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

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

Grand, Steve. Creation. Cambridge: Harvard University Press, 2001. A computer scientist writes a user-friendly encounter with a quickening universe that intrinsically organizes itself.

We now have quite a towering hierarchy of more and more sophisticated forms of persistence: photons, particles, atoms, molecules, autocatalytic networks, self-reproducing systems, adaptive systems, intelligence and mind. On top of that…we can perhaps add society as another level of being. A society is a self-sustaining emergent phenomenon that comes into existence among populations of communicating and interdependent organisms, just as an organism is an emergent phenomenon that comes into being among populations of interdependent cells. (60)

Heylighen, Francis, et al. Chemical Organization Theory as a General Modeling Framework for Self-Sustaining Systems.. Systems. 12/4, 2024. FH and Shima Beigi, Vrije Universiteit Brussel and Tomas Veloz, Universidad Tecnológica Metropolitana, Santiago, Chile post a latest edition (search FH) of this ongoing thought process this collaborative group. In regard, its accomplishment provides support for an autocatalytic cosmopoiesis which originates life and long after engenders our personal retrospect.

This paper summarizes and reviews the Chemical Organization Theory (COT), a formalism for complex, self-organizing systems across multiple disciplines. Its elements are resources and reactions whose networks arrange themselves into invariant subnetworks. Altogether they provide a simple model of a natural autopoiesis which persistently recreates and recycles its own components. Application domains of COT include the origin of life, systems biology, cognition, ecosystems, Gaia versions, sustainability, consciousness, and social systems. (Excerpt)

Heylighen, Francis, et al. Chemical Organization Theory as a Universal Modeling Framework for Self-Organization, Autopoiesis and Resilience. pespmc1.vub.ac.be/Papers/COT-applicationsurvey. In 2015, with Shima Beigi and Tomas Veloz, Vrije Universiteit Brussel, Evolution, Complexity & Cognition Group (ecco.vub.ac.be), researchers propose an independent complex dynamic system that appears in similar effect everywhere across nature and society. While the paper opens by saying that John Holland’s complex adaptive systems via many interacting elements is in common use, another substantial version can be drawn from the University of Jena, Germany, biochemist Peter Dittrich and colleagues. By these later theories, a further measure of computational, modular, autopoietic, and resilience qualities can accrue. For original entries by PD, et al see Molecular Codes in Biological and Chemical Reaction Networks (2013) and Thermodynamics of Random Reaction Networks (2015) in PLoS One (search Dittrich) and e.g., Chemical Organization Theory in the Bulletin of Mathematical Biology (69/1199, 2007).

Chemical Organization Theory (COT) is a recently developed formalism inspired by chemical reactions. Because of its simplicity, generality and power, COT seems able to tackle a wide variety of problems in the analysis of complex, self-organizing systems across multiple disciplines. The elements of the formalism are resources and reactions, where a reaction maps a combination of resources onto a new combination. The resources on the input side are “consumed” by the reaction, which “produces” the resources on the output side. Thus, a reaction represents an elementary process that transforms resources into new resources. Reaction networks tend to self-organize into invariant subnetworks, called “organizations”, which are attractors of their dynamics. These are characterized by closure (no new resources are added) and self-maintenance (no existing resources are lost). Thus, they provide a simple model of autopoiesis: the organization persistently recreates its own components. Organizations can be more or less resilient in the face of perturbations, depending on properties such as the size of their basin of attraction or the redundancy of their reaction pathways. Concrete applications of organizations can be found in autocatalytic cycles, metabolic or genetic regulatory networks, ecosystems, sustainable development, and social systems. (Abstract)

Hill, Craig and Djamaladdin Musaev, eds. Complexity in Chemistry and Beyond. Berlin: Springer, 2013. Reviewed also in Systems Chemistry, the editors are Emory University chemists, these proceedings from a NATO Science for Peace and Security 2012 conference held in Baku, Azerbaijan. An overview by the University of Augsburg philosopher Klaus Mainzer alludes that such a nascent “supramolecular chemistry,” by way intrinsic self-organization and self-assembly, implies that biology seems to be inherently coded into elementary particulate, atomic matter. By way of these autocatalytic “potentialities” of material systems, an old “creation ex nihilo” does not hold, indeed something rather than nothing is going on in this a quickening cosmos from molecules to minds we have found. For a concurrent accord, see herein Young Sun, Early Earth and the Origins of Life by Muriel Gargaud, et al, which avers the same vitality.

Hisata, Yusei, et al. In-silico-assisted derivatization of triarylboranes for the catalytic reductive functionalization of aniline-derived amino acids and peptides.. Nature Communications.. 15/3708, 2024. As the abstract notes, Osaka University computational chemists employ novel AI methods as a way to further discern, analyze and prove nature’s innate, spontaneous biochemical self-making origins and proactive propensities.

Cheminformatics-based machine learning (ML) has been employed to determine optimal reaction conditions, including catalyst structures, in the field of synthetic chemistry. However, such ML-focused strategies have remained largely unexplored in the context of catalytic molecular transformations using Lewis-acidic main-group elements. Here, the construction of a triarylborane library and its application to the catalytic reductive alkylation of aniline-derived amino acids and C-terminal-protected peptides with aldehydes and H2 is reported. A theoretical and experimental approach identified the optimal borane which exhibits compatibility toward aniline derivatives in the presence of 4-methyltetrahydropyran.

Catalysis is a fact of our daily lives. A wide variety of important commercial chemical substances are currently produced on both the fine and bulk scales in the presence of molecular catalysts that have been optimized based on specific factors such as efficiency, toxicity, cost, or a combination thereof. Recent advancements in cheminformaticsbased machine learning (ML) offer chemists a way to bypass traditional Edisonian empiricism and develop more efficient approaches to optimizing catalysts1–4 . Several groups have reported successful demonstrations of ML-driven optimizations of homogeneous catalysts such as phosphoric acids and Lewis-basic ligands for metal-based catalysts involving phosphines, N-heterocyclic carbenes, and nitrogen-based ligands5–18 (1)

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)

Howlett, Michael and Stephen Fletcher.. From autocatalysis to survival of the fittest in self-reproducing lipid systems. Nature Reviews Chemistry.. August, 2023. Oxford University researchers add a further influence by perceptions that even precursor biochemical formations seem to exhibit innate self-making qualities. We also note in this issue an article From Alchemist to AI Chemist by Rebecca Greenaway, et al about “Reimaging the training of the next generation in the era of digital chemistry, automation, robotics and artificial intelligence.”

Studying autocatalysis in which molecules drive their own formation might help explain the emergence of chemical systems with biological traits. When coupled to other processes, autocatalysis can lead to complex systems-level behaviour in simple phases such as Lipids which collectively show supramolecular and mesoscale dynamics. Here we discuss such reactivity as a source of primitive chemical evolution, chemotaxis, temporally controllable materials and continuous synthesis. Many examples also spawn synthetic systems that emulate life by way of as metabolism and homeostasis, with structural complexity and out-of-equilibrium models. (Excerpt)

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)

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