III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

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

This January 2018 section reports an increasing notice of how a natural universe to human evolutionary emergence seems to be facilitated by life’s autocreative biochemical self-initiation. As popularly known, a catalyst is a (bio)chemical agent which can effect a reaction without itself being changed in the process. An autocatalytic term has become a general identifier for this procedure, and has gained usage because something like this does seem to be going on. A pioneer theorist since the 1970s has been Stuart Kauffman (search) which he has articulated in books and collegial papers to this day. Lately the concept is advanced by biomathematicians such as Wim Hordijk and Michael Steel, along with Liane Gabora, Nathaniel Virgo, Guenther Witzany, Sara Walker, Leroy Cronin, Addy Pross, and others herein.

In November 2019, another phase or mode of a self-making natural genesis will be included here, namely “bootstrap universe” theories. With a once and future casting, the concept began with Geoffrey Chew in the 1960s, but while notable it was set aside. As entries here especially by Natalie Wolchover and others cite, a strong revival has occurred because a lively cosmos seems to actually be doing something like this. New contributions by Nima Arkani-Hamed, David Poland, Gui Pimental and others (cited below, and posted on the arXiv eprint site). If one queries “bootstrap” there it gets over 3,000 hits. The Simons Foundation perceptively funds such efforts and conference (Perimeter Institute). Indeed this ecosmic placement seems to be expecting us (as Freeman Dyson would say) because there is some necessary, vivifying act we all are to carry out.

2020: Another essential feature of a genesis ecosmos is an array of self-creative phenomena which activate and enliven its ongoing development. Living systems from their earliest rediments appear to pervasively initiate and catalyze themselves by innately responsive biochemicals and bioprocesses at every instance. That is to say, a wholly self-making, autopoietic, spontaneity by way of its own internal agencies becomes apparent.

A companion perception is the recent recovery of a 1960s physical bootstrap model mostly from Geoffrey Chew, as described by Natalie Wolchover. A significant implication may be that we regnant human beings, both personally and collectively, ought to be inspired and moved to take up a role and mission as Earthomo and Earthosmic catalystic cocreators.

Adamski, Paul, et al. From Self-Replication to Replicator Systems en Route to de Novo Life. Nature Reviews Chemistry. 4/8, 2020.
Blokhuis, Alex, et al. Universal Motifs and the Diversity of Autocatalytic Systems. Proceedings of the National Academy of Sciences. 41/25230, 2020.
Dufour, Gwenaelle and Steven Charnley. Astrochemical Bistability: Autocatalysis in Oxygen Chemistry. Astrophysical Journal. 887.1, 2019.
Fontana, Walter. From Computation to Life: The Challenge of a Science of Organization. www.walterfontana.zone/writings
Hordijk, Wim. Autocatalytic Sets and Chemical Organizations: Modeling Self-Sustaining Reaction Networks at the Origin of Life. New Journal of Physics. January, 2018.
Kutner, Corinna, et al. The Photophysics of Nucleic Acids: Consequences for the Emergence of Life. ChemSystemsChem. 4/6, 2022.
Lancet, Doron. Systems Protobiology: Origin of Life by Mutually Catalytic Networks. Life. July, 2018.

Peng, Zhen, et al. The Hierarchical Organization of Autocatalytic Reaction Networks and its Relevance to the Origin of Life. PLOS Computational Biology. September, 2922.
Piotto, Stefano, et al. Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions. Life. Online April 4, 2019.
Preiner, Martina, et al. Catalysts, Autocatalysis and the Origin of Metabolism. Interface Focus. October, 2019.
Teuscher, Christof. Revisiting the Edge of Chaos. Biosystems. May 2022.
Wolchover, Natalie.Cosmic Triangles Open a Window to the Origin of Time. Quanta. October 29, 2019
Xavier, Joana, et al. Autocatalytic Chemical Networks at the Origin of Metabolism. Proceedings of the Royal Society B. March, 2020.

2030: Into the 2020s, as the newreferences note, a broad realization has arisen that catalytic activities whence all manner of biochemical and metabolic reactions enhance, iterate, and propel themselves. In this regard, they altogether have a premier animative role. As a result the real presence of a self-making, autocreative ecosmos becomes actually evident.

