autocatalysis model of culture is culturally diachronical, the semiosphere is, however, a synchronical one. In both cases, the natural philosophical cytology of the 19th century was Lotman’s semiotical meta-language. (shrink)

Autocatalytic networks have been used to model the emergence of self‐organizing structure capable of sustaining life and undergoing biological evolution. Here, we model the emergence of cognitive structure capable of undergoing cultural evolution. Mental representations (MRs) of knowledge and experiences play the role of catalytic molecules, and interactions among them (e.g., the forging of new associations) play the role of reactions and result in representational redescription. The approach tags MRs with their source, that is, whether they were acquired through (...) social learning, individual learning (of pre‐existing information), or creative thought (resulting in the generation of new information). This makes it possible to model how cognitive structure emerges and to trace lineages of cumulative culture step by step. We develop a formal representation of the cultural transition from Oldowan to Acheulean tool technology using Reflexively Autocatalytic and Food set generated (RAF) networks. Unlike more primitive Oldowan stone tools, the Acheulean hand axe required not only the capacity to envision and bring into being something that did not yet exist, but hierarchically structured thought and action, and the generation of new MRs: the concepts EDGING, THINNING, SHAPING, and a meta‐concept, HAND AXE. We show how this constituted a key transition toward the emergence of semantic networks that were self‐organizing, self‐sustaining, and autocatalytic, and we discuss how such networks replicated through social interaction. The model provides a promising approach to unraveling one of the greatest anthropological mysteries: that of why development of the Acheulean hand axe was followed by over a million years of cultural stasis. (shrink)

This year we celebrated Stuart Kauffman’s 80th birthday. Kauffman has contributed many original ideas to science. One of them is that of autocatalytic sets in the context of the origin of life. An autocatalytic set is a self-sustaining chemical reaction network in which all the molecules mutually catalyze each other’s formation from a basic food source. This notion is often seen as a “counterargument” against the dominant genetics-first view of the origin of life, focusing more on metabolism instead. (...) The original notion was introduced back in 1971, but it has taken several decades for this idea to really catch on. Thanks to theoretical as well as experimental progress in more recent research on autocatalytic sets, especially over the past 15 years, the idea now seems to be gaining significant interest and support. In this tribute to Kauffman’s work and ideas, a brief history of research on autocatalytic sets is presented. (shrink)

The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given the set of elements, the reactions between them (chemical or otherwise), and with various elements catalysing certain reactions, a Reflexively Autocatalytic F-generated (RAF) set is a subset R′\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$'$$\end{document} of reactions that is self-generating from a given food set, and with each reaction in (...) R′\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$'$$\end{document} being catalysed from within R′\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$'$$\end{document}. RAF theory has been applied to various phenomena in theoretical biology, and a key feature of the approach is that it is possible to efficiently identify and classify RAFs within large systems. This is possible because RAFs can be described as the (nonempty) subsets of the reactions that are the fixed points of an (efficiently computable) interior map that operates on subsets of reactions. Although the main generic results concerning RAFs can be derived using just this property, we show that for systems with at least 12 reactions there are generic results concerning RAFs that cannot be proven using the interior operator property alone. (shrink)

The organization of the complex mixed-mode oscillations generated, in a three-dimensional variable space, by an autocatalytic process formalized as a cubic monomial is analyzed. The generation of the temporal patterns is elucidated by complementary approaches dealing with the three-variable differential continuous system itself and with successive discrete applications modelling its first return map. The extent to which the underlying bifurcation structures could constitute a fingerprint of autocatalytic processes is discussed in connection with the modelling of biological systems.

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear reactions (...) are required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)

An idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicators (...) generate self-similar structure, but because the process happens in a piecemeal manner, through bottom-up interactions rather than a top-down code, they replicate with low fidelity, and acquired characteristics are inherited. Just as polymers catalyze reactions that generate other polymers, the retrieval of an item from memory can in turn trigger other items, thus cross-linking memories, ideas, and concepts into an integrated conceptual structure. Worldviews evolve idea by idea, largely through social exchange. An idea participates in the evolution of culture by revealing certain aspects of the worldview that generated it, thereby affecting the worldviews of those exposed to it. If an idea influences seemingly unrelated fields this does not mean that separate cultural lineages are contaminating one another, because it is worldviews, not ideas, that are the basic unit of cultural evolution. (shrink)

