Autocatalytic chemical networks at the origin of metabolism
Joana C . XavierProceedings of the Royal Society B: Biological Sciences
Sign up for access to the world's latest research
checkGet notified about relevant papers
checkSave papers to use in your research
checkJoin the discussion with peers
checkTrack your impact
Abstract
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here, we identify reflexively autocatalytic food-generated networks (RAFs)—self-sustaining networks that collectively catalyse all their reactions—embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H 2 and CO 2 provided with small-molecule catalysts generate acetyl-CoA as well as amino acids and bases, the monomeric components of protein and RNA, but amino acids and bases without organic catalysts do not generate metabolic RAFs. This suggests that RAFs identify attributes of biochemical origins conserved i...
Related papers
Autocatalytic chemical networks preceded proteins and RNA in evolution
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic molecule sets that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic molecule sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here we identify reflexively autocatalytic food-generated networks (RAFs) - self-sustaining networks that collectively catalyze all their reactions - embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H2 and CO2 generate amino acids and bases, the monomeric components of protein and RNA, and acetyl-CoA, but amino acids and bases do not generate metabolic RAFs, indicating that small-molecule catalysis preceded polymers in biochemical evolution. RAFs uncover intermediate stages in the origin of metaboli...
Autocatalysis Before Enzymes: The Emergence of Prebiotic Chain Reactions
Advances in Artificial Life, ECAL 2013, 2013
How could complex, enzyme-or ribozyme-like molecules first have arisen on planet Earth? Several authors have suggested autocatalytic cycles as a partial answer to this question, since such reactions exhibit the lifelike property of exponential growth while being composed of relatively simple molecules. However, a question remains as to the likelihood of an autocatalytic cycle forming spontaneously in the absence of highly specific catalysts. Here we show that such cycles form readily in a very simple model that includes no direct catalysis reactions. Catalytic effects nevertheless emerge as properties of the reaction network. This suggests that the conditions for the formation of such cycles are not difficult to achieve. The resulting cycles solve the problem of specificity not by being small and simple but by being large and complicated, suggesting that early prebiotic metabolisms could have been extremely complex. We predict that this phenomenon can be reproduced in wet chemistry. We discuss the challenges involved in this, as well as the implications for how we view the origins of life.
The structure of autocatalytic networks, with application to early biochemistry
Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organisation of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualise RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide...
Autocatalytic Networks at the Basis of Life’s Origin and Organization
Life, 2018
Life is more than the sum of its constituent molecules. Living systems depend on a particular chemical organization, i.e., the ways in which their constituent molecules interact and cooperate with each other through catalyzed chemical reactions. Several abstract models of minimal life, based on this idea of chemical organization and also in the context of the origin of life, were developed independently in the 1960s and 1970s. These models include hypercycles, chemotons, autopoietic systems, (M,R)-systems, and autocatalytic sets. We briefly compare these various models, and then focus more specifically on the concept of autocatalytic sets and their mathematical formalization, RAF theory. We argue that autocatalytic sets are a necessary (although not sufficient) condition for life-like behavior. We then elaborate on the suggestion that simple inorganic molecules like metals and minerals may have been the earliest catalysts in the formation of prebiotic autocatalytic sets, and how RAF...
Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life
Proceedings of the National Academy of Sciences, 2010
A basic property of life is its capacity to experience Darwinian evolution. The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first “living” systems and may have led to the evolution of an RNA world.
Chasing the tail: The emergence of autocatalytic networks
Bio Systems, 2017
A ubiquitous feature of all living systems is their ability to sustain a biochemistry in which all reactions are coordinated by catalysts, and all reactants (along with the catalysts) are either produced by the system itself or are available from the environment. This led to the hypothesis that 'autocatalytic networks' play a key role in both the origin and the organization of life, which was first proposed in the early 1970s, and has been enriched in recent years by a combination of experimental studies and the application of mathematical and computational techniques. The latter have allowed a formalization and detailed analysis of such networks, by means of RAF theory. In this review, we describe the development of these ideas, from pioneering early work of Stuart Kauffman through to more recent theoretical and experimental studies. We conclude with some suggestions for future work.
Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2014
The deep dichotomy of archaea and bacteria is evident in many basic traits including ribosomal protein composition, membrane lipid synthesis, cell wall constituents, and flagellar composition. Here we explore that deep dichotomy further by examining the distribution of genes for the synthesis of the central carriers of one carbon units, tetrahydrofolate (H 4 F) and tetrahydromethanopterin (H 4 MPT), in bacteria and archaea. The enzymes underlying those distinct biosynthetic routes are broadly unrelated across the bacterial-archaeal divide, indicating that the corresponding pathways arose independently. That deep divergence in one carbon metabolism is mirrored in the structurally unrelated enzymes and different organic cofactors that methanogens (archaea) and acetogens (bacteria) use to perform methyl synthesis in their H 4 F-and H 4 MPT-dependent versions, respectively, of the acetyl-CoA pathway. By contrast, acetyl synthesis in the acetyl-CoA pathwayfrom a methyl group, CO 2 and reduced ferredoxinis simpler, uniform and conserved across acetogens and methanogens, and involves only transition metals as catalysts. The data suggest that the acetyl-CoA pathway, while being the most ancient of known CO 2 assimilation pathways, reflects two phases in early evolution: an ancient phase in a geochemically confined and non-free-living universal common ancestor, in which acetyl thioester synthesis proceeded spontaneously with the help of geochemically supplied methyl groups, and a later phase that reflects the primordial divergence of the bacterial and archaeal stem groups, which independently invented genetically-encoded means to synthesize methyl groups via enzymatic reactions. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
The origin and evolution of modern metabolism
International Journal of Biochemistry & Cell Biology, 2009
One fundamental goal of current research is to understand how complex biomolecular networks took the form that we observe today. Cellular metabolism is probably one of the most ancient biological networks and constitutes a good model system for the study of network evolution. While many evolutionary models have been proposed, a substantial body of work suggests metabolic pathways evolve fundamentally by recruitment, in which enzymes are drawn from close or distant regions of the network to perform novel chemistries or use different substrates. Here we review how structural and functional genomics has impacted our knowledge of evolution of modern metabolism and describe some approaches that merge evolutionary and structural genomics with advances in bioinformatics. These include mining the data on structure and function of enzymes for salient patterns of enzyme recruitment. Initial studies suggest modern metabolism originated in enzymes of nucleotide metabolism harboring the P-loop hydrolase fold, probably in pathways linked to the purine metabolic subnetwork. This gateway of recruitment gave rise to pathways related to the synthesis of nucleotides and cofactors for an ancient RNA world. Once the TIM /␣-barrel fold architecture was discovered, it appears metabolic activities were recruited explosively giving rise to subnetworks related to carbohydrate and then amino acid metabolism. Remarkably, recruitment occurred in a layered system reminiscent of Morowitz's prebiotic shells, supporting the notion that modern metabolism represents a palimpsest of ancient metabolic chemistries.
The Origins of Life: The Managed-Metabolism Hypothesis
Foundations of Science, 2018
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.
Related topics
Cited by
The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors
Microorganisms
The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing...
The structure of autocatalytic networks, with application to early biochemistry
Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organisation of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualise RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide...
The metabolic network of the last bacterial common ancestor
Communications Biology
Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-...
Modeling a Cognitive Transition at the Origin of Cultural Evolution Using Autocatalytic Networks
Cognitive Science
LG acknowledges funding from Grant 62R06523 from the Natural Sciences and Engineering Research Council of Canada. We thank Russell Gray for drawing our attention to the paper by Stout et al. that inspired this one. We thank Claes Andersson and anonymous reviewers for comments, and thank Conner Gibbs for assistance with the manuscript.
Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives
Life
Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models.
Modeling Discontinuous Cultural Evolution: The Impact of Cross-Domain Transfer
Frontiers in Psychology, 2022
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 (“foodset-derived”) nodes from existing ones (the “foodset.”) 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 Löwenmen...
A Dynamic Autocatalytic Network Model of Therapeutic Change
Entropy
Psychotherapy involves the modification of a client’s worldview to reduce distress and enhance well-being. We take a human dynamical systems approach to modeling this process, using Reflexively Autocatalytic foodset-derived (RAF) networks. RAFs have been used to model the self-organization of adaptive networks associated with the origin and early evolution of both biological life, as well as the evolution and development of the kind of cognitive structure necessary for cultural evolution. The RAF approach is applicable in these seemingly disparate cases because it provides a theoretical framework for formally describing under what conditions systems composed of elements that interact and ‘catalyze’ the formation of new elements collectively become integrated wholes. In our application, the elements are mental representations, and the whole is a conceptual network. The initial components—referred to as foodset items—are mental representations that are innate, or were acquired through...
