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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Organic Universe
Earth Life Emerge
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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet Incubator Lifescape

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

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)

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.

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