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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator LifescapeA. UniVerse Alive: An Organic, Self-Made, Encoded, Familial Procreativity Gordon, Richard and Alexei Sharov, eds. Habitability of the Universe before Earth. Amsterdam: Academic Press/Elsevier, 2017. The veteran theoretical biologist editorial team (search each) gather a unique collection in the later 2010s which professes a natural cosmic conduciveness for organic chemicals to form and complexify on the way to life’s cellular evolutionary development on a special bioplanet. The main parts are Physical and Chemical Constraints, Predicting Habitability, Life in the Cosmic Scale, and System Properties of Life. Altogether the work is a grand affirmation to date of a true procreative universe. Choice chapters are Life before its Origin on Earth by Julian Chela-Flores, The Emergence of Structured, Living, and Conscious Matter in the Evolution of the Universe by Dorian Aur and Jack Tuszynski, Earth before Life by Caren Marzban, et al, Cosmic Evolution of Biochemistry by Aditya Chopra and Charles Lineweaver, and The Habitability of Our Evolving Galaxy by Michael Gowanlock and Ian Morrison. Habitability of the Universe before Earth examines the times and places on Earth that might have provided suitable environments for life to occur. The universe changed considerably during the vast epoch between the Big Bang 13.8 billion years ago and the first evidence of life on Earth 4.3 billion years ago, providing significant time and space to contemplate where, when and under what circumstances life might have arisen. No other book covers this cosmic time period from the point of view of its potential for life. It covers a broad range of laboratory and field research into the origins and evolution of life on Earth, life in extreme environments and the search for habitable environments in our solar system and beyond, including exoplanets, exomoons and astronomical biosignatures. Griffith, Elizabeth, et al. Ocean-Atmosphere Interactions in the Emergence of Complexity in Simple Chemical Systems. Accounts of Chemical Research. 45/12, 2012. Biophysicists Griffith, with Veronica Vaida, University of Colorado, and Adrian Tuck, Imperial College, London, quantify an astute observation that this aqueous-air interface, by way of aerosol vesicular sprays, is an ideal incubator for biomolecules and cells to complexify and evolve. As the quotes aver, it is notable that this work assumes an intrinsic milieu of nonequilibrium energies which serve to generate life’s nested scales of self-similar networks. In regard, as the condensed matter realm of statistical physics lately becomes pregnant with quickening life and mind, it portends a grand revolutionary genesis cosmos. The prebiotic conversion of simple organic molecules into complex biopolymers necessary for life can only have emerged on a stage set by geophysics. The transition between “prebiotic soup,” the diverse mixture of small molecules, and complex, self-replicating organisms requires passing through the bottleneck of fundamental chemistry. In this Account, we examine how water–air interfaces, namely, the surfaces of lakes, oceans, and atmospheric aerosols on ancient Earth, facilitated the emergence of complex structures necessary for life. In addition, we provide a statistical mechanical approach to natural selection and emergence of complexity that proposes a link between these molecular mechanisms and macroscopic scales. Very large aerosol populations were ubiquitous on ancient Earth, and the surfaces of lakes, oceans, and atmospheric aerosols would have provided an auspicious environment for the emergence of complex structures necessary for life. The fluctuating exposure of the large, recycling aerosol populations to radiation, pressure, temperature, and humidity over geological time allows complexity to emerge from simple molecular precursors. We propose an approach that connects chemical statistical thermodynamics and the macroscopic world of the planetary ocean and atmosphere. (Abstract excerpts) Gruebele, Martin and Devarajan (Dave) Thirumalai. Perspectives: Reaches of Chemical Physics in Biology. Journal of Chemical Physics. 139/12, 2013. In this second decade of the 2ist century, senior University of Illinois and University of Maryland biophysicists introduce a special section on the Chemical Physics of Biological Systems as material cosmos and developmental life become once more an integral genesis. As an example, it is inferred that the self-assembly of proteins can be newly explained by way of statistical mechanics, which fulfills Ervin Schrodinger’s 1940’s prescience. While a “Biological Physics” is broached, work remains to sort out and clear up with a consistent, natural literacy and indeed philosophy, e.g., the phrase “molecular machinery” is still bandied. A typical paper herein is “Combinatoric Analysis of Heterogeneous Stochastic Self-Assembly” by Maria D’Orsogna, et al.
