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

D. Non-Equilibrium Thermodynamics of Living Systems

Nigmatullin, Ramil and Mikhail Prokopenko. Thermodynamic Efficiency of Interactions in Self-Organizing Systems. arXiv:1912.08948. As the century enters its third decade, we cite this posting by University of Sydney complexity scientists as an example of how it has become assumed and affirmed that a natural cosmic genesis does proceed to internally organize itself into quickening complexities from cosmic phenomena to our own intelligent phase.

The emergence of global order in complex systems with locally interacting components is most striking at criticality, where small changes in control parameters result in a global re-organization. We introduce a measure of thermodynamic interaction efficiency in self-organizing systems to quantify the change in order per unit work carried out or extracted. Our analysis formalizes an intuitive understanding of thermodynamic efficiency across diverse self-organizing dynamics in physical, biological and social domains. (Excerpt)

Ord, Alison, et al, eds. Patterns in our Planet: Defining New Concepts for the Applications of Multi-scale Non-equilibrium Thermodynamics to Earth-system Science. Philosophical Transactions of the Royal Society A. 368/3, 2010. An Introduction to a special issue on topics such as self-organized criticality in earthquake dynamics, geophysical flows, and a coupled biosphere-climate model. Yet despairing 2010 books by, e.g., Carroll and Gleiser, over a 19th century entropic arrow of time do not even mention this robust 21st century science of an animate universe that could just as well be seen as spontaneously winding itself up in a way we are just beginning to fathom.

Although non-equilibrium thermodynamics began to grow in the 1930s (Onsager 1931; Prigogine 1955; Truesdell 1969), it has had something of a resurgence in the physical sciences in recent years, embracing ideas from classical solid mechanics and stimulated by advances in computer performance. Non-equilibrium thermodynamics has now advanced to a stage where it is beginning to offer a unifying approach to understanding and modelling coupled phenomena and complex systems as a whole. (3)

Ouldridge, Thomas. The Importance of Thermodynamics for Molecular Systems, and the Importance of Molecular Systems for Thermodynamics. arXiv:1702.00360. An Imperial College London bioengineer first surveys chemical and stochastic versions as a theoretical basis, and applies these generative propensities as a way to better quantify and understand living, biomolecular, cellular, organic phenomena.

Improved understanding of molecular systems has only emphasised the sophistication of networks within the cell. Simultaneously, the advance of nucleic acid nanotechnology, a platform within which reactions can be exquisitely controlled, has made the development of artificial architectures and devices possible. Vital to this progress has been a solid foundation in the thermodynamics of molecular systems. In this pedagogical review and perspective, I will discuss how thermodynamics determines both the overall potential of molecular networks, and the minute details of design. I will then argue that, in turn, the need to understand molecular systems is helping to drive the development of theories of thermodynamics at the microscopic scale. (Abstract)

Pavlos, Georgios, et al. Universality Tsallis Non-Extensive Statistics and Fractal Dynamics for Complex Systems. Chaotic Modeling and Simulations (CMSIM). 2/2, 2012. We note this new online International Journal of Nonlinear Science, based in Eastern Europe, and this paper by Democritus University of Thrace and Aristotle University of Thessaloniki physicists as an example of the many places, ways and vernaculars that the nonlinear revolution is robustly underway. They speak of a “general, cosmic Ordering Principle,” a turn from reduction to integral self-organization, and so on. Constantino Tsallis (search) is a Greek-Brazilian thermodynamics theorist. See also Nonlinear Self-Organization Dynamics of a Metabolic Process of the Krebs Cycle by Valery Grytsay and Iryna Musatenko in the July 2014 issue.

Pinero, Jordi and Ricard Sole. Nonequilibrium Entropic Bounds for Darwinian Replicators. Entropy. 20/2, 2018. Akin to Spinney, et al below, ICREA Complex Systems Lab, Universitat Pompeu Fabra, Barcelona theorists join 21st century thermodynamic insights from Gavin Crooks, Susanne Still, Jeremy England, Anthony Bartolotta and others in search of better explanations of how life actually began. An aim of these entries is to finesse and unify the many geometric, self-similar, energetic, dissipative, informational, dynamical, Bayesian versions now in the theoretical mix.

Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other classes of replicators. On the other hand, the presence of thermodynamical constrains for these systems remain an open question. This is largely due to the lack of a general theory of out of statistical methods for systems far from equilibrium. Nonetheless, a first approach to this problem has been put forward in a series of novel developements in non-equilibrium physics, under the rubric of the extended second law of thermodynamics. The work presented reviews this theoretical framework and briefly describes the three fundamental replicator types in prebiotic evolution: parabolic, Malthusian and hyperbolic. (Abstract)

Poudel, Ram, et al, eds. Thermodynamics 2.0: Bridging the Natural and Social Sciences, Part 1. Philosophical Transactions of the Royal Society A. July, 2023. RP, Appalachian State University, NC, UMass, Amherst, Assumption University, MA, Memorial University of Newfoundland, and Yildiz Technical University, Turkey introduce the topical issue as a frontier contribution by way of this theoretical resource to the historic endeavor to achieve a grand, credible synthesis of universe and humanverse. Typical authoritative entries are Philosophy of Thermodynamics by Arto Annila, Thermodynamics, Organisms and Behavior by Ben De Bari, et al, A Thermodynamic Basis for Teleological Causality, by Terrence Deacon, and Miguel Garcia-Valdecasas, Poudel, Ram. A Unified Science of Matter, Life and Evolution by Ram Poudel and Toward a Universal Theory of Stable Evolution by Peter Van.

Some Part II, August papers are Stochastic thermodynamics: dissipativity, accumulativity, energy storage and entropy production by Manuel Lanchares and Wassim M. Haddad, and The agency of observation not to be neglected’: complementarity, causality and the arrow of events in quantum and quantum-like theories by Arkady Plotnitsky

Thermodynamics is a universal science. The language of thermodynamics is energy and its derivatives such as entropy, power and information. A more unified system of human knowledge that encompasses both life and matter is inevitable. Indeed, this knowledge has been in the making within various branches of science for a while. This theme issue is an effort in that direction, one where we consider the unity of science within the language of thermodynamics. This two-part issue includes both theoretical and applied advances for bridging the natural and social sciences with an emphasis on methods sourced from thermodynamics and quantum theory. (Issue Preface)

In this theme issue we consider the unity of science within the language of thermodynamics. Eleven articles consider theoretical and applied advances for bridging the natural and social sciences with emphasis on methods sourced from thermodynamics and quantum theory. A universal science would recognize no boundary between non-living and living.. Our understanding of science can have many limitations that follow our culture and understanding of nature. Just as our brain is divided in two with the right and left hemispheres, so are our sciences divided in two with the natural and social sciences: one facing the West and the other facing the East, to paraphrase Iain McGilchrist. We believe that thermodynamics may be able to provide such an ontological foundation and help bridge the natural and social sciences toward their unity. (2)

The thermodynamics of organisms and life is examined by Dilip Kondepudi and colleagues and Terrence Deacon et al. Both Dilip and Terry build their argument on dissipative structures in thermodynamics introduced first by Ilya Prigogine. Organisms are not machines but exhibit intentionality or goal-directed behavior, which is also known as teleology. Terry explains teleological causality in organisms in terms of a codependent structure. Two or multiple self-organizing processes linked by a shared substrate can develop toward a self-sustaining targeted state. This natural model of teleological causation, however, is applicable to the far-from-equilibrium dissipative dynamics of self-organized processes. (4)

Prigogine, Ilya. From Being to Becoming. San Francisco: Freeman, 1980. A definitive statement of the revolutionary theories of nonequilibrium thermodynamics by their Nobel laureate founder. As a result, the old physics of a closed, static equilibrium is replaced by an open, dynamical emergence of a cosmic genesis. Living systems are “dissipative structures” that flourish due to their sustenance by a flow and dissipation of energy and information.

Prigogine, Ilya. Nonlinear Science and the Laws of Nature. International Journal of Bifurcation and Chaos. 7/9, 1997. In an irreversibly developing universe, the arrow of an “evolutionary thermodynamics” can justify the directional rise of life.

Pross, Addy. How Can a Chemical System Act Purposefully? Bridging Between Life and Non-Life. Journal of Physical Organic Chemistry. 21/7-8, 2008. Endorsed by Stuart Kauffman, the Ben-Gurion University chemist provides his latest views on an apparent innate propensity of chemical matter to spontaneously give rise to life’s ramifying evolution. This Abstract tells how and why.