This paper uses autocatalytic networks to model discontinuous cultural transitions involving cross-domain transfer, using as an illustrative example, artworks inspired by the oldest-known uncontested example of figurative art: the carving of the Hohlenstein-Stadel Löwenmensch, or lion-human. Autocatalytic networks provide a general modeling setting in which nodes are not just passive transmitters of activation; they actively galvanize, or “catalyze” the synthesis of novel nodes from existing ones This makes them uniquely suited to model how new structure grows out of (...) earlier structure, i.e., cumulative, generative network growth. They have been used to model the origin and early evolution of biological life, and the emergence of cognitive structures capable of undergoing cultural evolution. We conducted a study in which six individual creators and one group generated music, prose, poetry, and visual art inspired by the Hohlenstein-Stadel Löwenmensch, and answered questions about the process. The data revealed four through-lines by which they expressed the Löwenmensch in an alternative art form: lion-human hybrid, subtracting from the whole to reveal the form within, deterioration, and waiting to be found with a story to tell. Autocatalytic networks were used to model how these four spontaneously derived through-lines form a cultural lineage from Löwenmensch to artist to audience. We used the resulting data from three creators to model the cross-domain transfer from inspirational source to creative product. These four spontaneously-generated threads of cultural continuity formed the backbone of this Löwenmensch-inspired cultural lineage, enabling culture to evolve even in the face of discontinuity at the level conventional categories or domains. We know of no other theory of cultural evolution that accommodates cross-domain transfer or other forms of discontinuity. The approach paves the way for a broad scientific framework for the origins of evolutionary processes. (shrink)

Ultimately we will only understand biological agency when we have developed a theory of the organization of biological processes, and science is still a long way from attaining that goal. It may be possible nonetheless to develop a list of necessary conditions for the emergence of minimal biological agency. The authors offer a model of molecular autonomous agents which meets the five minimal physical conditions that are necessary (and, we believe, conjointly sufficient) for applying agential language in biology: autocatalytic (...) reproduction; work cycles; boundaries for reproducing individuals; self-propagating work and constraint construction; and choice and action that have evolved to respond to food or poison. When combined with the arguments from preadaptation and multiple realizability, the existence of these agents is sufficient to establish ontological emergence as against what one might call Weinbergian reductionism. Minimal biological agents are emphatically not conscious agents, and accepting their existence does not commit one to any robust theory of human agency. Nor is there anything mystical, dualistic, or non-empirical about the emergence of agency in the biosphere. Hence the emergence of molecular autonomous agents, and indeed ontological emergence in general, is not a negation of or limitation on careful biological study but simply one of its implications. (shrink)

In 1972, we proposed a theory of biological pattern formation in which concentration maxima of pattern forming substances are generated through local self- enhancement in conjunction with long range inhibition. Since then, much evidence in various developmental systems has confirmed the importance of autocatalytic feedback loops combined with inhibitory interaction. Examples are found in the formation of embryonal organizing regions, in segmentation, in the polarization of individual cells, and in gene activation. By computer simulations, we have shown that the (...) theory accounts for much of the regulatory phenomena observed, including signalling to regenerate removed parts. These self- regulatory features contribute to making development robust and error-tolerant. Furthermore, the resulting pattern is, to a large extent, independent of the details provided by initial conditions and inducing signals. (shrink)

Preface -- Prolegomenon : Hayek's three unsettling theses -- Beyond human nature -- Beyond moral justification -- Beyond human governance -- Three enquiries on the open society -- The rise of a normative species -- A natural history of moral order -- The "starting point" -- The egalitarian revolution -- Self-interest, reciprocity and altruism -- Internalized, enforced, social rules -- The other side of morality -- Cultural evolution -- Part I : the rise and fall of inequality -- A complex (...) moral species -- The diversity and self-organized complexity -- Liberalism and the open society -- Understanding diversity -- Autocatalytic diversity -- Diversity and complexity -- Too much complexity? -- The morality of self-organization -- The social contract -- A self-organization model -- Moral diversity In the open society -- Part II: the complexities of self-governance -- Self-governance -- Macro control -- Macro structure -- Strategic dilemmas and polycentricity -- Meso-level goal pursuit -- Sectoral policy -- Self-governance from the bottom-up : simplifying the problems of governance -- Our moral nature and governance in the open society -- Liberal democracy -- Epilogue -- Appendix A -- Appendix B. (shrink)

The paper addresses the formation of striking patterns within originally near-homogenous tissue, the process prototypical for embryology, and represented in particularly purist form by cut sections of hydra regenerating, by internal reorganisation of the pre-existing tissue, a complete animal with head and foot. The essential requirements are autocatalytic, self-enhancing activation, combined with inhibitory or depletion effects of wider range – “lateral inhibition”. Not only de-novo-pattern formation, but also well known, striking features of developmental regulation such as induction, inhibition, and (...) proportion regulation can be explained on this basis. The theory provides a mathematical recipe for the construction of molecular models with criteria for the necessary non-linear interactions. It has since been widely applied to different developmental processes. (shrink)