The Expected Number of Viable Autocatalytic Sets in Chemical Reaction Systems
Artificial Life, 2021
The emergence of self-sustaining autocatalytic networks in chemical reaction systems has been studied as a possible mechanism for modeling how living systems first arose. It has been known for several decades that such networks will form within systems of polymers (under cleavage and ligation reactions) under a simple process of random catalysis, and this process has since been mathematically analyzed. In this paper, we provide an exact expression for the expected number of self-sustaining autocatalytic networks that will form in a general chemical reaction system, and the expected number of these networks that will also be uninhibited (by some molecule produced by the system). Using these equations, we are able to describe the patterns of catalysis and inhibition that maximize or minimize the expected number of such networks. We apply our results to derive a general theorem concerning the trade-off between catalysis and inhibition, and to provide some insight into the extent to whi...
Undefining life's biochemistry: implications for abiogenesis
Journal of The Royal Society Interface, 2022
In the mid-twentieth century, multiple Nobel Prizes rewarded discoveries of a seemingly universal set of molecules and interactions that collectively defined the chemical basis for life. Twenty-first-century science knows that every detail of this Central Dogma of Molecular Biology can vary through either biological evolution, human engineering (synthetic biology) or both. Clearly the material, molecular basis of replicating, evolving entities can be different. There is far less clarity yet for what constitutes this set of possibilities. One approach to better understand the limits and scope of moving beyond life's central dogma comes from those who study life's origins. RNA, proteins and the genetic code that binds them each look like products of natural selection. This raises the question of what step(s) preceded these particular components? Answers here will clarify whether any discrete point in time or biochemical evolution will objectively merit the label of life's ...
Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)
Frontiers in Microbiology, 2021
Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95–97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol−1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core’s reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 ...
Role of geochemical protoenzymes (geozymes) in primordial metabolism: specific abiotic hydride transfer by metals to the biological redox cofactor NAD +
The FEBS Journal
Hydrogen gas, H 2 , is generated in serpentinizing hydrothermal systems, where it has supplied electrons and energy for microbial communities since there was liquid water on Earth. In modern metabolism, H 2 is converted by hydrogenases into organically bound hydrides (H-), for example, the cofactor NADH. It transfers hydrides among molecules, serving as an activated and biologically harnessed form of H 2. In serpentinizing systems, minerals can also bind hydrides and could, in principle, have acted as inorganic hydride donors-possibly as a geochemical protoenzyme, a 'geozyme'-at the origin of metabolism. To test this idea, we investigated the ability of H 2 to reduce NAD + in the presence of iron (Fe), cobalt (Co) and nickel (Ni), metals that occur in serpentinizing systems. In the presence of H 2 , all three metals specifically reduce NAD + to the biologically relevant form, 1,4-NADH, with up to 100% conversion rates within a few hours under alkaline aqueous conditions at 40°C. Using Henry's law, the partial pressure of H 2 in our reactions corresponds to 3.6 mM, a concentration observed in many modern serpentinizing systems. While the reduction of NAD + by Ni is strictly H 2-dependent, experiments in heavy water (2 H 2 O) indicate that native Fe can reduce NAD + both with and without H 2. The results establish a mechanistic connection between abiotic and biotic hydride donors, indicating that geochemically catalysed, H 2-dependent NAD + reduction could have preceded the hydrogenase-dependent reaction in evolution. Abbreviations 1 H-NMR, proton nuclear magnetic resonance, an analytical method to characterise and quantify hydrogen-containing molecules; Co, cobalt; Fd ox /Fd red , oxidised/reduced ferredoxins; Fe, iron; LUCA, the last universal common ancestor, a theoretical cell based on phylogenetic reconstructions of the most conserved genetic setup between bacteria and archaea; NAD + /NADH, oxidised and reduced form of nicotinamide adenine dinucleotide; Ni, nickel.
A Testable Theory for the Emergence of the Classical World
Entropy
The transition from the quantum to the classical world is not yet understood. Here, we take a new approach. Central to this is the understanding that measurement and actualization cannot occur except on some specific basis. However, we have no established theory for the emergence of a specific basis. Our framework entails the following: (i) Sets of N entangled quantum variables can mutually actualize one another. (ii) Such actualization must occur in only one of the 2N possible bases. (iii) Mutual actualization progressively breaks symmetry among the 2N bases. (iv) An emerging “amplitude” for any basis can be amplified by further measurements in that basis, and it can decay between measurements. (v) The emergence of any basis is driven by mutual measurements among the N variables and decoherence with the environment. Quantum Zeno interactions among the N variables mediates the mutual measurements. (vi) As the number of variables, N, increases, the number of Quantum Zeno mediated mea...
