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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet Incubator Lifescape

1. Ecosmopoiesis: An Autocatalytic, Bootstrap Self-Made UniVerse

Hordijk, Wim. Autocatalytic Sets and Chemical Organizations: Modeling Self-Sustaining Reaction Networks at the Origin of Life. New Journal of Physics. Online January, 2018. In a paper for a Focus on the Origin of Life collection (see below), Hordijk, Konrad Lorenz Institute, Mike Steel, University of Canterbury, and Peter Dittrich, Friedrich Schiller University continue forward with intricate theoretical insights about how living systems in some spontaneous ways get themselves going on an evolutionary developmental trajectory. See also Autocatalytic Networks in Biology by Mike Steel, et al in the Journal of the Royal Society Interface (February 2019) and Molecular Diversity Required for the Formation of Autocatalytic Sets by Hordijk, Steel, and Stuart Kauffman in Life (March 1, 2019).

Two related but somewhat different approaches have been proposed to formalize the notion of a self-sustaining chemical reaction network. One is the notion of collectively autocatalytic sets, formalized as RAF theory, and the other is chemical organization theory. Both formalisms have been argued to be relevant to the origin of life. RAF sets and chemical organizations are defined differently, but previously some relationships between the two have been shown. Here, we refine and explore these connections in more detail. In particular, we show that so-called closed RAFs are chemical organizations, but that the converse is not necessarily true. We end with a discussion of why and how closed RAFs could be important in the context of the origin and early evolution of life. (Abstract)

How does life begin? This question has been haunting the human history for millennia and there could not be a bigger question to find an answer to. Historically, scientists have approached the question from the geological point of view, then the empirical evolutionary theory came along and more recently genetics has been used to provide clues to this question. Fast progress has been made across other branches of science, including macromolecular chemistry, biochemistry and biophysics, biogeochemistry, nanoscience, and statistical physics. The scope of this focus collection will cover the transition from non-living matter to living matter from diverse perspectives, ranging from the conditions on early Earth and other Earth-like planets to the chemical and physical principles of the origins of life to more complex aspects such as genetic evolution. (Focus on the Origin of Life scope)

Hordijk, Wim. Autocatalytic Sets: From the Origin of Life to the Economy. BioScience. 63/11, 2013. We cite this paper as a synoptic example of such theories by the Swiss computational biologist. An extensive publication with collaborators before and since is on his website, search Philippe Nghe, et al for a 2015 entry. Our interest is also in the implied sense of an innately “autocreative” cosmos. In some deep way, the incredible natural universe that human acumen is quantifying seems to be involved in its own autocatalytic being and becoming. Does this procreation then want us to realize that we are to take it forth from here?

The origin of life is one of the most important but also one of the most difficult problems in science. Autocatalytic sets are believed to have played an important role in the origin of life. An autocatalytic set is a collection of molecules and the chemical reactions between them, such that the set as a whole forms a functionally closed and self-sustaining system. In this article, I present an overview of recent work on the theory of autocatalytic sets and on how this theory can be used to study the probability of emergence, the overall structure, and the further evolution of such systems, both in simple mathematical models and in real chemical systems. I also describe some (still speculative) ideas of how this theory can potentially be applied to living systems in general and perhaps even to social systems such as the economy. (Abstract)

Hordijk, Wim and Mike Steel. Chasing the Tail: The Emergence of Autocatalytic Networks. Biosystems. 152/1, 2017. Konrad Lorenz Institute for Evolution and Cognition Research, Austria and University of Canterbury, New Zealand biomathematicians continue to identify and finesse just how life gets going by way of self-activating processes. Again the presence of endemic interconnective topologies is a significant factor. See also Tractable Models of Self-Sustaining Autocatalytic Networks by Steel and Hordijk at arXiv:1801.03953.

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. (Abstract)

Hordijk, Wim, et al. Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World. Life. 8/3, 2018. In a Systems Protobiology: Origin of Life by Mutually Catalytic Networks issue (Lancet), University of Amsterdam and Newcastle University bioscientists emphasize that life’s evident autopoietic urge to self-initiate and evolve is further facilitated by the presence of multiple, integrally bounded entities. These module-like forms proceed to actively join in viable associations. A computational model is then cited which quantifies how this may happen.

Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so-called protocells. However, these previous studies have so far not explicitly modeled the emergence and dynamics of autocatalytic sets in populations of compartments in a spatial environment. Here, we use a recently developed software tool to simulate exactly this scenario, as an important first step towards more realistic simulations and experiments on autocatalytic sets in protocells. (Abstract)

Hunding, Alex, et al. Compositional Complementarity and Prebiotic Ecology in the Origin of Life. BioEssays. 28/4, 2006. An international group coordinated by Robert Root-Bernstein moves beyond the gene or metabolism first version to propose that life arose not by a single entity or event but via conducive pre-biotic ecosystems. Biochemical precursors that complement each other fuse into networks and systems of increasing viable complexity. These diverse, interactive molecular communities then bootstrap a Darwinian evolution impelled by dynamic self-assembly.

In sum, self-organization, reproduction and inheritable variations emerge from composomal systems when they are kept away from equilibrium by coupling their assembly, chemistry and fission-fusion processes to an external free energy source in such a way as to evolve compartmentalization and autocatalysis. (405) The theme of this paper is that the co-evolution of populations of molecularly diverse aggregates (composomes) selected on the basis of molecular complementarity and the emergence of modular functionality forms a basis for addressing some of the issues raised by the origin of life….In this picture, life emerged as a functioning ecological system through a process of integration from diverse components, not as a single entity that subsequently evolved by an as-yet-unknown process into an ecologically diverse system. Rather, we have described a continuous process by which increasingly complex, integrated, self-replicating, autocatalytic, modular systems evolve new properties in tandem with their environments. (409-410)

Jee, Ah-Young, et al. Catalytic Enzymes are Active Matter. Proceedings of the National Academy of Sciences. 115/E10812, 2018. Center for Soft and Living Matter, Institute for Basic Science, South Korea researchers including Tsvi Tlusty cite theoretical and experimental reasons why this biological substance can well exhibit spontaneous activity.

Using a microscopic theory to analyze experiments, we demonstrate that enzymes are active matter. Superresolution fluorescence measurements—performed across four orders of magnitude of substrate concentration—show that catalysis boosts the motion of enzymes to be superdiffusive for a few microseconds, enhancing their effective diffusivity over longer timescales. Occurring at the catalytic turnover rate, these fast ballistic leaps maintain direction over a duration limited by rotational diffusion, driving enzymes to execute wormlike trajectories by piconewton forces. These findings violate the classical paradigm that chemical reaction and motility are distinct processes, and suggest reaction–motion coupling as a general principle of catalysis. (Abstract excerpt)

Kamimura, Atsushi and Kunihiko Kaneko. Molecular Diversity and Network Complexity in Growing Protocells. arXiv:1904.08094. University of Tokyo, Universal Biology Institute researchers continue their project (search KK) to explain how life gained its cellular vitalities by here adding an important presence of catalytic activities.

A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell. (Abstract excerpt)

Kolchinsky, Artemy. A Thermodynamic Threshold for Darwinian Evolution. arXiv:2112.02809. The author has a 2015 doctorate in Informatics of Complex Systems from Indiana University, then some years at SFI, and is now at the Universal Biology Institute of Tokyo University where he studies intersects between information, physics and an animated nature. This entry proceeds with an emphasis on self-making, ecosmo-poiesis features of a genesis universe which seems to involved with its own autocatalytic cocreation.

Understanding the thermodynamics of Darwinian evolution has important implications for biophysics, evolutionary biology, and the origin of life. We show that for autocatalytic replicators in a nonequilibrium steady state, the critical selection coefficient is lower bounded by the Gibbs free energy dissipation. This bound presents a fundamental threshold for Darwinian evolution, which is complementary to other thresholds that may arise from finite population sizes, mutation rates, etc. Our results apply to a large class of molecular replicators, including many autocatalytic sets and multistep mechanisms. (Excerpt)

Kutner, Corinna, et al. The Photophysics of Nucleic Acids: Consequences for the Emergence of Life. ChemSystemsChem. 4/6, 2022. Harvard Smithsonian Center for Astrophysics quantify even more explanatory reasons about an innate vitality which serves to engender an increasing, oriented series of complex biomolecules and procreative processes.