The goal of synthetic biology is to create artificial organisms. To achieve this it is essential to understand what life is. Metabolism-replacement systems, or (M, R)-systems, constitute a theory of life developed by Robert Rosen, characterized in the statement that organisms are closed to efficient causation, which means that they must themselves produce all the catalysts they need. This theory overlaps in part with other current theories, including autopoiesis, the chemoton, and autocatalytic sets, all of them invoking some idea (...) of closure. A simple model of an (M, R)-system has been implemented in the computer, and behaves in ways that may shed light on the requirements for a prebiotic self-organizing system. In addition to a trivial steady state in which nothing happens, it can establish a non-trivial steady state in which all intermediates have finite concentrations, with their rates of degradation balanced by their rates of synthesis. The system can be regenerated from the set of food components plus a single intermediate, and maintain itself in that state indefinitely, despite continuous degradation. At the very low compartment volumes that may have existed in prebiotic conditions, for example in cavities in minerals, or in micelles formed by simple amphiphiles, statistical fluctuations in the numbers of molecules need to be taken into account. With the stochastic approach there is no non-trivial steady state in strict mathematical terms, because the system will always collapse to the trivial state after sufficient time. However, the average time before collapse is so long for volumes greater than $10^{-19}\;{\textsc{l}}$ (much smaller than the volume of the order of $10^{-15}\;{\textsc{l}}$ for a typical bacterial cell) that for practical purposes the self-maintaining state of non-null concentrations becomes significant, recalling the situation of bistability that is observed in deterministic analysis. In turn, there exists a minimum size below which the self-organizing system cannot maintain itself on chemically relevant time scales. The value of the critical volume depends on the particular concentrations and rate constants assumed, but the principle could apply generally. (shrink)

This paper considers questions of continuity and change in education from the perspective of complexity theory, introducing the field to educationists who might not be familiar with it. Given a significant degree of complexity in a particular environment (or ‘dynamical system’), new properties and behaviours, which are not necessarily contained in the essence of the constituent elements or able to be predicted from a knowledge of initial conditions, will emerge. These concepts of emergent phenomena from a critical mass, associated with (...) notions of lock‐in, path dependence, and inertial momentum, suggest that it is in the dynamic interactions and adaptive orientation of a system that new phenomena, new properties and behaviours, emerge. The focus thus shifts from a concern with decontextualised and universalised essence to contextualised and contingent complex wholes. This is where complexity theory seeks the levers of history. The paper posits the notion of inertial momentum as the conceptual link between the principle of emergent phenomena as developed principally in the natural sciences and the notion of socio‐historical change in human society. It is argued that educational and institutional change is less a consequence of effecting change in one particular factor or variable, and more a case of generating momentum in a new direction by attention to as many factors as possible. Complexity theory suggests, in other words, that what it might take to change a school's inertial momentum from an ethos of failure is massive and sustained intervention at every possible level until the phenomenon of learning excellence emerges from this new set of interactions among these new factors, and sustains itself autocatalytically. The paper concludes with a summary consideration of the conditions that contribute to the emergence of new properties and behaviours in a system. (shrink)

Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, (...) and the more generic category of Darwinian evolution on the other. We argue that Hull’s and Dawkins’ replicator/interactor distinction of entities is a sufficient, but not necessary, condition for Darwinian evolution to take place. We conceive the origin of genes as a separation between different types of molecules in a thermodynamic state space, and employ a notion of reproducers. (shrink)

Whenever the state of a biological system is not determined solely by present conditions but depends on its past history, we can say that the system has memory. Bacteria and bacteriophage use a variety of memory mechanisms, some of which seem to convey adaptive value. A genetic type of heritable memory is the programmed inversion of specific DNA sequences, which causes switching between alternative patterns of gene expression. Heritable memory can also be based on epigenetic circuits, in which a system (...) with two possible steady states is locked in one or the other state by a positive feedback loop. Epigenetic states have been observed in a variety of cellular processes, and are maintained by diverse mechanisms. Some of these involve alternative DNA methylation patterns that are stably transmitted to daughter molecules and can affect DNA–protein interactions (e.g., gene transcription). Other mechanisms exploit autocatalytic loops whereby proteins establish the proper conditions for their continued synthesis. Template polymers other than nucleic acids (e.g., components of the cell wall) may also propagate epigenetic states. Non‐heritable memory is exemplified by parasitic organisms that bear a signature of their previous host, such as host‐controlled modification of phage DNA or porin hitchhiking in predatory bacteria. The heterogeneous nature of the examples known may be indicative of widespread occurrence of memory mechanisms in bacteria and phage. However, the actual extent, variety and potential selective value of prokaryotic memory devices remain open questions, still to be addressed experimentally. BioEssays 24:512–518, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Reaction network is a promising framework for representing complex systems of diverse and even interdisciplinary types. In this approach, complex systems appear as self-maintaining structures emerging from a multitude of interactions, similar to proposed scenarios for the origin of life out of autocatalytic networks. The formalism of chemical organization theory mathematically specifies under which conditions a reaction network is stable enough to be observed as a whole complex system. Such conditions specify the notion of organization, crucial in COT. In (...) this paper, we show that the structure and operation of organizations can be advanced towards a formal framework of resilience in complex systems. That is, we show that there exist three fundamental types of change defined for reaction networks, and that these perturbations not only provide a general representation of perturbations in the context of resilience but also pave the ground to formalize different forms of resilient responses. In particular, we show that decomposing the network’s operational structure into dynamically decoupled modules allows to formalize what is the impact of a perturbation and to what extent any potential compensation to that perturbation will be successful. We illustrate our approach with a toy model of a farm that operates in a sustainable way producing milk, eggs, and/or grains from other resources. With the help of simulations, we analyze the different types of perturbations and responses that the farm can undergo and how that affects its sustainable operation. (shrink)

