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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Procreative Organic Habitable UniVerse

2. An Autocatalytic, Bootstrap EcosmoVerse

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)

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)

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.

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)

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