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

A. UniVerse Alive: An Organic, Self-Made, Encoded, Familial Procreativity

Ellis, George F. R.. Physics and the Real World. Foundations of Physics. 36/2, 2006. A brief version appeared in Physics Today, July 2005. An exercise to better relate and square physical reality with the presence of risen life. But what kind of universe is Ellis trying to describe. Not the moribund megaverse of string theory whereof human beings are the most fleeting, insignificant anomaly. By such inherent animate properties cosmic matter is seen to develop into emergent modular hierarchies of sentient and creative entities, in so many words a natural genesis.

The challenge to physics is to develop a realistic description of causality in truly complex hierarchical structures, with top-down causation and memory effects allowing autonomous higher levels of order to emerge with genuine causal powers. (227)

Eschenmoser, Albert. The Search for the Chemistry of Life’s Origin. Tetrahedron. 63/12821, 2007. In this “International Journal for the Rapid Publication of Full Original Research Papers and Critical Reviews in Organic Chemistry,” the emeritus Swiss chemist offers as much a philosophical update upon a natural materiality that increasingly appears as fundamentally biological in kind, innately fertile with an evolutionary gestation, just now evident a personal humankind at the late verge of its own discovery.

Yet, contemporary chemistry, as a branch of natural science, cannot escape having become as much biology as biology has become molecular, a welcome development considering that the supreme expression of the chemical potential of matter is found in living organisms. (12821) An understanding of what it means for chemical matter to be alive at the level of lowest possible complexity is one of the goals to be attained; the philosophical impact on mankind’s thinking when chemists actually will be able to experimentally demonstrate the validity of the scientific postulate that life can emerge from non-life is another. (12821)

The central message to be taken from the wealth of experimental observations in prebiotic chemistry of the last half century is the insight that all major types of low-molecular weight building blocks of living organism, amino acids, sugard, and nucleobases,…are elementary organic molecules in the sense that their formation from (essentially) the elements and excess energy can proceed under an extraordinarily broad variety of conditions as a deterministic expression of matter’s organochemical potential. (12822)

Fondi, R. Evolutionism and Holism: Two Different Paradigms for the Phenomenon of Biological Evolution. International Journal of Ecodynamics. 1/3, 2007. A typical article to here present a new journal with this editorial purpose: to relate ecosystems to evolutionary thermodynamics in order to arrive at satisfactory solutions for sustainable development. The array of papers in the first two volumes, as its abstract conveys, evoke a dynamically alive natural genesis.

Besides, during the 20th century, the conceptual transformations produced by restricted and general relativity, quantum mechanics, cosmology, information theory, research into consciousness, chaos– complexity theory, evolutionary thermodynamics and biosemiotics have radically changed the scientific picture of reality. It is therefore necessary to adopt a more suitable and up-to-date paradigm, according to which nature is not seen anymore as a mere assembly of independent things, subject to the Lamarckian-Darwinian dialectics of ‘chance and necessity’, but as: (1) an extremely complex system with all its parts dynamically coordinated; (2) the evolution of which does not obey the logic of a deterministic linear continuity but that of an indeterministic global discontinuity; and (3) in which the mind or psychic dimension, particularly evident in semiotic aspects of the biological world, is an essential and indissoluble part. On the basis of its characteristics, the new paradigm can be generically named holistic, organicistic or systemic.

Fraser, Mariam, et al. Inventive Life: Approaches to the New Vitalism. Theory, Culture & Society. 22/1, 2005. An issue Introduction on a revived sense of nature’s fertile essence due to its phenomenal propensity for self-developing complexity. But as noted elsewhere, papers in this journal hold to a postmodernism that disavows a greater, knowable reality and tends to take commentaries on prior writings as real, rather than an actual vitality itself.

Freeland, Stephen and Gayle Philip. What Can the Origin of Life on Earth Tell Us About the Cosmos? Journal of Cosmology. Volume 10, 2010. NASA Astrobiology Institute, University of Hawaii, researchers muse that a steady, broad-based increase in evidence for a “life friendly” natural cosmos bodes well for a new, revised universe, indeed a “cosmogony,” which can include its inherent biological essence. See also the author’s article “Did Evolution Select a Nonrandom “Alphabet” of Amino Acids?” in Astrobiology (11/3, 2011) which argues that the latest findings imply these vital, optimum biochemicals could not have arise by chance.

Friston, Karl. Life as We Know It. Journal of the Royal Society Interface. 6/10, 2013. The Wellcome Trust Centre theoretical neuroscientist expands his frontier studies, as many today, to rightly (re)join, root in, and explain living systems by way of a suitable physical substrate and ground which itself is under theoretical revision as much more spontaneously active. Through cast in technical arcana, see quotes and definitions below, the quest is to articulate a cosmic material nature as an integral source via its own innate qualities for evolving organisms and inquisitive people to inevitably appear, wonder, and discover.

