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VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

2. The Origins of Life

Ross, David and David Deamer. Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis. Life. Online July, 2016. We cite this entry by an SRI International researcher and the senior UC Santa Cruz biochemist for itself, and to record the Emergence of Life: From Chemical Origins to Synthetic Biology issue, edited by Pier Luigi Luisi, which it is included in. See also therein The Role of Lipid Membranes in Life’s Origin by Deamer and Coevolution Theory of the Genetic Code by Tze-Fei Wong, et al. Some other special collections on this open site are The Landscape of the Emergence of Life, The Origin and Evolution of the Genetic Code, and The Origins and Early Evolution of RNA.

Ruelle, David. The Origin of Life Seen From the Point of View of Non-Equilibrium Statistical Mechanics. arXiv:1701.08388. The Rutgers University mathematician has been a pioneer systems theorist since the 1960s and was co-coiner with Floris Takens (1940-2010) of the widely used phrase strange attractor. This latest note seeks to clarify earlier thermodynamic versions of this approach by noting new work by Gavin Crooks, Christopher Jarzynski and Jeremy England (search each). It then proposes a series of steps by which living systems may arise from this conducive, natural environment. An evident surmise, if to admit, is an innately conducive, life entailing, genesis cosmos.

The purpose of the present note is to attempt a more precise discussion of the above remarks by using basic ideas of non-equilibrium statistical mechanics. In view of this we have just presented some accepted or acceptable ideas on pre-biological or pre-metabolic systems. Note that one such system may occupy several distinct regions of space (just as biological species may consist of different individuals). But pre-metabolic systems have a discrete structure: we are not thinking of a homogeneous pre-biological soup. (4)

Ruiz-Mirazo, Kepa and Alvaro Moreno. Reflections on the Origin of Life: More than an “Evolutionary” Problem. Metode Science Studies. Volume 6, 2016. In this University of Valencia online journal, University of the Basque Country researchers in the Science Philosophy and Logic group and Biology Philosophy Cognition group (which AM founded) pick up on Thomas Nagel’s 2012 work Mind and Cosmos which contends that a mechanist evolution by selection alone misses a key mental, generative feature. In regard, an evident need for a prior source force is specified as nature’s physical (lawful) propensity to organize into emergent, self-sustained scales of complexity and consciousness. As a result, the article achieves one of the clearest and most strident inclusions of (essentially) a natural genetic code. See also Chemical Roots of Biological Evolution by K. Ruiz-Mirazo, et al in Open Biology (April 2017, herein).

This paper argues that the question of the origin of life cannot be explained by appealing exclusively to Darwinian evolutionary mechanisms, as many experts tend to assume, but requires a profound change in perspective. Accordingly, we highlight the fact that, in order to operate as a diversification force (and indirectly, a force for a potential increase in complexity), natural selection requires a number of conditions to be met in order for it to be possible: specifically, self-sustained and self-(re-)productive chemical organisation within a sufficiently large phenotypic space (that is, a wide range of functions). Therefore, we suggest an extension of the self-organising paradigm towards a self-(re-)productive one as an alternative to the main proposals regarding the origin of life, based on molecular populations subject to Darwinian evolution. Such a paradigm would adequately portray the specificity of the biological phenomenon (metabolic and cellular dimensions) and would be relevant before, during, and after natural selection started to operate. (Abstract)

Ruiz-Mirazo, Kepa, et al. Chemical Roots of Biological Evolution: The Origins of Life as a Process of Development of Autonomous Functional Systems. Open Biology. April, 2017. In this Royal Society journal, Spanish astrobiologists K R-M, Carlos Briones and Andres de la Escosura exercise a meld of “systems chemistry with evolutionary theory” along with innate organizational agencies to reach a complete, plausible explanation. A main theme of this extended collegial endeavor is to view life’s oriented development as facilitated by a biochemical autocatalysis toward an enhanced free individuality. As a result, an increasing self control of kinetic, energetic, creative, and spatial dimensions leads to a finesse of the major evolutionary transition scales.

