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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Procreative Organic Habitable UniVerse

2. An Autocatalytic, Bootstrap EcosmoVerse

ABSCICON Astrobiology Science Conference 2015: Habitability, Habitable Worlds, and Life. www.hou.usra.edu/meetings/abscicon2015. Reviewed much more in Astrobiology, a premier biannual conference for this cosmic quest. We add an apropos Abstract for this new section.

Recent years have witnessed dramatic advances in our understanding of the early steps in the transition from a prebiotic world to a world transformed by a biotic component. These early steps are presumed to include the evolution of collectively autocatalytic networks of molecules, as well as the evolution of protocells that define the boundary between living and non-living matter. Since the earliest cellular life, innovations caused by gene duplication and divergence, novel gene fusions/fission, and transfer of genes between phylogenetically distinct groups have led to an explosive diversification of the metabolic and regulatory networks within cells, enabling colonization of new environmental niches as well as new mechanisms for cooperative interactions between cells. The hierarchy of life — genes within genomes, organelles within cells, cells within organisms, and organisms within societies — is not a starting condition of the evolutionary process, but an outcome of a series of major transitions in which units of low complexity combine to form units of high complexity. (The Origin and Subsequent Evolution of Life Plenary Session)

Systems Chemistry. www.esf.org/conferences/08267. An October 2008 meeting held at Maratea, Italy by the European Science Foundation as part of its Action CM0703: Systems Chemistry initiative. This website will direct to the extensive program, which includes, e.g., George Cody: Geomimetic Biochemistry; Steven Benner: Systems Chemistry that Creates “Life;” Donna Blackmond: Chemical and Physical Models for the Evolution of Biological Homochirality; Peter Schuster: The Advent of Information and combinatorial Complexity; and Eors Szathmary: The Origin of the Genetic Code. Immediately followed by Chembiogenesis 2008 (Google) in the same venue, these efforts achieves a further rooting of living dynamics into conducive molecular realms. But the deeper ground of the physical cosmos remains absent and barren, a “systems physics” turn has yet to be taken.

Systems chemistry is the joint effort of prebiotic and supramolecular chemistry assisted by computer science from theoretical chemistry, biology, and complex systems research to tackle dynamic supersystem integration including at least one autocatalytic subsystem. It is the bottom-up pendant of systems biology towards synthetic biology. The integration approach will necessarily link to the question of asymmetric autocatalysis and chiral symmetry breaking, while the key challenge is to find the roots of Darwinian evolvability in chemical systems.

Adamski, Paul, et al. From Self-Replication to Replicator Systems en Route to de Novo Life. Nature Reviews Chemistry. 4/8, 2020. Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Institute of Evolution, MTA Centre for Ecological Research, Hungary including Eors Szathmary and Sijbren Otto provide a latest exercise with regard to how the Darwinian evolution model might be reconciled and joined with increasing scientific evidence that an array of self-generative systems are in effect prior to selections. It is now recognized that a common cellular formation can be defined (see Abstract), which is here seen as due to a self-replicative process, aka collective autocatalysis. Life’s natural emergence is further traced to far-from-equilibrium energies and nonlinear complex dynamics. In so many words and ways, these original agencies are well known to be at work to impel and guide life’s oriented development before winnowings take place.

The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. Both the de novo synthesis and origin of life require the functional integration of three key characteristics — replication, metabolism and compartmentalization — into a system that is out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate these vital aspects. We analyse how far experimental self-replicators have come in terms of Darwinian evolution and also cover models of replicator communities. Successful models rely on a collective metabolism and the formation of compartments suggesting that the invention and integration of these two features is driven by evolution. (Abstract)

Attwater, James and Philipp Holliger. Origins of Life: The Cooperative Gene. Nature. 491/48, 2012. A news note on “Spontaneous Network Formation among Cooperative RNA Replicators” by Nilesh Valdya, et al in the same issue, wherein Portland State, Harvard, and Stanford University researchers report that active nets of RNA molecules actually appear to mutually help assemble one another. This finding seems to suggest that “cooperation may be as old as life itself.” Niles Lehman, a Portland State coauthor is also engaged with his group (search) with studies of Abiogenesis, the rooting of life in its fertile chemical ground.