Metabolic homeostasis and growth in abiotic cells
Metabolism constitutes the core chemistry of life. How it began on the early Earth and whether it had a cellular origin is still uncertain. A leading hypothesis for life’s origins postulates that metabolism arose from geochemical CO2-fixing pathways, driven by inorganic catalysts and energy sources, long before enzymes or genes existed. The acetyl-CoA pathway and the reductive tricarboxylic acid cycle are considered ancient reaction networks that hold relics of early carbon-fixing pathways. Although transition metals can promote many steps of these pathways, whether they form a functional metabolic network in abiotic cells has not been shown. Here, we formulate a nonenzymatic carbonfixing network from these pathways and determine its functional feasibility in abiotic cells by imposing the fundamental physico-chemical constraints of the early Earth. Using first principles, we show that abiotic cells could have sustainable steady carbon-fixing cycles that perform a systemic function o...
Prebiotic decluttering: the thermodynamic tail-wind to asymmetric autocatalysis
International Journal of Astrobiology
I outline a general thermodynamic condition for the earliest steps in the origin of life based on fluctuation theorems developed in the last two decades. I argue that the exponentially developing loop of asymmetric autocatalysis and thermodynamic tail-wind condition (TTC) in the prebiotic clutter was a key to a particular trajectory of decluttering via a sequence of early symmetry breaking events. Such decluttering was bound to result, most prominently, in homochiral amino acids and homochiral sugars composing nucleotides as the TTC exponentially favoured asymmetric autocatalytic processes over catalytic and symmetric autocatalytic processes in the clutter. I describe the loop's structure, including its chemical and physical properties, and explain that the TTC/asymmetric autocatalysis loop intersected with multiple chemical, geological and climatological feedback loops, thus providing conditions for the propagation of living systems as we know them.
The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life
PLOS Computational Biology
Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds.” We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks an...
An Autocatalytic Network Model of Conceptual Change
Topics in Cognitive Science, 2021
In Reflexively Autocatalytic Foodset-generated (RAF) networks, nodes are not just passive transmitters of activation; they actively galvanize, or 'catalyze' the synthesis of novel ('foodset-derived') nodes from existing ones (the 'foodset'). Thus, RAFs are uniquely suited to modeling how new structure grows out of currently available structure, and analyzing phase transitions in potentially very large networks. RAFs have been used to model the origins of evolutionary processes, both biological (the origin of life) and cultural (the origin of cumulative innovation), and may potentially provide an overarching framework that integrates evolutionary and developmental approaches to cognition. Applied to cognition, the foodset consists of information obtained through social learning or individual learning of pre-existing information, and foodset-derived items arise through mental operations resulting in new information. Thus, mental representations are not just propagators of spreading activation; they trigger the derivation of new mental representations. To illustrate the application of RAF networks in cognitive science, we develop a step-by-step process model of conceptual change (i.e., the process by which a child becomes an active participant in cultural evolution), focusing on childrens' mental models of the shape of the Earth. Using results from (Vosniadou & Brewer, 1992), we model different trajectories from the Flat Earth model to the Spherical Earth model, as well as the impact of other factors, such as pretend play, on cognitive development. As RAFs increase in size and number, they begin to merge, bridging previously compartmentalized knowledge, and get subsumed by a giant RAF (the maxRAF) that constrains and enables the scaffolding of new conceptual structure. At this point, the cognitive network becomes self-sustaining and self-organizing. The child can reliably frame new knowledge and experiences in terms of previous ones, and engage in recursive representational redescription, and abstract thought. We suggest that individual differences in the reactivity of mental representations, i.e., their proclivity to trigger conceptual change, culminates in different cognitive networks and concomitant learning trajectories.
Related papers
The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life
PLOS Computational Biology
Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds.” We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks an...
Catalysts, autocatalysis and the origin of metabolism
Interface Focus
If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO 2 , N 2 and H 2 . Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H 2 –CO 2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, th...
Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions
Life
The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory.
On the Origin of Metabolic Pathways
Journal of Molecular Evolution, 1999
The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO 2 to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking from preexisting pathways as well as prebiotic compounds from the environment.
The Origin and Evolution of Metabolic Pathways: Why and How did Primordial Cells Construct Metabolic Routes?