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided.

Ruiz-Mirazo, Kepa, et al. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chemical Reviews. 114/1, 2014. Reviewed more Systems Chemistry, Spanish scientists extensively presage a revolutionary genesis cosmos.

Russell, Michael. First Life. American Scientist. January-February, 2006. The thermal vents of the Hadean seas indeed served as incubators for complex biochemicals on the way to bounded, replicating cells.

Billions of years ago, deep under the ocean, the pores and pockets in minerals that surrounded warm, alkaline springs catalyzed the beginnings of life. (32)

Russell, Michael, et al. The Drive to Life on Wet and Icy Worlds. Astrobiology. 14/4, 2014. A 14 member team from Cal Tech, JPL, Precambrian Ecosystem Laboratory, Japan, University of Illinois, CNRS France and more, including Elbert Branscomb and Wolfgang Nitschke, claims that the vectorial formation of living, evolving systems is impelled from their onset by far-from-equilibrium energy gradients. The paper summarizes years of research and results, with over 400 references, albeit with machine metaphors, in support of this thermal theory. The article is the latest of a series in international journals, especially Biochimica et Biophysica Acta (BBA) - Bioenergetics, from this broad European and American collaboration. A special issue of BBA above, The Evolutionary Aspects of Bioenergetic Systems (1827/2, 2013), introduced by Nitschke, contends this source precedes and subsumes an optional RNA or metabolism emphasis by their common thermodynamic drives. Later in the same journal, Free Energy Conversion in the LUCA: Quo Vadis? (Online December 2013), presses this “origin of energy metabolism” approach. Another summary is The Inevitable Journey to Being in Philosophical Transactions of the Royal Society B (368/1622, 2013) by MR, WN, and EB, Abstract below.

This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life’s operations calls into question the idea of ‘‘prebiotic chemistry.’’ It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors—such as pyrophosphate synthetase and the like driven by these gradients—that make life work. (Article Abstract)

In systems driven far from equilibrium, self-organized dynamic structures, acting as engines (i.e., ‘‘free energy converters’’), arise spontaneously. Their effect is invariably to accelerate the rate at which the driving disequilibrium generates entropy and is thereby dissipated. Tellingly, the Universe itself, at the moment of its Big Bang birth, was by a vast measure the most extreme example, known or conceivable, of a far-from-equilibrium system, born as it was in a condition of disequilibrium so great as to be virtually inestimable. From this pinnacle of improbability, it could only, as the second law of thermodynamics demands, go endlessly ‘‘down’’ to ever increasing total entropy. (3)

Indeed, the history of the Universe has been ‘‘nothing but’’ the playing out of the dynamics of accelerated entropy production via emergent, self-organizing engines. All the dynamic structures and processes of the Universe, both great and small, from galactic superclusters to burning and dying stars, black holes, the writhing pirouettes of quasar jets, planetary systems, convective currents in myriad guises, to the poppies on the cool green hills of Earth — all are engines all contributing members of this great self-organizing cascade of accelerated entropy production. (3)

Life is evolutionarily the most complex of the emergent symmetry-breaking, macroscopically organized dynamic structures in the Universe. Members of this cascading series of disequilibria-converting systems, or engines in Cottrell's terminology, become ever more complicated—more chemical and less physical—as each engine extracts, exploits and generates ever lower grades of energy and resources in the service of entropy generation. Each one of these engines emerges spontaneously from order created by a particular mother engine or engines, as the disequilibrated potential daughter is driven beyond a critical point. Exothermic serpentinization of ocean crust is life's mother engine. It drives alkaline hydrothermal convection and thereby the spontaneous production of precipitated submarine hydrothermal mounds. Here, the two chemical disequilibria directly causative in the emergence of life spontaneously arose across the mineral precipitate membranes separating the acidulous, nitrate-bearing CO2-rich, Hadean sea from the alkaline and CH4/H2-rich serpentinization-generated effluents. Essential redox gradients—involving hydrothermal CH4 and H2 as electron donors, CO2 and nitrate, nitrite, and ferric iron from the ambient ocean as acceptors—were imposed which functioned as the original ‘carbon-fixing engine’. (The Inevitable Journey to Being)