The origin of life on Earth remains one of the great unsolved mysteries. A new study suggests that cooperation among molecules could have contributed to the transition from inanimate chemistry to biology. (Attwater, 48) Cooperation operates at all scales of life, from whole organisms, such as wolves hunting in packs, to individual cells acting in a coordinated fashion during development or organ function. (48)

The origins of life on Earth required the establishment of self-replicating chemical systems capable of maintaining and evolving biological information. In an RNA world, single self-replicating RNAs would have faced the extreme challenge of possessing a mutation rate low enough both to sustain their own information and to compete successfully against molecular parasites with limited evolvability. Thus theoretical analyses suggest that networks of interacting molecules were more likely to develop and sustain life-like behaviour. Here we show that mixtures of RNA fragments that self-assemble into self-replicating ribozymes spontaneously form cooperative catalytic cycles and networks. We find that a specific three-membered network has highly cooperative growth dynamics. When such cooperative networks are competed directly against selfish autocatalytic cycles, the former grow faster, indicating an intrinsic ability of RNA populations to evolve greater complexity through cooperation. We can observe the evolvability of networks through in vitro selection. Our experiments highlight the advantages of cooperative behaviour even at the molecular stages of nascent life. (Vaidya, Abstract, 72)

Bissette, Andrew and Stephen Fletcher. Mechanisms of Autocatalysis. Angewandte Chemie International Edition. 52/12800, 2013. Oxford University chemists note the propensity of natural phenomena to bootstrap itself out of available materials into emergent organic complexities, especially at life’s origin. By these lights, an “autocatalytic cosmos” comes to mind. Search autocatalysis here for more usages, and Bissette in Mind over Matter for a case of human intention taking on a role of cosmic catalysts.

Self-replication is a fundamental concept. The idea of an entity that can repeatedly create more of itself has captured the imagination of many thinkers from von Neumann to Vonnegut. Beyond the sciences and science fiction, autocatalysis has found currency in economics and language theory. Autocatalysis is central to the propagation of life and intrinsic to many other biological processes. This includes the modern conception of evolution, which has radically altered humanity’s image of itself. Organisms can be thought of as imperfect self-replicators which produce closely-related species, allowing for selection and evolution. Hence, any consideration of self-replication raises one of the most profound questions of all: what is life? Minimal self-replicating systems have been studied with the aim of understanding the principles underlying living systems, allowing us to refine our concepts of biological fitness and chemical stability, self-organization and emergence, and ultimately to discover how chemistry may become biology. (Abstract)

Blokhuis, Alex, et al. Universal Motifs and the Diversity of Autocatalytic Systems. Proceedings of the National Academy of Sciences. 41/25230, 2020. Systems biochemists AB and David Lacoste, Paris Sciences et Lettres University and Philippe Nghe, CNRS Chimie Biologie Innovation post a wide-ranging study to a notable extent that this self-creative organic process is seen to play a more important, pervasive role in life’s evolution than previously thought. By way of analogy, the vital presence of a beneficial symbiosis was also sidelined until recent times. Into the later 2010s, it is becoming evident that from earliest origins, life’s precursor biochemical networks grew and evolved in complexity because of these innate agencies. See also An Ecological Framework for the Analysis of Prebiotic Chemical Reaction Networks by Zhen Peng, et al in the Journal of Theoretical Biology (Vol. 507, 2020).

Autocatalysis, the ability of chemical systems to make more of themselves, is a hallmark of living systems, as it underlies metabolism, reproduction, and evolution. Here, we present a unified theory of autocatalysis based on stoichiometry. This allows us to identify essential motifs of autocatalytic networks, namely, autocatalytic cores, which come in five categories. In these networks, internal catalytic cycles are found to favor growth. The stoichiometry approach furthermore reveals that diverse autocatalytic networks can be formed with multiple compartments. Overall, these findings suggest that autocatalysis is a richer and more abundant phenomenon than previously thought. (Significance)

In this way, autocatalysis can emerge from reaction schemes as simple as a bimolecular reaction. The principle is more general, however: Autocatalysis may also emerge from coupling phases with physical–chemical conditions conducive to different reactions, as observed in liquid–solid and solid–gas interfaces. Overall, our framework shows that autocatalysis comes in a diversity of forms and can emerge in unexpected ways, indicating that autocatalysis in chemistry must be more widespread than previously thought. This invites a search for further extensions of autocatalysis, which provides new vistas for understanding how chemistry may complexify toward life. (25235)

Braakman, Rogier and Eric Smith. The Compositional and Evolutionary Logic of Metabolism. Physical Biology. 10/1, 2013. Reviewed more in Systems Evolution, SFI scientists, notable vitas appended, entertain theoretical ways to join, root, join, and source, life’s genomic and biological scales within the geological substrates from which they naturally arose. Metabolic networks, broadly conceived, are seen to have a prominent generative, homeostasis-like role in this regard. Within the major evolutionary transitions, their universal, independent dynamics then animate and recur across many levels.