Evolution: Education and Outreach, 2012
The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present on the primordial Earth imposed an important selective pressure, favoring those primordial heterotrophic cells that became able to synthesize those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria, and Eukarya reveal that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the emergence of new metabolic abilities. Among these gene elongations, gene and operon duplications played a crucial role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence, giving rise to new genes coding for new metabolic abilities. Concerning the mechanisms of pathway assembly, both the analysis of completely sequenced genomes and directed evolution experiments strongly support the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis, suggests that other different hypothesis, i.e., the retrograde hypothesis, may account for the evolution of some steps within metabolic pathways.
Autocatalytic sets in E. coli metabolism
Journal of Systems Chemistry, 2015
Background: A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belonging to the set catalyze the synthesis of other members of the set. Given an external supply of starting molecules-the food set-and the conditions that (i) all reactions are catalyzed by at least one molecule, and (ii) each molecule can be constructed from the food set by a sequence of reactions, the system becomes a reflexively autocatalytic food-generated network (RAF set). Autocatalytic networks and RAFs have been studied extensively as mathematical models for understanding the properties and parameters that influence self-organizational tendencies. However, despite their appeal, the relevance of RAFs for real biochemical networks that exist in nature has, so far, remained virtually unexplored. Results: Here we investigate the best-studied metabolic network, that of Escherichia coli, for the existence of RAFs. We find that the largest RAF encompasses almost the entire E. coli cytosolic reaction network. We systematically study its structure by considering the impact of removing catalysts or reactions. We show that, without biological knowledge, finding the minimum food set that maintains a given RAF is NP-complete. We apply a randomized algorithm to find (approximately) smallest subsets of the food set that suffice to sustain the original RAF. Conclusions: The existence of RAF sets within a microbial metabolic network indicates that RAFs capture properties germane to biological organization at the level of single cells. Moreover, the interdependency between the different metabolic modules, especially concerning cofactor biosynthesis, points to the important role of spontaneous (non-enzymatic) reactions in the context of early evolution.
From prebiotic chemistry to cellular metabolism—The chemical evolution of metabolism before Darwinian natural selection
Journal of Theoretical Biology, 2008
It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin. r
An ecological framework for the analysis of prebiotic chemical reaction networks and their dynamical behavior
2020
It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. To explore this possibility, we formalize the dynamics of chemical reaction networks within the framework of chemical ecosystem ecology. To capture the idea that life-like chemical systems are maintained out of equilibrium by fluxes of energy-rich food chemicals, we model chemical ecosystems in well-mixed containers that are subject to constant dilution by a solution with a fixed concentration of food chemicals. Modelling all chemical reactions as fully reversible, we show that seeding an autocatalytic cycle (AC) with tiny amounts of one or more of its member chemicals results in logistic growth of all member chemicals in the cycle. This finding justifies drawing an instructive analogy between an AC and the population of a biologic...
An ecological framework for the analysis of prebiotic chemical reaction networks
Journal of Theoretical Biology, 2020
It is becoming widely accepted that very early in life's origin, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. To explore this possibility, we formalize the dynamics of chemical reaction networks within the framework of chemical ecosystem ecology. To capture the idea that lifelike chemical systems are maintained out of equilibrium by fluxes of energy-rich food chemicals, we model chemical ecosystems in wellmixed containers that are subject to constant dilution by a solution with a fixed concentration of food chemicals. Modelling all chemical reactions as fully reversible, we show that seeding an autocatalytic cycle with tiny amounts of one or more of its member chemicals results in logistic growth of all member chemicals in the cycle. This finding justifies drawing an instructive analogy between an autocatalytic cycle and the population of a biological species. We extend this finding to show that pairs of autocatalytic cycles can show competitive, predator-prey, or mutualistic associations just like biological species. Furthermore, when there is stochasticity in the environment, particularly in the seeding of autocatalytic cycles, chemical ecosystems can show complex dynamics that can resemble evolution. The evolutionary character is especially clear when the network architecture results in ecological precedence ("survival of the first"), which makes the path of succession historically contingent on the order in which cycles are seeded. For all its simplicity, the framework developed here is helpful for visualizing how autocatalysis in prebiotic chemical reaction networks can yield lifelike properties. Furthermore, chemical ecosystem ecology could provide a useful foundation for exploring the emergence of adaptive dynamics and the origins of polymer-based genetic systems.
Loading Preview
Sorry, preview is currently unavailable. You can download the paper by clicking the button above.