Scharf, Caleb, et al. A Strategy for Origins of Life Research. International Journal of Astrobiology. 15/12, 2015. With multiple contributors (30 men and 3 women), this is a summary review of an August 2015 Earth-Life Science Institute workshop at the Tokyo Institute of Technology. The main aspects such as definitions of life, how to assimilate meteorites, thermal vents, biochemicals, scales of aliveness, and so on, are dutifully covered. It is noted that the presence of spontaneous non-equilibrium self-organizing dynamics should also be considered. But it seems to me that a deep contradiction besets any such project that needs airing. While Scharf, a Columbia University astrobiologist and author (search), leads the well intentioned group, the endeavor goes forth in a moribund cosmos already dismissed as devoid of any creative essence, direction, or destiny. What does it matter whether life began this way or that, if animate evolution and our brave human reconstruction is yet all for naught.

Schopf, William, ed. Life’s Origin: The Beginnings of Biological Evolution. Berkeley: University of California Press, 2002. A synoptic survey from historical backgrounds to earth’s formation, biochemical precursors, polymerization, genetic information and ancient paleontology which reaches this conclusion:

So even though detailed understanding has yet to be achieved, the main story of life’s beginnings is abundantly clear: Life is a natural outcome of the evolution of cosmic matter ( Schopf, 3)

Schrum, Jason, et al. The Origins of Cellular Life. Atkins, John, et al, eds. RNA Worlds: From Life’s Origins to Diversity in Gene Regulation. Cold Spring Harbor: CSH Laboratory Press, 2011. With coauthors Ting Zhu and Nobel laureate Jack Szostak, Howard Hughes Medical Institute, Boston, integrative biologists reach a similar surmise to Andrew Pratt (2011), Eors Szathmary (2007), Tibor Ganti (search) and others that a defining propensity of living systems is the formation of whole, semi-autonomous entities, by way of hereditary instruction. Life’s iterative evolution can then be viewed, in our retrospect, as a progression of increasingly free, complex and smart “proto-cells.” (And all this surely augurs for a “social proto-cell” such as Sustainable Ecovillage herein avers.)

With coauthors Ting Zhu and Nobel laureate Jack Szostak, Howard Hughes Medical Institute, Boston, integrative biologists reach a similar surmise to Andrew Pratt (2011), Eors Szathmary (2007), Tibor Ganti (search) and others that a defining propensity of living systems is the formation of whole, semi-autonomous entities, by way of hereditary instruction. Life’s iterative evolution can then be viewed, in our retrospect, as a progression of increasingly free, complex and smart “proto-cells.” (And all this surely augurs for a “social proto-cell” such as Sustainable Ecovillage herein avers.)

Schuster, Peter. Origins of Life. Complexity. Early View: December, 2009. Recent advances are the confirmation of an RNA “genetics first” pathway, along with a growing sense of how conducive the prebiotic chemical milieu is. And a theoretical synthesis and reconstruction may finally be in sight if the active organizational role of complex systems phenomena can be factored in.

Despite rather pessimistic views uttered by opponents of a natural origin of life an impressive collection of data is available now. They all speak for a sequence of prebiotic events and processes leading from networks of dynamically related small molecules and amphiphiles to biological macromolecules, compartments, and eventually protocells. Not a single one of the suggested avenues to life seems to be plausible but taking them all together in a concerted view could provide the solution. (3)

Schuster, Peter and Peter Stadler. Networks in Molecular Evolution. Complexity. 8/1, 2003. With a subtitle “A Common Theme at All Levels,” this paper claims that the way biochemicals evolved into organic complexity is by a hierarchy of autocatalytic systems.

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