This paper presents a heuristic proof (and simulations of a primordial soup) suggesting that life—or biological self-organization—is an inevitable and emergent property of any (ergodic) random dynamical system that possesses a Markov blanket. This conclusion is based on the following arguments: if the coupling among an ensemble of dynamical systems is mediated by short-range forces, then the states of remote systems must be conditionally independent. These independencies induce a Markov blanket that separates internal and external states in a statistical sense. The existence of a Markov blanket means that internal states will appear to minimize a free energy functional of the states of their Markov blanket. Crucially, this is the same quantity that is optimized in Bayesian inference. In other words, they will appear to model—and act on—their world to preserve their functional and structural integrity, leading to homoeostasis and a simple form of autopoiesis. (Abstract)

“How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?” Erwin Schroedinger. (1944) The emergence of life—or biological self-organization—is an intriguing issue that has been addressed in many guises in the biological and physical sciences. This paper suggests that biological self-organization is not as remarkable as one might think—and is (almost) inevitable, given local interactions between the states of coupled dynamical systems. In brief, the events that ‘take place within the spatial boundary of a living organism’ (E.S.) may arise from the very existence of a boundary. (1)

In this section, we simulate a primordial soup to illustrate the emergence of biological self-organization. This soup comprises an ensemble of dynamical subsystems – each with its own structural and functional states – that are coupled through short-range interactions. These simulations are similar to simulations used to characterize pattern formation in dissipative systems; for example Turing instabilities; far from equilibrium systems; (e.g. Benard cells), percolation and reaction-diffusion systems. Self-assembly is another important example from chemistry that his biological connotations (e.g. for pre-biotic formation of proteins). (5)

Markov Blanket: In machine learning, the Markov blanket for a node in a Bayesian network is the set of nodes composed of 's parents, its children, and its children's other parents. In a Markov network, the Markov blanket of a node is its set of neighboring nodes. Ergodic: In mathematics, the term ergodic is used to describe a dynamical system which, broadly speaking, has the same behavior averaged over time as averaged over the space of all the system's states (phase space). In physics the term is used to imply that a system satisfies the ergodic hypothesis of thermodynamics. (Wikipedia)

Gaeta, Francesco. Definition of Life. Rizzotti, Martino, ed. Defining Life. Padova, Italy: University of Padova Press, 1996. The new nonequilibrium thermodynamics can explain a cosmos made for emergent life.

A continuous thread seems to link together the events of the history of the Universe, from the Big Bang to the advent of Homo sapiens. The striking continuity of the general pattern of evolution suggests that the Universe was pregnant with life since beginning, and the biosphere was right from the start pregnant of mankind. (102)

Gagliano, Monica. Seeing Green: The Re-Discovery of Plants and Nature’s Wisdom. Societies. Online March, 2013. A University of Western Australia, Center for Evolutionary Biology, Postdoctoral Research Fellow (UWA is Crawley near Perth, and might a lady scientist be better known as a “Mellow”) The journal is posted by the Multidisciplinary Digital Publishing Institute, Basel, Switzerland, www.mdpi.com/journal/societies. This perceptive contribution could be seen as an evocation of a “systems botany” to correct a prior over-emphasis of creaturely fauna, to the slight of equally sensitive, semiotic lushness of flora. Indeed trees and forest are graced with a communicative sociality that serves much the same for their survival and prosperity.

Coherent processes belong to a new way of looking at and understanding the reality of the world. This is largely the domain of quantum physics, but it seems that plants may provide an ideal starting model to develop an equivalent quantum domain in biology. In fact, the existence of coherent, non-localized phenomena has been previously reported in plants (e.g., quantum coherence in marine algae photosynthesis) and such an approach may be required and prove fruitful in understanding plant bioacoustics. Beyond its importance in plant biology and within the life sciences, I propose that coherence is a fundamental concept to assist us in rethinking the vegetal and reconnecting us to Nature. (152)

The concept of coherence is used in a variety of contexts and has been widely adopted by disciplines as diverse as linguistics, philosophy, economics, cognitive science, mathematics and physics. In physics, for example, coherence refers to a fundamental principle of a quantum field, a domain within which atoms and molecules are in sync with each others moving exactly together in space and time; in linguistics, it describes the cohesive links within a sentence that hold the text together and give it meaning. Evidently no matter the context, coherence is a term that implies some form of collective association within systems and among systems (as well as across systems or subsystems) in which individual units interact by connecting closely together (from the Latin word cohaereō — to cling together, to be closely connected with, to be in harmony). (152-153)