Life appears to be a natural property of matter, but the problem of its origin only arose after early scientists refuted continuous spontaneous generation. There is no chance of life arising ‘all at once’, we need the standard scientific incremental explanation with large numbers of small steps, an approach used in both physical and evolutionary sciences. The necessity for considering both theoretical and experimental approaches is emphasized. After describing basic principles that are available (including the Darwin-Eigen cycle), the search for (...) origins is considered under four main themes. These are the RNA-world hypothesis; potential intermediates between an RNA-world and a modern world via the evolution of protein synthesis and then of DNA; possible alternatives to an RNA-world; and finally the earliest stages from the simple prebiotic systems to RNA. The triplicase/proto-ribosome theory for the origin of the ribosome is discussed where triples of nucleotides are added to a replicating RNA, with the origin of a triplet code well-before protein synthesis begins. The length of the code is suggested to arise from the early development of a ratchet mechanism that overcomes the problem of continued processivity of an RNA-based RNA-polymerase. It is probable that there were precursor stages to RNA with simpler sugars, or just two nucleotides, but we do not yet know of any better alternatives to RNA that were likely to arise naturally. For prebiotic stages (before RNA) a flow-reactor model is suggested to solve metabolism, energy gradients, and compartmentation simultaneously – thus the intense interest in some form of flow reactor. If an autocatalytic cycle could arise in such a system we would be major steps ahead. The most likely physical conditions for the origin of life require further clarification and it is still unclear whether the origin of life is more of an entropy (information) problem (and therefore high temperatures would be detrimental), rather than a kinetic problem (where high temperatures may be advantageous). (shrink)

Explaining the emergence of life is perhaps central and the most challenging question in modern science. Within this area of research, the emergence and evolution of the genetic code is supposed to be a critical transition in the evolution of modern organisms. The canonical genetic code is one of the most dominant aspects of life on this planet, and thus studying its origin is critical to understanding the evolution of life, including life’s emergence. In this sense it is possible to (...) view the ribosome as a digital-to-analogue information converter. Why the translation apparatus evolved, is one of the enduring mysteries of molecular biology. Assuming the hypothesis that during the emergence of life evolution had to first involve autocatalytic systems, which only subsequently acquired the capacity of genetic heredity, in the present article we discuss some aspects and causes of the possible emergence of digital, discrete information arising from analogue information realized in the intra- and inter-molecular interactions throughout molecular evolution. How such reverse translation was achieved at a molecular level is still unclear. The results of such debates and investigations might shift current biological paradigms and might also have a momentous significance for modern philosophy in understanding our place in the universe. (shrink)

The close link between signaling by the developmental regulators of the Hedgehog family and cholesterol biochemistry has been known for some time. The morphogen is covalently attached to cholesterol in a peculiar autocatalytic reaction and embryonal disruption of cholesterol synthesis leads to malformations that mimic Hh signaling defects. Recently, it was furthermore shown that secreted Hh could hitchhike on lipoprotein particles to establish its morphogenic gradient in the developing embryo. Additionally, there is new evidence that the Hh‐receptor Patched transmits (...) the Hh signal by modulating the secretion of an inhibitory sterol molecule from the receiving cells. Here we present some of the most recent discoveries on the Hh–sterol link and discuss their implications from a systems design perspective. We predict that a robust functioning of the Hh pathway will require the involvement of more sterol metabolites, and these should be the subject of future research. BioEssays 29:1085–1094, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

