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

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

Gagrani, Praful. et al. The geometry and combinatorics of an autocatalytic ecology in chemical and cluster chemical reaction networks. arXiv:2303.14238. As an instance of a unified 2023 integrity in the making, this entry by University of Wisconsin biochemists including Eric Smith illumes a thorough confirmation of nature’s insistent propensity to evolve and procreate by all manner of ecosmo-poietic, self-initiated and process viabilities. A content table has sections like Autocatalytic Cycles, An Algorithmic Organization, Cluster Networks, Mathematical Bases and Future Progress. See also Bifurcation in Cellular Evolution by Diego Radillo-Ochoa, et al herein for another citation. As these current papers altogether attest, since the 1970s (S. Kauffman) a growing observance and record of life’s developmental emergence by way of internal agencies seems at last to have matured unto an evident discovery.

Developing a mathematical understanding of autocatalysis in chemical reaction networks has both theoretical and practical implications. For a certain “stoichiometric” autocatalysis, we show that it is possible to locate them in equivalence classes and quantify their behavior. We define cluster chemical reaction networks, so to coarse-grain via conservation laws. We find that the list of minimal autocatalytic subnetworks in a maximum cluster chemical reaction network grows exponentially in the number of species. (Excerpt)

Gartner, Florian and Erwin Frey. Design principles for fast and efficient self-assembly processes. Physical Review X. 14, 021004, 2024. Center for NanoScience, Ludwig-Maximilians-University physicists provide a latest theoretical explanations which substantiate nature’s characteristic tendency to actively organize itself into emergent, self-similar vitalities wherever it can. See also The role of mobility in epidemics near criticality by Beatrice Nettuno et al. at arXiv:2402.06505 from this group. And into springtime 2024, we begin to wonder if a sufficient confluence is being reached by our learned pediasphere about an actual discovery of a familial genesis and a worthy Earth.

Self-assembly is a fundamental concept in biology, and also nanotechnology. While significant recent progress has been made, less is known about kinetic constraints of dynamical properties like time efficiency. Here we investigate how the temporal straits of reversible self-assembly depend on the morphology of the systems. We find that the constituent shapes critically determines the formation time and how it scales with the size of the target structure. Using this method, we achieve an effective theory of the self-assembly kinetics, which we show exhibits an inherent scale invariance. We show how these insights on the kinetics of self-assembly processes can be used to design artificial self-assembly processes. (Excerpt)

Gatti, Roberto Cazzolla, et al. Niche Emergence as an Autocatalytic Process in the Evolution of Ecosystems. Journal of Theoretical Biology. 454/110, 2018. The lead author is a wildlife biologist and photographer with postings at Tomsk State University, Russia, and Purdue University. He is joined by senior systems scholars Brian Fath, Wim Hordijk, and Stuart Kauffman to post a novel argument about how the appearance of new animal species involves a construction of their own environmental niche. By this view, another way to perceive an evolutionary autocatalysis at generative work is achieved. See also Biodiversity is Autocatalytic by these authors in Ecological Modelling (346/70, 2017).

The utilisation of the ecospace and the change in diversity through time has been suggested to be due to the effect of niche partitioning, as a global long-term pattern in the fossil record. However, niche partitioning, as a way to coexist, could be a limited means to share the environmental resources and condition. Here, we propose that niche emergence, rather than niche partitioning, is what mostly drives ecological diversity. In particular, we view ecosystems in terms of autocatalytic sets: catalytically closed and self-sustaining reaction (or interaction) networks. We provide some examples of such ecological autocatalytic networks, how this can give rise to an expanding process of niche emergence (both in time and space), and how these networks have evolved over time. Furthermore, we use the autocatalytic set formalism to show that it can be expected to observe a power-law in the size distribution of extinction events in ecosystems. (Abstract)

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)

Harraz, Deiaa, et al. Homogeneous-heterogeneous bifunctionality in Pd-catalyzed vinyl acetate synthesis. Science. April 4, 2025. With regard to growing recognitions of nature’s self-initiating and sustaining material and functional propensities, we cite another instance as MIT and Harvard chemical biologists offer deeper insights to its pervasive presence and advantages. See also Catalysis at the crossroads by Cathy Tway and Sorin Filip in the same issue for an expert review. See also Proverbio, Daniele and Giulia Giordano. Resilience of the autocatalytic feedback loop for gene regulation by Daniele Proverbio and Giulia Giordano at arXiv:2504.03276 and Versatile BiFeO3 shining in piezocatalysis by Jian Dai, et al in the Journal of Advanced Ceramics, (14/3, 2025)

Mechanistic paradigms in catalysis posit that the active species remains either in a homogeneous or heterogeneous state during reactions. In this work, we show that a prominent industrial process, palladium (Pd)–catalyzed vinyl acetate synthesis, proceeds via interconversion of both heterogeneous and homogeneous during catalysis in a complementary manner. We found that heterogeneous, nanoparticulate Pd(0) serves as an active oxygen reduction electrocatalyst to form homogeneous Pd(II), which then catalyzes selective ethylene acetoxylation. (Harraz)

Approximately 90% of industrial chemical products use catalysts to speed up a reaction, minimize energy consumption, and reduce waste. They are classified into two main types. Homogeneous catalysts as the reactants decrease the activation energy by direct binding. while heterogeneous catalysts work by surface reactions. In this issue, Harraz et al. report an interconversion between homogeneous and heterogeneous catalysts within the same catalytic cycle of vinyl acetate synthesis. (Tway, Filip)

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)

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