One of life's most striking characteristics is its purposeful (teleonomic) character, a character already evident at the simplest level of life - a bacterial cell. But how can a bacterial cell, effectively an aqueous solution of an assembly of biomolecules and molecular aggregates within a membrane (that is itself a macromolecular aggregate), act purposefully? In this review, we discuss this fundamental question by showing that the somewhat vague concept of purpose can be given precise physicochemical characterization, and can be shown to derive directly from the powerful kinetic character of the replication reaction. At the heart of our kinetic model is the idea that the stability that governs replicating systems is a dynamic kinetic stability, one that is distinctly different to the thermodynamic stability that dominates the inanimate world. Accordingly, living systems constitute a kinetic state of matter as opposed to the thermodynamic states that dominate the inanimate world. Thus, the model is able to unite animate and inanimate within a single conceptual framework, yet is able to account for life's unique characteristics, amongst them its purposeful character. As part of that unification, it is demonstrated that key Darwinian concepts are special examples of more general chemical concepts. (Abstract)

Rajpurohit, Tanmay and Wassim Haddad. Stochastic Thermodynamics: A Dynamical Systems Approach. Entropy. Online December, 2017. Georgia Tech engineering theorists (search Haddad) post an intensely mathematical treatise for a later 2010s embellishment of natural, generative energies, broadly conceived, that make the cosmos and world go. We add quotes to help convey its essence and intent. Apropos the third entry, as scientists seek to unite atomic and astral realms, how might our middle/meso humankinder quantification be of equal cosmic import?

In this paper, we develop an energy-based, large-scale dynamical system model driven by Markov diffusion processes to present a unified framework for statistical thermodynamics predicated on a stochastic dynamical systems formalism. Specifically, using a stochastic state space formulation, we develop a nonlinear stochastic compartmental dynamical system model characterized by energy conservation laws that is consistent with statistical thermodynamic principles. (Abstract excerpt)

In an attempt to generalize classical thermodynamics to irreversible nonequilibrium thermodynamics, a relatively new framework has been developed that combines stochasticity and nonequilibrium dynamics. This framework is known as stochastic thermodynamics and goes beyond linear irreversible thermodynamics addressing transport properties and entropy production in terms of forces and fluxes via linear system response theory. Stochastic thermodynamics is applicable to nonequilibrium systems extending the validity of the laws of thermodynamics beyond the linear response regime by providing a system thermodynamic paradigm formulated on the level of individual system state realizations that are arbitrarily far from equilibrium. The thermodynamic variables of heat, work, and entropy, along with the concomitant first and second laws of thermodynamics, are formulated on the level of individual dynamical system trajectories using stochastic differential equations. (1)

In this paper, we combined thermodynamics and stochastic dynamical system theory to provide a system-theoretic foundation of thermodynamics. The proposed dynamical systems framework of thermodynamics can potentially provide deeper insights into the constitutive mechanisms that explain fundamental thermodynamic processes and describe acute microcosms and macrocosms in the ever-elusive pursuit of unifying the subatomic and astronomical domains. (45)

Roberts, Bryan. Reversing the Arrow of Time. arXiv.2212.03489. The author of this online 266 page volume is Director of the Centre for Philosophy of Natural and Social Sciences at the London School of Economics. We note for its merits and as an example of how a single human being seems readily capable of viewing an entire cosmological theoretic scenario.

The arrow of time refers to the curious asymmetry that distinguishes the future from the past. Here I contend there is a link between the symmetries of 'time’s course in physical theories, which has wide-ranging implications. This relation clarifies how we can learn about the symmetries of our world, what is real, and how to overcome pervasive illusions. (Editor)

Robledo, Alberto. Unifying Laws in Multidisciplinary Power-Law Phenomena. Gell-Mann, Murray and Constantino Tsallis, eds. Nonextensive Entropy – Interdisciplinary Applications. Oxford: Oxford University Press, 2004. An example of the worldwide discovery of a creative, organic universe, in need of translation.

Critical, power-law behavior in space and/or time manifests in a large variety of complex systems within physics and, nowadays, more conspicuously in other fields, such as biology, ecology, geophysics, and economics. Universality, the same power-law holding for completely different systems, is a consequence of the characteristic self-similar, scale-invariant property of criticality… (63)

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