Gusev, Victor and Dirk Schulze-Makuch. Genetic Code: Lucky Chance or Fundamental Law of Nature? Physics of Life Reviews. 1/3, 2004. Rather than a “frozen accident,” the prebiotic rise of life and DNA is seen to be written into a universe that is much more biological in kind as previously thought. See also Perlovsky in Part II, The Spiral of Science, for a note about this new journal. It becomes clear that the information code is intrinsically related to the physical laws of the universe, and thus life may be an inevitable outcome of our universe. The lack of success in explaining the origin of the code and life itself in the last several decades suggest that we miss something very fundamental about life, possible something fundamental about matter and the universe itself. (Abstract) Harms, Michael and Joseph Thornton. Evolutionary Biochemistry: Revealing the Historical and Physical Causes of Protein Properties. Nature Reviews Genetics. 14/8, 2013. Among the thousands of scientific papers each month, this entry by a University of Oregon, biophysicist, and a University of Chicago, geneticist, is worth especial notice for its proposal of a salutary 21st century reunion of a past divide, as the quotes say, between a ground materiality and developing life. Just now, as many entries here attest, this parting and fracture from the 1950s, and earlier 1700s, between physical cosmology and biological emergence, is finally coming together again into the single, indivisible universe it truly is and must be. In respect, a cosmic Copernican revolution could be seen as underway in our collaborative midst. The authors do not go that far, but intimate a resolve to the conflict of vicarious selection alone and an obviously necessary generative source. But while evolving organisms manifest an internal vital activity, such basic “physical properties” are not yet seen as endowed with their own agency. The work remains to scope out, name, and sufficiently explain this genesis universe where earth and peoples are meant to be. Maybe the missing crucial element is something like a similar natural genetic code. The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality — the purviews of evolutionary biology and biochemistry, respectively — are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do. (Abstract) Hazen, Robert. Evolution of Minerals. Scientific American. March, 2010. At the same while that authors Sean M. Carroll, Chris Impey, and Marcelo Gleiser conclude the multiverse to be without plan or point, scientific peer geochemist Hazen advocates a true cosmic genesis of which human persons have a central creative purpose. In addition to this popular article, see also Geosphere and Atmosphere herein, and the February 2010 Elements: An International Magazine of Mineralogy, Geochemistry, and Petrology for more technical info on how living systems via effects such as an increasing oxygenation served to engender new and more complex mineral compounds. A good site to reach it is http://elements.geoscienceworld.org/current.dtl. And in the same issue, appears a notable essay article by Hazen and Niles Eldredge on “Themes and Variations in Complex Systems.” Viewing minerals in an evolutionary context also elucidates a more general theme of evolving systems throughout the cosmos. Simple states evolve into increasingly complicated states in many contexts: the evolution of chemical elements in stars, mineral evolution in planets, the molecular evolution that leads to the origin of life, and the familiar biological evolution through Darwinian natural selection. (65) Genesis: The Scientific Quest for Life's Origins. http://scienceandreligion.hampshire.edu/videos.php. A presentation on November 3, 2011 by the Carnegie Institute of Washington and George Mason University mineral geologist at Hampshire College, Amherst, MA, in their Science and Religion lecture series. It is to be posted in full at the above website. The talk title is from Hazen’s 2005 book (search) which stands as a good synopsis of the organic revolution. By any lights today biological complexity spontaneously self-organizes and emerges from chemical matter, at every sequential stage, through dynamic interactions amongst many component agents. Hazen is lately involved with the Deep Carbon Observatory (Google) which is finding signs of “deep life” at high temperatures several miles into earth’s surface. His 2011 surmise further affirms a material reality naturally made to spawn and evolve life and people. “Life arises inevitably unto consciousness as the way a universe comes to know itself.” We quote the talk Abstract. How did life arise? Is life’s origin a cosmic imperative manifest throughout the cosmos, or is life an improbable accident, restricted to a few planets (or only one)? Scientists seek experimental and theoretical frameworks to deduce the origin of life. In this context the concept of emergent systems provides a unifying approach. Natural systems with many interacting components, such as molecules, cells or organisms, often display complex behavior not associated with their individual components. The origin of life can be modeled as a sequence of emergent events – the synthesis of biomolecules, the selection and organization of those small molecules into functional macromolecules, the emergence of self-replicating molecular systems, and the initiation of molecular natural selection – which transformed the lifeless geochemical world of oceans, atmosphere and rocks into a living planet.