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)

Baum, David, et al. The ecology–evolution continuum and the origin of life.. Journal of the Royal Society Interface. November, 2023. A veteran team of DB, Zhen Peng, and Praful Gagrani, University of Wisconsin, Emily Dodson, Michigan State University, Eric Smith, Georgia Tech and Alex Plum, UC San Diego system theorists (search names) continue on this year to an insightful synthesis which is able to explain and establish nature’s essential spontaneity fertile by identifying the primary presence of many dynamic, autocatalytic, self-making processes. As this section reports, since the 1970’s there have been growing perceptions of this finding, which is now, at last, well verified. See also Polyhedral geometry and combinatorics of an autocatalytic ecology in chemical and cluster chemical reaction networks by this group at arXiv:2303.14238. Here is still more vital evidence, so it seems, of an historic, integral PediaVerse discovery event.

Prior research on evolutionary mechanisms during the origin of life has mainly assumed populations of discrete entities with information encoded in genetic polymers. However recent advances in autocatalytic chemical ecology (ACEs) imply a broader basis that allows for adaptive complexification prior to genetic encoding or individual entities. When ACEs are organized in meta-ecosystems, whether they be cells or environmental patches, evolution, defined as changes in AC frequency over time, can occur. Such an adaptive evolution can then explain the emergence of self-bounded units (e.g. protocells) and genetic inheritance.. Recognizing the continuity between evolution and ecology by way of autocatalytic chemical processes suggests that life’s origin is a general and predictable outcome of driven chemical ecosystems rather than due to specific, rare conditions.

This new framework, chemical ecosystem ecology, suggests that the origin of life is best understood as a process whereby ACMEs change adaptively prior to the onset of Darwinian evolution, resulting in the acquisition of autopoiesis and genetic encoding. Such an insight may allow for the development of new formal theories of abiogenesis that avoid invoking the spontaneous emergence of complex genetic systems. Thus, by bringing together expertise in ecology, evolution and autocatalytic chemistry, it may become possible to quantify the de novo appearance of adaptively evolving chemical systems that begin to remove the boundary between life and non-life. (8)

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.

Cochrane, Wesley, et al. Cross-chiral exponential amplification of an RNA enzyme.. PNAS. 121/44, 2024. Salk Institute, La Jolla, CA researchers including Gerald Joyce contribute to a latest origin of life emphasis on nature’s dual orientation feature. In this paper, a further perception of innate catalytic activities is factored in. See also The astrochemical evolutionary traits of phospholipid membrane homochirality by Jana Bockova, et al in Nature Reviews Chemistry. (8/652, 2024) and Prebiotic chiral transfer from self-aminoacylating ribozymes may favor either handedness by John Kenchel, et al in Nature Communications (15/7980, 2024).

An RNA ligase ribozyme that catalyzes the joining of RNA molecules of the opposite chiral handedness was optimized for the ability to synthesize its own enantiomer from two component fragments. The mirror-image D- and L-ligases operate in concert to provide a system for cross-chiral replication, whereby they catalyze each other's synthesis and undergo mutual amplification. Unlike the nucleic acid replication that relies on pairing between complementary strands, cross-chiral mode relies on tertiary interactions between structured nucleic acids "across the mirror." There are no prior examples, in either biological or chemical systems, of cross-chiral replication enabling exponential amplification. (Excerpt)

A special form of autocatalysis, rarely seen outside of biology, involves self-replication with exponential growth. Biology relies on building blocks of the same chiral handedness, including nucleic acids that contain only D-sugars. Here, a system of cross-replicating RNAs was devised based on a ribozyme that joins two RNA fragments of opposite handedness to form its own enantiomer. The D- and L-ribozymes grow together exponentially and can be propagated indefinitely, demonstrating a form of autocatalytic self-replication that relies on an RNA enzyme and its mirror image. (News review)

Homochirality is a uniformity of chirality, or handedness. Objects are chiral when they cannot be superposed on their mirror images. In biology, 19 of the 20 natural amino acids are homochiral, being L-chiral (left-handed), while sugars are D-chiral (right-handed). Homochirality can also refer to enantiopure substances in which all the constituents are the same enantiomer (a right-handed or left-handed version of an atom or molecule).

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)

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