My main research is broadly in evolutionary ecology and focusing on key aspects of the ecological processes by which organisms are able to gather information on the variable conditions of their surrounding environment in order to survive. While I continue my research on the ecology of coral reef fishes and other marine creatures, I have also expanded my interests to plants with great emphases on elucidating how plants obtain and make use of information about their environment through learning and, how they communicate and what kind of information they share amongst themselves and other organisms. (Monica Gagliano website)

Garcia-Ruiz, Juan Manuel, et al. Mineral Self-Organization on a Lifeless Planet. Physics of Life Reviews. January, 2020. JM G-R, University of Granada, Laboratory for the Study of Crystallogenesis, Mark van Zuilen, University of Paris, Institute of Earth Physics, and Wolfgang Bach, University of Bremen, each a veteran geoscientist, post a decisive report to date that Earth’s primordial land and sea materiality has an intrinsic propensity to catalyze, vivify, and develop into a prebiotic chemical milieu. As the 2010 decade of intensely accelerating worldwide research comes to a fruitful close like this, it is becoming possible to quantify and affirm that an organic universal genesis, an oriented evolutionary gestation to our curious, learned humankinder, does indeed exist on its independent own. See also for example, Inorganic Reactions Self-organize Life-like Microstructures Far from Equilibrium Knoll, Pamela and Oliver Steinbock by Pamela Knoll and Oliver Steinbock in the Israel Journal of Chemistry (58/6, 2018).

It has been experimentally found that, under alkaline conditions, silica is able to induce the formation of self-assembled inorganic-inorganic composite materials similar in morphology, texture and nanostructure to hybrid biomineral structures that, millions of years later, life was able to self-organize. These mineral self-organized structures (MISOS) have been shown to be effective catalyzers for prebiotic chemical reactions and to create compartmentalization within the solutions where they form. We reason that, during the very earliest history of this planet, there was a geochemical scenario that inevitably led to the existence of a large array of simple and complex organic compounds, many of which were relevant to prebiotic chemistry.

The primal phase involves a silica-rich high-pH ocean and is powered by two main factors: a) a quasi-infinite source of carbon molecules synthesized abiotically from serpentinization reaction, and b) the formation of self-organized silica-metal mineral composites that catalyze the condensation of molecules in a methane-rich reduced atmosphere. We discuss the plausibility of this geochemical scenario, review the details of the formation of MISOS and its catalytic properties and the transition towards a slightly alkaline to neutral ocean. (Abstract)

Gardner, James. A New Dawn for Cosmology. What is Enlightenment?. June-August, 2006. Noted more in Current Vistas, the author of Biocosm updates his case that much of cosmological physics is misconceived because the universe is fundamentally organic in kind.

Gardner, James. Biocosm. Makawao, HI: Inner Ocean Publishing, 2003. A spectulative attempt to gather and express the dawning vision in science of an organic cosmic genesis. By this view, a inherently self-organizing universe results in intelligent, planetary entities who can intentionally continue this complex development onto solar, galactic and cosmic scales. The author provides a synthesis of many thinkers in this regard such as Lee Smolin, Stuart Kauffman, Christian de Duve, Martin Rees and Lynn Margulis. From these sources is described a teleological evolution whose life and cognition is involved with the ultimate ‘self-replication’ of the universe. A bit heavy on technology but one of the early signs of an epic shift to a life-friendly cosmos.

Goodwin, Jay, et al. Digital and Analog Chemical Evolution. Accounts of Chemical Research. 45/12, 2012. Goodwin, Anil Mehta and David Lynn (search), Emory University, NSF/NASA Center for Chemical Evolution researchers, highlight these dual reciprocal modes, as the quotes explain, as bytes and waves of interactivity. At the outset, the authors ask whether such lively, pervasive emergence could indeed be realized as an innate, complementary propensity of a spontaneous materiality. Some pages on, it closes via the second quote, that into the 21st century, this seems in fact to be intentionally so, at once affirming Darwin’s intuition, and Lawrence Henderson’s 1913 prescience of a cosmic and earthly environment inherently fit for biological growth (American Naturalist 47/2). And worth noting, with such sanction its human co-creators may commence to “reinvent” and embellish a new sustainable earth.

Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. (Abstract excerpt)

A functional approach that looks beyond the phylogenetic event horizon of ribosome emergence may allow us to fundamentally reinvent chemical evolution, and address an issue that dates back at least to Charles Darwin’s suggestion of the warm pond where living matter first emerged. His speculation implied that evolution was an inherent property of matter and that by deciphering the chemical thresholds and physical limitations necessary for the emergence of molecular order, we can unlock and deconvolute the most elaborate, elegant, and complex hierarchical forms of matter through chemical evolution. (2197)

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