Compositional complementarity and prebiotic ecology in the origin of life (original) (raw)
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Emergence of Self-Reproduction in Cooperative Chemical Evolution of Prebiological Molecules
The paper presents a model of coevolution of short peptides (P) and short oligonucleotides (N) at an early stage of chemical evolution leading to the origin of life. The model describes polymerization of both P and N types of molecules on mineral surfaces in aqueous solution at moderate temperatures. It is assumed that amino acid and nucleotide monomers were available in a prebiotic milieu, that periodic variation in environmental conditions between dry/warm and wet/cool took place and that energy sources were available for the polymerization. An artificial chemistry approach in combination with agent-based modeling was used to explore chemical evolution from an initially random mixture of monomers. It was assumed that the oligonucleotides could serve as templates for self-replication and for translation of peptide compositional sequences, and that certain peptides could serve as weak catalysts. Important features of the model are the short lengths of the peptide and oligonucleotide molecules that prevent an error catastrophe caused by copying errors and a finite diffusion rate of the molecules on a mineral surface that prevents excessive development of parasitism. The result of the simulation was the emergence of self-replicating molecular systems consisting of peptide catalysts and oligonucleotide templates. In addition, a smaller but significant number of molecules with alternative compositions also survived due to imprecise reproduction and translation of templates providing variability for further evolution. In a more general context, the model describes not only peptide-oligonucleotide molecular systems, but any molecular system containing two types of polymer molecules: one of which serves as templates and the other as catalysts.The presented coevolutionary system suggests a possible direction towards finding the origin of molecular functionality in a prebiotic environment.
Chemistry & Biodiversity, 2007
During the last two decades, the common school of thought has split into two, so that the problem of the origin of life is tackled in the framework of either the replication first paradigm or the metabolism first scenario. The first paradigm suggests that the life started from the spontaneous emergence of the first, supposedly RNA-based replicators and considers in much detail their further evolution in the socalled RNA world. The alternative hypothesis of metabolism first derives the life from increasingly complex autocatalytic chemical cycles. In this work, we emphasize the role of selection during the prebiological stages of evolution and focus on the constraints that are imposed by physical, chemical, and biological laws. We try to demonstrate that the replication first and metabolism first hypotheses complement, rather than contradict, each other. We suggest that life on Earth has started from a metabolism-driven replication; the suggested scenario might serve as a consensus scheme in the framework of which the molecular details of origin of life can be further elaborated. The key feature of the scenario is the participation of the UV irradiation both as driving and selecting forces during the earlier stages of evolution.
The origin and early evolution of life in chemical composition space
Journal of Theoretical Biology, 2018
Life can be viewed as a localized chemical system that sits on, or in the basin of attraction of, a metastable dynamical attractor state that remains out of equilibrium with the environment. Such a view of life allows that new living states can arise through chance changes in local chemical concentration ("mutations") that move points in space into the basin of attraction of a life state-the attractor being an autocatalytic sets whose essential ("keystone") species are produced at a higher rate than they are lost to the environment by diffusion, such that growth in expected. This conception of life yields several new insights and conjectures. (1) This framework suggests that the first new life states to arise are likely at interfaces where the rate of diffusion of keystone species is tied to a low-diffusion regime, while precursors and waste products diffuse at a higher rate. (2) There are reasons to expect that once the first life state arises, most likely on a mineral surface, additional mutations will generate derived life states with which the original state will compete. (3) I propose that in the resulting adaptive process there is a general tendency for higher complexity life states (i.e., ones that are further from being at equilibrium with the environment) to dominate a given mineral surface. (4) The framework suggests a simple and predictable path by which cells evolve and provides pointers on why such cells are likely to acquire particulate inheritance. Overall, the dynamical systems theoretical framework developed provides an integrated view of the origin and early evolution of life and supports novel empirical approaches.
Origins of Life: Chemistry and Evolution
Progress in understanding the origins of life will be enhanced if models and their predictions are clearly understood and explicitly articulated. Two distinct models can be used to explain the genesis of biopolymers during the origins of life. In one model, which has been pursued for nearly 50 years, RNA is the result of inherent chemical reactivities of prebiotic chemical species. RNA invented evolution. This model enables the prediction that if the conditions of the ancient earth are sufficiently constrained, chemists will discover the direct synthetic pathways that produced RNA. In a fundamentally different model, which is more recent, RNA and other biopolymers are proposed to be the result of prolonged, creative, selection-based changes that occurred during chemical evolution and overlap with early biological evolution. Evolution invented RNA. In this evolutionary model, inherent chemical reactivities are not necessarily relevant to the origins of life and do not predict biosynt...
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...
