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

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

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)

Kaltschnee, Lukas, et al. Parahydrogen-enhanced magnetic resonance identification of intermediates in [Fe]-hydrogenase catalysis. Nature Catalysis. Volume 51, December, 2024. We cite this work by thirteen mainly MPI Terrestrial Microbiology researchers as a way to convey the deep degree that autocatalytic processes seem to be an essential procedure of an inherently self-making, cocreative reality. (My first patent in 1962 with Ed Reisman was for a battery and fuel cell catalyst. I have followed the science since, along with a stint at the Engelhard Corp. (now BASF) where rare earth oxides were used in diesel engines.)

Understanding the catalytic mechanism of hydrogenases (see below) can help to establish industrial (bio)catalytic hydrogen production and conversion. Here we introduce so-far undetectable intermediates of [Fe]-hydrogenase in its catalytic cycle by a NMR technique based on parahydrogen. We found that its catalytic conversion leads to enhanced NMR signals which encode information during catalysis. This work demonstrates the hitherto unexploited power of parahydrogen-induced polarization (PHIP) to study catalytic mechanisms of hydrogenases. (Excerpt)

Hydrogenases are enzymes that catalyze the reversible oxidation of molecular hydrogen into protons and electrons, and the reverse reaction. They are found in many organisms, including plants, and play a central role in microbial energy metabolism.

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)

Lipka-Bartosik, Patryk, et al. Catalysis in quantum information theory.. Reviews of Modern Physics. 96/025005, 2024. PL-B, University of Geneva, Henrik Wilming, Leibniz University and Nelly H. Y. Ng, Nanyang Technological University, Singapore post the latest glimpses of nature’s universal self-making propensities as they even become evident in these deepest realms. See also All states are universal catalysts in quantum thermodynamics by Pl-B and Paul Skrzypczyk at arXiv:2006.16290.

Catalysts open up new reaction pathways that can speed up chemical reactions while not consuming the catalyst. A similar phenomenon has been discovered in quantum information science, where physical transformations become possible by utilizing a quantum degree of freedom that returns to its initial state at the end of the process. In this review, a comprehensive overview of the concept of catalysis in quantum information science is presented and its applications in various physical contexts are discussed.

In this section we formalize the concept of catalysis in a general manner. We then describe the paradigm of resource theories, and argue that it provides a convenient set of tools allowing for a systematic study of catalytic effects. Finally, we summarize the most relevant mathematical tools and techniques that will be used throughout this review. We emphasize that this section focuses on generic features of catalysis which are valid irrespectively of the particular physical setting. (4)

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)

Nghe, Philippe, et al. Prebiotic Network Evolution. Molecular BioSystems. 11/3206, 2015. Reviewed in Origin of Life, in a Royal Society of Chemistry journal, after decades of origin of life studies to identify many relevant components, this premier paper with eight authors including Stuart Kauffman, Sara Walker, Wim Hordijk, and Niles Lehman can now aver an equally important presence of interconnective dynamics which altogether initiate the cellular ascent of organisms. “Collective autocatalytic sets” as an independent source prior to biochemistry, composed of characteristic “entity nodes and relational edges,” are seen to empower a “self-sustaining” vital organization.

Palyi, Gyula, et al, eds. Advances in Asymmetric Autocatalysis. Cambridge, MA: Academic Press, 2017. University of Modena, Italy and University of Pannonia, Hungary editors gather chapters about life’s deep propensity to catalyze, activate, organize itself by way of intrinsic, recurrent drives, structures and processes all the way from universe to us. A typical chapter is The Importance of Parachirality in Life Science by Noriko Fujii, et al.

Asymmetric autocatalysis is a chemical reaction which leads from achiral starting materials to chiral products, and in which the product accelerates its own formation reaction (conventional catalysis) and promotes the prevalence of its own chiral configuration (asymmetric induction). The book contains expert-contributed chapters that describe the most exciting recent developments in the field of the Soai reaction and in related topics, ranging from mechanistic studies and theoretical research, to practical problems in chiral syntheses and products.

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