Brown, Mark, et al. Energy Hierarchy and Transformity in the Universe. Ecological Modelling. 178/1-2, 2004. An article in a special issue to review and expand on the work of the late systems ecologist Howard Odum. Through his legacy and perspective, stratified autocatalytic processes are found to characterize both environmental and cosmic scales.

Coveney, Peter, et al. Theory, Modelling and Simulation in Origin of Life Studies. Chemican Society Reviews. 41/5430, 2012. Reviewed much more in Origin of Life, in a special section on “Prebiotic Chemistry,” Coveney, and Jacob Swadling, University College London computational chemists, Jonathan Wattis, University of Nottingham mathematician, and Christopher Greenwell, Durham University earth scientist review past and further orientations for this broad, significant field.

Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the “systems chemistry” level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life. (Abstract)

Cronin, Leroy and Sara Imari Walker. Beyond Prebiotic Chemistry. Science. 352/1174, 2016. A University of Glasgow chemist and Arizona State University astrophysicist contribute to the nascent revolution in origin of life studies, akin to other fields such as genomics, that after a long period of identifying elemental pieces like rudimentary RNA, a presence of equally real dynamic networks which serve to organize and vitalize need be factored in. This advance to join components and connections, along with their informational content, augurs for finding “universal laws of life.” Search for the Philippe Nghe, et al paper Prebiotic Network Evolution for another example.

How can matter transition from the nonliving to the living state? The answer is essential for understanding the origin of life on Earth and for identifying promising targets in the search for life on other planets. Most studies have focused on the likely chemistry of RNA (1), protein (2), lipid, or metabolic “worlds” (3), and autocatalytic sets (4), including attempts to make life in the lab. But these efforts may be too narrowly focused on the biochemistry of life as we know it today. A radical rethink is necessary, one that explores not just plausible chemical scenarios but also new physical processes and driving forces. Such investigations could lead to a physical understanding not only of the origin of life but also of life itself, as well as to new tools for designing artificial biology. (Summary)

Dufour, Gwenaelle and Steven Charnley. Astrochemical Bistability: Autocatalysis in Oxygen Chemistry. Astrophysical Journal. 887.1, 2019. NASA Goddard researchers quantify the natural presence and formative contribution of self-activating chemical reactions to an ecosmic materiality as it proceeds to evolve and develop in animate complexity.

The origin of bistable solutions in the kinetic equations describing the chemistry of dense interstellar clouds is explained as being due to the autocatalysis and feedback of oxygen nuclei from the oxygen dimer. We show that these processes can produce the bistable solutions found in previous studies, as well as the dependence on various model parameters such as the helium ionization rate and the sulfur depletion. (Abstract)

We have demonstrated that interstellar chemistry is bistable due to the interaction of several autocatalytic processes involving molecular oxygen. By deconstructing a known bistable solution into ever simpler reduced models through omission of chemical elements, and then artificially removing selected reactions, we have identified four distinct modes of autocatalysis that can occur in dense molecular clouds. (6)

Dunn, Ian. Searching for Molecular Solutions: Empirical Discovery and Its Future. New York: Wiley, 2010. The Australian geneticist author is now Director of Research at CytoCure in Boston “where the focus is improving the recognition of melanoma cells by the immune system.” Such medical progress can be aptly achieved by a reinterpretation of genomes in terms of literary and linguistic metaphors, a grand parallel lately verified. The well-organized, accessible work has various sections entitled How to be a Librarian, Primordial Alphabet Soup, and On Molecular Translations, hence a textual nature we are invited to read. In such perspective, life’s evolution is also to be recast by way the “new sciences of complexity and self-organizing systems.”

But a simpler view is that spontaneous order increases the size and versatility of the toolbox upon which natural selection can act, where the tools are self-organized autocatalytic molecular sets acting as supramolecular building blocks. (42-43) Thus, the arrangement of complex genetic circuits, up to the level of entire genomes, may result in part from the self-organizational properties of complex systems. (43)

The analogy of protein sequences with linguistics has indeed been well noted and has applications in the analysis of protein organization using similar approaches as with general computational linguistic. (353) In any event, emphasizing the centrality of alphabets is simply another way of framing the common notion of “life as information,” where information equates with semantics. (355) In the language analogy, structurally distinct proteins with analogous functions would constitute synonymous words or phrases. The same function in one “biological language” (such as folded protein sequences) is often “translatable” into another (such as folded RNA sequences). (357)

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