Coenzyme world model of the origin of life
The origin of life means the emergence of heritable and evolvable self-reproduction. However the mechanisms of primordial heredity were different from those in contemporary cells. Here I argue that primordial life had no nucleic acids; instead heritable signs were represented by isolated catalytically active selfreproducing molecules, similar to extant coenzymes, which presumably colonized surfaces of oil droplets in water. The model further assumes that coenzyme-like molecules (CLMs) changed surface properties of oil droplets (e.g., by oxidizing terminal carbons), and in this way created and sustained favorable conditions for their own self-reproduction. Such niche-dependent self-reproduction is a necessary condition for cooperation between different kinds of CLMs because they have to coexist in the same oil droplets and either succeed or perish together. Additional kinds of hereditary molecules were acquired via coalescence of oil droplets carrying different kinds of CLMs or via modification of already existing CLMs. Eventually, polymerization of CLMs became controlled by other polymers used as templates; and this kind of template-based synthesis eventually resulted in the emergence of RNA-like replicons. Apparently, oil droplets transformed into the outer membrane of cells via engulfing water, stabilization of the surface, and osmoregulation. In result, the metabolism was internalized allowing cells to accumulate free-floating resources (e.g., animoacids, ATP), which was a necessary condition for the development of protein synthesis. Thus, life originated from simple but already functional molecules, and its gradual evolution towards higher complexity was driven by cooperation and natural selection.
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. But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes. Recent theoretical work shows that “compositional genomes” (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts. Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggr...
The origins and physical roots of life’s dual – metabolic and genetic – nature
Life Science Press, 2017
This review paper aims at a better understanding of the origin and physical foundation of life's dual-metabolic and genetic-nature. First, I give a concise 'top-down' survey of the origin of life, i.e., backwards in time from extant DNA/RNA/protein-based life over the RNA world to the earliest, pre-RNA stages of life's origin, with special emphasis on the metabolism-first versus gene/replicator-first controversy. Secondly, I critically assess the role of minerals in the earliest origins of bothmetabolism and genetics. And thirdly, relying on the work of Erwin Schrödinger, Carl Woese and Stuart Kauffman, I sketch and reframe the origin of metabolism and genetics from a physics, i.e., thermodynamics, perspective. I conclude that life's dual nature runs all the way back to the very dawn and physical constitution of life on Earth. Relying on the current state of research, I argue that life's origin stems from the congregation of two kinds of sources of negentropy-thermodynamic and statistical negentropy. While thermodynamic negentropy (which could have been provided by solar radiation and/or geochemical and thermochemical sources), led to life's combustive and/or metabolic aspect, the abundant presence of mineral surfaces on the prebiotic Earth-with their selectively adsorbing and catalysing (thus 'organizing') micro-crystalline structure or order-arguably provided for statistical negentropy for life to originate, eventually leading to life's crystalline and/or genetic aspect. However, the transition from a prebiotic world of relatively simple chemical compounds including periodically structured mineral surfaces towards the complex aperiodic and/or informational structure, specificity and organization of biopolymers and biochemical reaction sequences remains a 'hard problem' to solve.
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...
Prebiological evolution and the physics of the origin of life
Physics of Life Reviews, 2005
The basic tenet of the heterotrophic theory of the origin of life is that the maintenance and reproduction of the first living systems depended primarily on prebiotically synthesized organic molecules. It is unlikely that any single mechanism can account for the wide range of organic compounds that may have accumulated on the primitive Earth, suggesting that the prebiotic soup was formed by contributions from endogenous syntheses in reducing environments, metal sulphide-mediated synthesis in deep-sea vents, and exogenous sources such as comets, meteorites and interplanetary dust. The wide range of experimental conditions under which amino acids and nucleobases can be synthesized suggests that the abiotic syntheses of these monomers did not take place under a narrow range defined by highly selective reaction conditions, but rather under a wide variety of settings. The robustness of this type of chemistry is supported by the occurrence of most of these biochemical compounds in the Murchison meteorite. These results lend strong credence to the hypothesis that the emergence of life was the outcome of a long, but not necessarily slow, evolutionary processes. The origin of life may be best understood in terms of the dynamics and evolution of sets of chemical replicating entities. Whether such entities were enclosed within membranes is not yet clear, but given the prebiotic availability of amphiphilic compounds this may have well been the case. This scheme is not at odds with the theoretical models of self-organized emerging systems, but what is known of biology suggest that the essential traits of living systems could have not emerged in the absence of genetic material able to store, express and, upon replication, transmit to its progeny information capable of undergoing evolutionary change. How such genetic polymer first evolved is a central issue in origin-of-life studies.