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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

2. The Origins of Life

Lahav, Noam. Biogenesis. New York: Oxford University Press, 1999. A proficient technical survey of the state of life’s biomolecular, genetic and protocellular origin.

Larson, Brian, et al. The Chemical Origin of Behavior is Rooted in Abiogenesis. Life. Online November, 2012. An online definition of Abiogenesis is “a natural organic phenomenon by which living organisms spontaneously arose from nonliving matter.” Coauthor Niles Lehman, Portland State University Chemistry Chair, with grad students Larson and Paul Jensen, join the mission to extend life’s regnant activity ever deeper into a conducive fertile ground. In regard, as a precursor “informational” source becomes more evident, suitable molecules then seem to make relative “choices” such as better “folding pathways” within a variable environment. Such an appreciation of an “anthropomorphic” biochemical materiality then contributes to a deep, true continuity between human and universe. Might one surmise that a dynamic cosmos of contingency and choice, a self-creating and selecting procreative genesis, could soon be in the offing?

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of choice. RNA polymers of sufficient length meet the criteria for behavioral chemistry and therefore are capable of making a choice. (Abstract)

Once Nature had the capacity to synthesize information-bearing macromolecules though, the stochasticity of the system became embodied into the “behavior” of the molecules because now there was the possibility that a molecule was the system! In essence, a system requires both a genotype and a phenotype to be able to display behavior. The “self” is now clearly defined; however, it can be a single self-replicating molecule or a network of related cooperators. Here we are using the example of RNA as the informational polymer, but the same conclusions were to apply if other polymers, or even inorganic lattices or compositional sets of macromolecules such as lipids, were the ancestral genotypes. Clearly, the advent of compartmentalization (protocellular life) would further enhance the establishment of a bounded genotype, thereby firmly entrenching behavior. (315)

Lazcano, Antonio. The Origins of Life. Natural History. February, 2006. A popular glimpse of the “heterotrophic” theory whereby “the first living entities evolved “abiotically” from nonliving organic molecules on the primitive Earth.” In this primal phase, a prebiotic soup cooked complex molecules such as amino acids. Although self-catalyzing systems are mentioned, this approach seems to labor within an inorganic, inanimate universe. Protein synthesis is seen as “machinery” leading to an RNA world.

Letelier, Juan-Carlos, et al. From L'Homme Machine to Metabolic Closure: Steps Toward Understanding Life. Journal of Theoretical Biology. Online July, 2011. For a 50th Anniversary Review of this journal’s tenure, Universidad de Chile (Letelier), and CRNS, France (Maria Cardenas and Athel Cornish-Bowden), biologists provide a unique history of many efforts to define the phenomenon of life. Julien Offray de La Mettrie’s (1707-1751) title mechanical manifesto leads to Nicolas Rashevshy’s (1899-1972) relational biology, Robert Rosen’s (1934-1998) M,R systems, and onto cybernetics, chemotons, hypercycles, autocatalysis, autopoiesis, systems biology. From our late vantage, by a re-evaluation and synthesis of these precursors, the essence of life appears much to be a bounded metabolic organization, with a penchant for self-construction. The article wraps up with the quoted paragraph, for a definitive discovery still eludes.

As for whether biology really needs a theory of the living state, we conclude by quoting (Carl) Woese (2004, search), who wrote that “without an adequate technological advance (sequencers, etc.) the pathway of progress is blocked, and without an adequate guiding vision there is no pathway, there is no way ahead.” Of course we need the technological advances that we have seen in the past 60 years, bu we also need a guiding vision.

