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

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

Dufour, Dufour and Steven Chamley. New Bistable Solutions in Molecular Cloud Chemistry: Nitrogen and Carbon Autocatalysis. arXiv:2304.14477. NASA Goddard astrochemists describe further quantifications of these self-making biocreative processes across the celestial raiment. As a quote adds, a natural affinity can then be viewed with life’s Earthly developmental evolution.

Nonlinear chemical systems far from thermodynamic equilibrium, such as those commonly found in astrophysical environments, can in principle exhibit multistability and complex dynamical evolution, including bistability, oscillations and chaos. Many chemical models of dense interstellar clouds have been developed since the early 1970s with astrochemical bistability first detected as steady-state solutions to their gas-phase kinetics. When a bifurcation occurs as a control parameter is varied, a nonlinear system may switch from a single stable solution to multiple simultaneous possible solutions, among which two at least are stable. (1) The fact that several autocatalyses are embedded in gas-phase interstellar chemistry, and yet only become active for certain combinations of the external control parameters, is consistent with the definition of autocatalysis in general chemical systems. (11)

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)

Egel, Richard. Life’s Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives. Life. Online November, 2012. Reviewed also in Organic Cosmos, the emeritus University of Copenhagen Biocenter geneticist achieves an insightful advocacy of the imminent (re)connection of biology with physics, of evolved organic entities with vital material substrates. An innovative context recalls the prescient insights of Jeffery Wicken, (1942-2002) as in his main work Evolution, Thermodynamics, and Information, (Oxford, 1987), who taught at Penn State for many years and is seen as laying out theoretical pathways to such a resolution. A 1995 companion paper by philosopher Iris Fry (search) is also availed to contrast these options – “continuity thesis or natural-law camp” vs. “happy accident or almost miracle.” From 2012, Egel’s affirms that the gulf between life and land has been bridged, - rather than improbable chance, living beings are now known to spontaneously arise and complexify by way of dynamical, self-organizing autocatalytic, integrative forces. The project goes on, which this site seeks to document, to better name, give credence to, and empower this cosmic Copernican revolution from mechanics to vitality, dark to light ages, from precarious nothing to an ordained teleological gestation.

Farnsworth, Keith, et al. Unifying Concepts of Biological Function from Molecules to Ecosystems. Oikos. 126/10, 2017. Farnsworth and Tancredi Caruso, Queen’s University, Belfast, with Larissa Albantakis, University of Wisconsin contribute to a vital, overdue synthesis across ecological theories by way of clarifying definitions, and a range of complexity principles such as autocatalysis and emergent scales. With common, simplified terms in place, the presence of universal formative principles across nature’s tangled bank can at last be realized. See also A Comprehensive Framework for the Study of Species Co-Occurrences, Nestedness and Turnover by Werner Ulrich, et al in the November issue.

The concept of function arises at all levels of biological study and is often loosely and variously defined, especially within ecology. This has led to ambiguity, obscuring the common structure that unites levels of biological organisation, from molecules to ecosystems. Here we build on already successful ideas from molecular biology and complexity theory to create a precise definition of biological function which spans levels of biological organisation and can be quantified in the unifying currency of biomass, enabling comparisons of functional effectiveness (irrespective of the specific function) across the field of ecology. We give precise definitions of ecological and ecosystem function that bring clarity and precision to studies of biodiversity–ecosystem function relationships and questions of ecological redundancy. This type of network structure is that of an autocatalytic set of functional relationships, which also appears at biochemical, cellular and organism levels of organisation, creating a nested hierarchy. This enables a common and unifying concept of function to apply from molecular interaction networks up to the global ecosystem. (Abstract)

Fontana, Walter and Phillpp Honegger. Translation of a 1971 Paper by Otto Rossler and a Commentary. arXiv:2209.04731.. Otto Rossler’s paper is a landmark in the chemical landscape that was all but missed despite providing a consequential refinement of the idea of generalized autocatalysis, which refers to a system that facilitates its own growth. Harvard Medical School system biologists (search WF) post a once and future survey over 50 years about how many domains across a long evolutionary development can be factually appreciated as a catalytic process by which living systems proceed to make themselves The author’s commentary continues from Rossler onto classic versions by Manfred Eigen, Stuart Kauffman, Tibor Ganti and others.

Froese, Tom. et al. From Autopoiesis to Self-Organization: Toward an Enactive Model of Biological Regulation. bioRxiv June 9, 2023. TF, Natalya Weber, and Ivan Spurov, Okinawa Institute of Science, and Takashi Ikegami, University of Tokyo propose a latest 2020s agency–like feature by which this 50 year sense of some cosmopoietic process within an actual self-making and sustaining evolutionary universe gain valid acceptance. (As a personal note, I heard cofounder Francisco Varela’s first talk in the USA in the 1970s, and in 1992 at Amherst College about his coauthored The Embodied Mind book.) But alas the recent Enactivism school has affinities but its dense Wikipedia page also has clarity issues.

The theory of autopoiesis has been influential in many areas of theoretical biology, and especially artificial life and origins of life. However, it still does not fit well with mainstream models because clear definitions have not been worked out. But the perception has lately been advanced by the enactive approach to life and mind. Hidden complexity in the original autopoiesis has been explicated by qualities related to self-individuation: precariousness, adaptivity, and agency. Herein we also highlight their interplay with thermodynamics: reversibility, path-dependence and self-optimization. (Abstract)

Fry, Iris. The Role of Natural Selection in the Origin of Life. Origins of Life and Evolution of Biospheres. 41/1, 2011. Reviewed more in Origin of Life, as the quote avers, an iconic sorting has arisen between an emphasis on discrete nucleotide molecules – ‘gene-first’, or in favor of primal autocatalytic, self-organizational processes – ‘metabolism first.’ A necessity for the gene group is the formation of membrane enclosed compartments or proto-cells to house such RNA informants.

Gabora, Liane and Mike Steel. Autocatalytic Networks in Cognition and the Origin of Culture. Journal of Theoretical Biology. Online July, 2017. University of British Columbia, and University of Canterbury, New Zealand, scholar biologists attempt a novel avail of this creative natural phenomena as a way to explain how human cultural societies came to be. A central guide is Merlin Donald’s four stages of hominid evolution from episodic to worldwide minds. The paper is also posted at iarXiv:1703.05917./i

It has been proposed that cultural evolution was made possible by a cognitive transition brought about by onset of the capacity for self-triggered recall and rehearsal. Here we develop a novel idea that models of collectively autocatalytic networks, developed for understanding the origin and organization of life, may also help explain the origin of the kind of cognitive structure that makes cultural evolution possible. In our setting, mental representations (memories, concepts, ideas) play the role of 'molecules', and 'reactions' involve the evoking of one representation by another through remindings, associations, and stimuli. In this paper, we propose and study a simple and explicit cognitive model that gives rise naturally to autocatylatic networks, and thereby provides a possible mechanism for the transition from a pre-cultural episodic mind to a mimetic mind. (Abstract excerpt)

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)

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)

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