We hypothesize that life began not with the first self‐reproducing molecule or metabolic network, but as a prebiotic ecology of co‐evolving populations of macromolecular aggregates (composomes). Each composome species had a particular molecular composition resulting from molecular complementarity among environmentally available prebiotic compounds. Natural selection acted on composomal species that varied in properties and functions such as stability, catalysis, fission, fusion and selective accumulation of molecules from solution. Fission permitted molecular replication based on composition rather than linear structure, while fusion (...) created composomal variability. Catalytic functions provided additional chemical novelty resulting eventually in autocatalytic and mutually catalytic networks within composomal species. Composomal autocatalysis and interdependence allowed the Darwinian co‐evolution of content and control (metabolism). The existence of chemical interfaces within complex composomes created linear templates upon which self‐reproducing molecules (such as RNA) could be synthesized, permitting the evolution of informational replication by molecular templating. Mathematical and experimental tests are proposed. BioEssays 28: 399–412, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Deacon speculates on the origin of interpretation of signs using autocatalytic origin of life models and Peircean terminology. I explain why interpretation evolved only later as a triadic intervention between symbols and actions. In all organisms the passive one-dimensional genetic informational symbol sequences are converted to active functional proteins or nucleic acids by three-dimensional folding. This symbol grounding is a direct symbol-to-action conversion. It is universal throughout all evolution. Folding is entirely a lawful physical process, leaving neither freedom nor (...) necessity for interpretation. Similarly, the initial converse action-to-symbol conversion of sensory inputs also leaves no freedom for interpretation until after the action-to-symbol conversion. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a (...) result, the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism. Graphical Abstract. (shrink)

Development is a process whereby a relatively unspecified system comprised of loosely connected lower level parts becomes organized into a coherent, higher-level agency. Its temporal corollaries are growth, increasingly deterministic behavior, and a progressive reduction of developmental potential. During immature stages with relatively low specification and high potential, development is largely controlled by local interactions from the “bottom-up,” whereas during more highly specified stages with reduced potential, emergent autocatalytic processes exert “top-down” control. Robert Ulanowicz has shown that this phenomenology (...) of ascendency follows thermodynamic principles and can be described quantitatively using information theory, providing a general theory of development. However, the theory has not found a wide audience among developmental biologists, as genetic determinism encourages the popular reductionistic perception that ontogeny is controlled entirely by molecular mechanisms that exert efficient causality from the bottom-up. Nonetheless, measurements of metabolic rates and mRNA complexity in developing embryos, as well as functional analyses of gene regulatory systems, indicate that ontogeny fits the paradigm of developmental ascendency. Beyond informing biomedical research and the interpretation of large datasets obtained by systems-biological approaches, developmental ascendency helps explain the origin of life, and, being independent of scale, provides an overarching explanation for phylogenetic change that contextualizes Darwinian evolution. (shrink)

It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein‐dominated membranes on their own. In a metabolism‐first context, “autocatalytically closed” sets of statistical peptides could organize a self‐maintaining protometabolism, assisted by an unfolding set of ribotide‐related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet‐drying cycles and an early onset of photosynthetic activities are considered (...) most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide‐dominated vesicles were engaged in light harvesting, together with isoprenoid‐tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have formed a contiguous layer covering the mineral sediment, held in place by colloidal coherence of a hydrogel matrix. This unconventional scenario assumes a late onset of cellular individualization – perhaps from within, resembling endosporogenesis. (shrink)

This essay presents a scenario of the origin of life that is based on analysis of biological architecture and mechanical design at the microstructural level. My thesis is that the same architectural and energetic constraints that shape cells today also guided the evolution of the first cells and that the molecular scaffolds that support solid-phase biochemistry in modern cells represent living microfossils of past life forms. This concept emerged from the discovery that cells mechanically stabilize themselves using tensegrity architecture and (...) that these same building rules guide hierarchical self-assembly at all size scales (Sci Amer 278:48–57;1998). When combined with other fundamental design principles (e.g., energy minimization, topological constraints, structural hierarchies, autocatalytic sets, solid-state biochemistry), tensegrity provides a physical basis to explain how atomic and molecular elements progressively self-assembled to create hierarchical structures with increasingly complex functions, including living cells that can self-reproduce. BioEssays 22:1160–1170, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

A three-variable biochemical prototype involving two enzymes with autocatalytic regulation proposed by Decroly and Goldbeter (1987) is analyzed using a topological approach. A two-branched manifold, a so-called template, is thus identified. For certain control parameter values, this template is a horseshoe template with a global torsion of two half-turns. This implies that the bifurcation diagram can be described using the usual sequences associated with a unimodal map with a differentiable maximum as well as exemplified by the logistic map. Moreover, (...) a type-I intermittency associated with a saddle-node bifurcation is exhibited. The dynamics from a single time series are also investigated to determine whether it is possible to investigate the dynamics of this biochemical model from the measure of a single concentration. (shrink)