Hazen, Robert.
Symphony in C: Carbon and the Evolution of (Almost) Everything.
New York: Norton,
2019.
The veteran geochemist director of the Deep Carbon Observatory at the Carnegie Institute, Washington and prolific, collegial author (search) writes a lyrical tribute to the most important element for the biochemical evolutionary occasion of creatures and peoples. He is also a member of a symphony orchestra as a trumpeter, so chose to arrange the work in four Earth, Air, Fire and Water movements about these prime ways carbon serves this purpose. He also led the discovery (RH 2008) of the vital role played by diverse mineral surfaces in life’s origin, whose compositions are seen evolve in tandem with biospheric and atmospheric systems (see VI. B. 1. Geosphere). Herdewijn, Piet and M. Volkan Kisakürek. On Chemistry Leading to Life's Origin. Chemistry & Biodiversity. 4/4, 2007. An editorial for a special issue with this title wherein senior scientists such as Christian de Duve, Gunter Wachtershauser, Sandra Pizzarello, Pier Luigi Liusi, and Andre Brack try to put down roots into a newly perceived fecund materiality whose propensities for non-equilibrium, dynamic self-organization appear to be increasingly conducive for life and evolution. Ho, Mae-Wan. Organism and Psyche in a Participatory Universe. Loye, David, ed. The Evolutionary Outrider. Westport, CT: Praeger, 1998. In the process philosophy tradition of Bergson and Whitehead, a biophysicist professes that space-time is organic in kind, whole organisms are the proper subject and its motive drive is not conflict but relational love.
Huber, Florian, et al.
Emergent Complexity of the Cytoskeleton: From Single Filaments to Tissue.
Advances in Physics.
62/1,
2013.
With Keywords such as “self-organization, self-assembly, emergent properties, multifunctionality,” this 112 page issue, with 600 references, could illustrate the worldwide revolution in the physical and biological sciences. As the Abstract and quotes note, University of Leipzig biophysicists show how living systems from polymers to people can be described by the same complex dynamic system concepts and principles that traditional physics, in some translation, has now adopted and assimilated. The paper itself, within evolutionary biology, also signifies a turn to admit generative natural phenomena, prior to selection alone. Despite their overwhelming complexity, living cells display a high degree of internal mechanical and functional organization which can largely be attributed to the intracellular biopolymer scaffold, the cytoskeleton. Being a very complex system far from thermodynamic equilibrium, the cytoskeleton's ability to organize is at the same time challenging and fascinating. The extensive amounts of frequently interacting cellular building blocks and their inherent multifunctionality permits highly adaptive behavior and obstructs a purely reductionist approach. Nevertheless the physics approach has already proved to be extremely successful in revealing very fundamental concepts of cytoskeleton organization and behavior. This review aims at introducing the physics of the cytoskeleton ranging from single biopolymer filaments to multicellular organisms. Throughout this wide range of phenomena, the focus is set on the intertwined nature of the different physical scales (levels of complexity) that give rise to numerous emergent properties by means of self-organization or self-assembly. (Abstract) Ianeselli, Alan, et al. Physical Non-Equilibria for Prebiotic Nucleic Acid Chemistry. Nature Reviews Physics. January, 2023. As the Abstract says, seven Ludwig Maximilians University biophysicists including Dieter Braun proceed with research studies to an extent that it well appears our ecosmos environs seems to be innately graced with a robust life-bearing fertility. By this view, its evolutionary emergence is just now reaching its planetary phase of our intelligent retrospective. The second quote is from Braun’s website, which provides an apt context. The prebiotic replication of DNA and RNA is a complex interplay between chemistry and the environment. Factors that have effects include temperature, monovalent and bivalent ions, the pH of water, ultraviolet irradiation and gaseous CO2. We discuss primordial conditions for the replicative reactions on the early Earth, such as heated rock pores, hydrothermal vents, evaporating ponds, icy regimes, and ultraviolet irradiation. Our expectation is that the nonlinear autonomous evolution dynamics provided by microfluidic non-equilibria make the origin of life understandable and experimentally testable. (Abstract)
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