Absorption of ultraviolet (UV) radiation can trigger a variety of photophysical and photochemical reactions in nucleic acids. In the prebiotic era, on the surface of the early Earth, UV light could have played a major role in the selection of biomolecules via a balance between synthetic and destructive pathways. As nucleic acid monomers assembled into polymers, their non-enzymatic replication hinged on a photo-stability and self-repair of lesions by UV charge transfer. This review summarizes the photophysical processes in nucleic acids and their implications for chemical and genetic selection at the emergence of life and the origin of translation. (Abstract)

Lancet, Doron. Systems Protobiology: Origin of Life by Mutually Catalytic Networks. Life. Online July, 2018. A Special Issue proposal by the Weizmann Institute of Science geneticist, which is open for papers until February 2019. Its intent is to be a space for extensive reviews and integrations of the equal presence and importance at life’s onset of active network phenomena along with biochemical, nucleotide molecules. We cite an edited write up, from which one might surmise that the particulate, nodal RNA mode and their metabolic, linked interconnections arose in tandem as archetypal complements. See Hordijk, et al above for an initial paper.

NASA’s definition of minimal life asserts that “Life is a self-sustaining chemical system capable of Darwinian evolution.” A majority opinion (RNA first) contends that self-sustaining and replicating capacities can only be attained via templating biopolymers, which copy sequence information. An alternative approach (metabolism first) claims that life began with mutually-catalytic networks, endowed with self-sustaining and reproduction capabilities, via network structures. RNA first implies that a single type of molecule with high internal complexity could jump-start life, later recruiting metabolism and enclosure. Metabolism first takes the stand that life was a multi-component network of diverse interacting molecules right from the beginning. In published research it is shown that such networks constitute not only a catalysis-based metabolism, but also compartmental and replication traits. This scenario is obviously much more life-like, and is analyzable by tools of the newly emerging disciplines of Systems Biology and Systems Chemistry. This special issue proposes a “Systems Protobiology”, as a composite merger for research to define and understand early protocellular life forms. (Proposal edits)

Liu, Yu and David Sumpter. Spontaneous Emergence of Self-Replication in Chemical Reaction Systems. arXiv:1801.05872. Uppsala University mathematicians contribute theoretical explanations about innate originations of living systems by way of an array of multi-catalytic agencies and processes. Cosmic material nature thus appears to be graced with such fertile, life-bearing propensities from universe to us, we peoples whom may reconstruct in wonderment.

Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? We set up a general model for chemical reaction systems that properly accounts for energetics, kinetics and the conservation law. We find that (1) some systems are collectively-catalytic where reactants are transformed into end products with the assistance of intermediates, while some others are self-replicating where different parts replicate each other and the system self-replicates as a whole; (2) many alternative chemical universes often contain one or more such systems; (3) it is possible to construct a self-replicating system where the entropy of some parts spontaneously decreases, in a manner similar to that discussed by Schrodinger; (4) complex self-replicating molecules can emerge spontaneously and relatively easily from simple chemical reaction systems through a sequence of transitions. (Abstract)

Lockwood, Michael. The Labyrinth of Time: Introducing the Universe. Cambridge: Cambridge University Press, 2007. Amongst a standard review of quantum and relativity physics and cosmology is a chapter on the surprising occurrence, in this frame, of life’s autocatalytic, corporeal complex systems and sapient knowledge. Such an incongruity is then seen to be of sufficient import as to presage a transformative paradigm shift in our understanding of universe and human. A good example of the juxtaposition of waning and waxing cosmologies.

The emergence of order is far from being unique to the living world. Indeed, we have already, …encountered a non-biological illustration of the general principle that we are exploring here: the formation, by way of gravitational clumping, of galaxies, stars, and planetary systems. Suppose we separate off the universe’s gravitational degrees of freedom, thereby treating the ambient gravitational field as the ‘environment’ in which matter and (non-gravitational) radiation act out their parts in the cosmic play. Then the way in which the rich structures that comprise the subject matter of astronomy come into existence and maintain themselves in being. Even at a cosmic scale, the universe reveals itself as a self-organizing system. (260)

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