Radical Embodied Cognition is an anti-representationalist approach to the nature of basic cognition proposed by Daniel Hutto and Erik Myin. While endorsing REC’s arguments against a role for contentful representations in basic cognition we suggest that REC’s ‘teleosemiotic’ approach to intentional targeting results in a ‘grey area’ in which it is not clear what kind of causal-explanatory concept is involved. We propose the concept of constraint-evading surrogacy as a conceptual basis for REC’s account of intentional targeting. The argument is developed (...) via a reconsideration of Peter Godfrey-Smith’s ‘environmental complexity thesis’. We show how constraint-evading surrogacy clarifies REC’s account of intentionality by specifying the role of external natural signs and certain internal states. We argue that the resulting view of intentionality can be extended to proto-biotic autocatalytic systems, offering support for the life-mind continuity thesis. We leave open the question of whether it is helpful to consider constraint-evading surrogacy to be a form of representation, but we suggest that there is a prima facie case for such a view. (shrink)

Mechanical reductionism, which deals entirely with homogeneous variables, will constrain and enable the activities of richly heterogeneous living systems, but it cannot determine their outcomes. Such indeterminism owes to problems with dimensionality, dynamical logic, intractability, and insufficiency. The order in any living structure arises via an historical series of contingencies that were selected endogenously by stable autocatalytic processes in tandem with, and usually in opposition to, conventional external influences (natural selection). The development of living communities thereby resembles a Heraclitean (...) dialectic between processes that build up and those that tear down. Investigating this unconventional dynamic requires metaphysical assumptions that are complementary to those that have guided science over the past three centuries. The new dynamics can be represented in terms of weighted networks of interacting processes, which facilitate the statement of testable hypotheses. Network analysis thereby implements and tests ideas that heretofore could only be addressed as verbal propositions. (shrink)

Ultimately we will only understand biological agency when we have developed a theory of the organization of biological processes, and science is still a long way from attaining that goal. It may be possible nonetheless to develop a list of necessary conditions for the emergence of minimal biological agency. The authors offer a model of molecular autonomous agents which meets the five minimal physical conditions that are necessary (and, we believe, conjointly sufficient) for applying agential language in biology: autocatalytic (...) reproduction; work cycles; boundaries for reproducing individuals; self-propagating work and constraint construction; and choice and action that have evolved to respond to food or poison. When combined with the arguments from preadaptation and multiple realizability, the existence of these agents is sufficient to establish ontological emergence as against what one might call Weinbergian reductionism. Minimal biological agents are emphatically not conscious agents, and accepting their existence does not commit one to any robust theory of human agency. Nor is there anything mystical, dualistic, or non-empirical about the emergence of agency in the biosphere. Hence the emergence of molecular autonomous agents, and indeed ontological emergence in general, is not a negation of or limitation on careful biological study but simply one of its implications. (shrink)

Like the information patterns that evolve through. biological processes, mental representations or memes evolve through adaptive exploration and transformation of an information space through variation, selection, and transmission. However since memes do not contain instructions for their replication our brains do it for them, strategically, guided by a fitness landscape that reflects both internal drives and a worldview that forms through meme assimilation. This paper presents a tentative model for how an individual becomes a meme evolving agent via the emergence (...) of an autocatalytic network of sparse, distributed memories, and discusses implications for complex creative thought processes and why they are unique to humans. A hypothetical scenario for the evolutionary dynamics of a given meme in a society of interacting individuals is presented. (shrink)

A simple molecular system is described consisting of the reciprocal linkage between an autocatalytic cycle and a self-assembling encapsulation process where the molecular constituents for the capsule are products of the autocatalysis. In a molecular environment sufficiently rich in the substrates, capsule growth will also occur with high predictability. Growth to closure will be most probable in the vicinity of the most prolific autocatalysis and will thus tend to spontaneously enclose supportive catalysts within the capsule interior. If subsequently disrupted (...) in the presence of new substrates, the released components will initiate production of additional catalytic and capsule components that will spontaneously re-assemble into one or more autocell replicas, thereby reconstituting and sometimes reproducing the original. In a diverse molecular environment, cycles of disruption and enclosure will cause auto-cells to incidentally encapsulate other molecules as well as reactive substrates. To the extent that any captured molecule can be incorporated into the autocatalytic process by virtue of structural degeneracy of the catalytic binding sites, the altered autocell will incorporate the new type of component into subsequent replications. Such altered autocells will be progenitors of “lineages” with variant characteristics that will differentially propagate with respect to the availability of commonly required substrates. Autocells are susceptible to a limited form of evolution, capable of leading to more efficient, more environmentally fitted, and more complex forms. This provides a simple demonstration of the plausibility of open-ended reproduction and evolvability without self-replicating template molecules or maintenance of persistent nonequilibrium chemistry. This model identifies an intermediate domain between prebiotic and biotic systems and bridges the gap from nonequilibrium thermodynamics to life. (shrink)

Many in science are disposed not to take biosemiotics seriously, dismissing it as too anthropomorphic. Furthermore, biosemiotic apologetics are cast in top-down fashion, thereby adding to widespread skepticism. An effective response might be to approach biosemiotics from the bottom up, but the foundational assumptions that support Enlightenment science make that avenue impossible. Considerations from ecosystem studies reveal, however, that those conventional assumptions, although once possessing great utilitarian value, have come to impede deeper understanding of living systems because they implicitly depict (...) the evolution of the universe backward. Ecological dynamics suggests instead a smaller set of countervailing postulates that allows evolution to play forward and sets the stage for tripartite causalities, signs, and interpreters—the key elements of biosemiosis—to emerge naturally out of the interaction of chance with configurations of autocatalytic processes. Biosemiosis thereby appears as a fully legitimate outgrowth of the new metaphysic and shows promise for becoming the supervenient focus of a deeper perspective on the phenomenon of life. (shrink)

Purpose: This, the second part of a two-part paper, describes how the concerns of enactive cognitive science have been realized in actual research: methodological issues, proposed explanatory mechanisms and models, some of the potential as both a theoretical and applied science, and several of the major open research questions. Findings: Despite some skepticism about "mechanisms" in constructivist literature, enactive cognitive science attempts to develop cognitive formalisms and models. Such techniques as feedback loops, self-organization, autocatalytic networks, and dynamical systems modeling (...) are used to develop alternatives to cognitivist models. A number of technical similarities are starting to emerge in the different models being proposed. Research Implications: The need to resolve the interplay between autonomy and coupling with the environment suggests the need for further technical research. And the reintroduction of first-person concerns into cognitive science raises some questions of method, particularly with regard to the relationship between first-person experience, neuroscience, and methods of description, analysis, and explanation. Results to date suggest that insights from enactive cognitive science could lead to innovations in the design of artifacts. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a (...) result, the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

To discover a unifying theory of biology, it is necessary first to believe in its existence and second to seek its elements. Such a theory would explain the regulation of the cell cycle, differentiation and the origin of life. Some elements of the theory may be obtained by considering both eukaryotic and prokaryotic cell cycles. These elements include cytoskeletal proteins, calcium, cyclins, protein kinase C, phosphorylation, transcriptional sensing, autocatalytic gene expression and the physical properties of lipids. Other more exotic (...) candidate elements include the dynamic enzoskeleton, ATP generation, mechanotransduction, the piezoelectric effect and resonance. Bringing these disparate elements together — and discovering others — will require extensive collaborations between specialists from different sciences. This can only be achieved within the context of an integrated approach to biology. (shrink)

The biochemical mechanism by which the phytochrome family of plant sensory photoreceptors transmit perceived informational light signals downstream to transduction pathway components is undetermined. The recent sequencing of the entire genome of the cyanobacterium Synechocystis, however, has revealed a protein that has an NH2‐terminal domain with striking sequence similarity to the photosensory NH2‐terminal domain of the phytochromes, and a COOH‐terminal domain strongly related to the transmitter histidine kinase module of bacterial two‐component sensors. The Synechocystis protein is capable of autocatalytic (...) chromophore ligation and exhibits photoreversible light‐absorption changes analogous to the phytochromes, indicating its capacity to function as an informational photoreceptor. Together with earlier observations that the COOH‐terminal domains of the plant phytochromes also have sequence similarity to the histidine kinases, these data suggest that the cyanobacteria utilize photoregulated histidine kinases as a sensory system and that the plant phytochromes may be evolutionary descendants of these photoreceptors. (shrink)

The fate of root epidermal cells is controlled by a complex interplay of transcriptional regulators, generating a genetically determined, position‐biased arrangement of root hair cells. This pattern is altered during postembryonic development and in response to environmental signals to confer developmental plasticity that acclimates the plant to the prevailing conditions. Based on the hypothesis that events downstream of this initial mechanism can modulate the pattern installed during embryogenesis, we have developed a reaction diffusion model that reproduces the root hair patterning (...) previously observed experimentally. Under all growth conditions, an almost equal spacing between root hair forming cells was observed both in vitro and in silico, indicating that long‐range intercellular communication is crucial for the trichoblasts' decision to form a root hair. We assume that a hair growth promoter (HGP) is upregulated in root‐hair‐forming cells by a trichoblast‐specific component. Once established, HGP production is self‐enhancing. The autocatalytic regulation of HGP is antagonized by an HGP‐produced hair growth inhibitor (HGI). HGI is exported from trichoblasts and diffuses to neighboring cells, where it inhibits further HGP production and promotes the non‐hair cell fate. Under conditions of phosphate deficiency, we hypothesise that HGP production is increased and HGI diffusion rate is reduced, leading to a position‐independent formation of extra root hairs. BioEssays 30:75–81, 2008. © 2007 Wiley Periodicals, Inc. (shrink)

The temporal behaviour of the nonlinear compartmental model we have developed for rat calcium metabolism is discussed with respect to the theoretical properties of the self-oscillating autocatalytic subunit around which the model is constructed. Depending on the approximations made, this subunit is described by a minimal two-variable model, SU2, or by a three-variable one, SU3. The diversity of the theoretical dynamic behaviours possible with SU2 is greatly increased with SU3. But the identification of SU3 parameter values in three different (...) experimental situations reveals that biological constraints efficiently preserve a simple circadian rhythm for bone metabolism. This analysis indicates the significant contribution of the available bone crystal pool to the dynamic organization of this tissue, and hence to extracellular calcium homeostasis. (shrink)

The improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or autocell). Since replication occurs without a self-assembly code, acquired characteristics are inherited. Moreover, there is no strict distinction between alive and dead; one can only infer that an autocell was alive if it replicates. These features of early life render natural selection inapplicable to the description of its change-of-state because (...) they defy its underlying assumptions. Moreover, natural selection describes only randomly generated novelty; it cannot describe the emergence of form at the interface between organism and environment. Self-organization is also inadequate because it is restricted to interactions amongst parts; it too cannot account for context-driven change. A modified version of selection theory or self-organization would not work because the description of change-of-state through interaction with an incompletely specified context has a completely different mathematical structure, i.e. entails a non-Kolmogorovian probability model. It is proposed that the evolution of early life is appropriately described as lineage transformation through context-driven actualization of potential, with self-organized change-of-state being a special case of no contextual influence, and competitive exclusion of less fit individuals through a selection-like process possibly (but not necessarily) playing a secondary role. It is argued that natural selection played an important role in evolution only after genetically mediated replication was established. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a (...) result, the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

This paper considers questions of continuity and change in education from the perspective of complexity theory, introducing the field to educationists who might not be familiar with it. Given a significant degree of complexity in a particular environment , new properties and behaviours, which are not necessarily contained in the essence of the constituent elements or able to be predicted from a knowledge of initial conditions, will emerge. These concepts of emergent phenomena from a critical mass, associated with notions of (...) lock‐in, path dependence, and inertial momentum, suggest that it is in the dynamic interactions and adaptive orientation of a system that new phenomena, new properties and behaviours, emerge. The focus thus shifts from a concern with decontextualised and universalised essence to contextualised and contingent complex wholes. This is where complexity theory seeks the levers of history. The paper posits the notion of inertial momentum as the conceptual link between the principle of emergent phenomena as developed principally in the natural sciences and the notion of socio‐historical change in human society. It is argued that educational and institutional change is less a consequence of effecting change in one particular factor or variable, and more a case of generating momentum in a new direction by attention to as many factors as possible. Complexity theory suggests, in other words, that what it might take to change a school's inertial momentum from an ethos of failure is massive and sustained intervention at every possible level until the phenomenon of learning excellence emerges from this new set of interactions among these new factors, and sustains itself autocatalytically. The paper concludes with a summary consideration of the conditions that contribute to the emergence of new properties and behaviours in a system. (shrink)

The improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or protocell). Since replication occurs without a self-assembly code, acquired characteristics are inherited. Moreover, there is no strict distinction between alive and dead; one can only infer that a protocell was alive if it replicates. These features of early life render natural selection inapplicable to the description of its change-of-state because (...) they defy its underlying assumptions. Moreover, natural selection describes only randomly generated novelty; it cannot describe the emergence of form at the interface between organism and environment. Self-organization is also inadequate because it is restricted to interactions amongst parts; it too cannot account for context-driven change. A modified version of selection theory or self-organization would not work because the description of change-of-state through interaction with an incompletely specified context has a completely different mathematical structure, i.e. entails a non-Kolmogorovian probability model. It is proposed that the evolution of early life is appropriately described as lineage transformation through context-driven actualization of potential (CAP), with self-organized change-of-state being a special case of no contextual influence, and competitive exclusion of less fit individuals through a selection-like process possibly (but not necessarily) playing a secondary role. It is argued that natural selection played an important role in evolution only after genetically mediated replication was established. (shrink)

An idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicators (...) generate self-similar structure, but because the process happens in a piecemeal manner, through bottom-up interactions rather than a top-down code, they replicate with low fidelity, and acquired characteristics are inherited. Just as polymers catalyze reactions that generate other polymers, the retrieval of an item from memory can in turn trigger other items, thus cross-linking memories, ideas, and concepts into an integrated conceptual structure. Worldviews evolve idea by idea, largely through social exchange. An idea participates in the evolution of culture by revealing certain aspects of the worldview that generated it, thereby affecting the worldviews of those exposed to it. If an idea influences seemingly unrelated fields this does not mean that separate cultural lineages are contaminating one another, because it is worldviews, not ideas, that are the basic unit of cultural evolution. (shrink)