Lilley, David and John Sutherland. The Chemical Origins of Life and its Early Evolution. Philosophical Transactions of the Royal Society B. 366/2853, 2011. University of Dundee and MRC Laboratory of Molecular Biology researchers introduce a full issue on increasing accessible primeval seedings and stirrings of life’s earthly emergence, lately bent on reconstructing itself via our human phenomenon. In addition to Hanczyc above, “Prebiotic Chemistry: A New Modus Operandi” by Matthew Powner and John Sutherland cites an original “systems chemistry” that forms vesicular membranes, while Robert Pascal and Laurent Boiteau in “Energy Flows, Metabolism and Translation” continue their work on a thermodynamic basis for cellular compartments, information, and metabolism. And many authors and articles seem by inference to be on the verge of admitting an inherent cosmic and earthly predisposition for life to get going from nature’s deepest material recesses and ancient ages.

Can we look at contemporary biology and couple this with chemical insight to propose some plausible mechanisms for the origin of life on the planet? In what follows, we examine some promising chemical reactions by which the building blocks for nucleic acids might have been created about a billion years after the Earth formed. This could have led to self-assembling systems that were based on an all-RNA metabolism, where RNA is both catalytic and informational. (Abstract, 2853)

Lynn, David, et al. Origins of Chemical Evolution. Accounts of Chemical Research. 45/12, 2012. This significant topical issue is reviewed much more in Organic Universe, where several articles are also noted separately.

Markovitch, Omer, et al. Chemical Heredity as Group Selection at the Molecular Level. arXiv:1802.08024. As many similar studies nowadays, systems biochemists OM, University of Groningen with Olaf Witkowski and Nathaniel Virgo, Earth-Life Science Institute, Tokyo, proceed to root life’s multilevel evolutionary phenomena such as selection, replication, autocatalysis, and especially cooperative groups deeply and firmly into fertile, active physical matter. In one more way, the extant natural cosmos is becoming wholly organic in kind.

Many examples of cooperation exist in biology. In chemical systems however we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. The biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology. (Abstract excerpts)

Arguing that it is possible to apply biology tools on chemical systems, together with the present example help portray a route to further deepen the connections between chemistry
and biology, as much as such connections exist. For the origins of life, this supports a view of a continuous transition from the prebiotic chemistry towards present-day biology. The picture we imagine is that selection on ensembles of molecules gives rise to cooperative processes between molecules; this provides a starting point from which the complexity of biology can develop. (15)

Mathis, Cole, et al. Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation. Life. Online October, 2017. Mathis, Sanjay Ramprasad, and Sara Imari Walker, Arizona State University, with Niles Lehman, Portland State University, find that nature’s network topologies and dynamics are in effect even at this early nucleotide phase because they provide cooperative benefits. The entry is for The RNA World and the Origin of Life issue, see also Evolutionary Conflict Leads to Innovation (Paulien Hogeweg) and The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture (Paul Higgs). In further regard, see Topological and Thermodynamic Factors that Influence the Evolution of Small Networks of Catalytic RNA Species by Niles Lehman, et al in the journal RNA (23/7, 2017).

Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life. (Abstract)

Mathis, Cole, et al. The Emergence of Life as a First Order Phase Transition.. arXiv:1503.02776. Astrophysicists Mathis, ASU, Tanmoy Bhattacharya, SFI, and Sara Imari Walker, ASU, assume an inherently organic cosmos whereof “life is a phase of matter.” By this frontier scientific view, a non-equilibrium universe is seen to spontaneously evolve and develop by way of information and replication. Again in 2015, we move closer to a revolutionary natural genesis as its genetic narrative begins to breakthrough unto its own recognition.

We demonstrate a phase transition from non-life to life, defined as non-replicating and replicating systems respectively, and characterize some of its dynamical properties. The transition is first order and demonstrates many characteristics one might expect from a newly emergent biosphere. During the phase transition the system experiences an explosive growth in diversity, with restructuring of both the extant replicator population and the environment. The observed dynamics have a natural information-theoretic interpretation, where the probability for the transition to occur depends on the mutual information shared between replicators and environment. Through the transition, the system undergoes a series of symmetry breaking transitions whereby the information content of replicators becomes increasingly distinct from that of their environment. Thus, the replicators that nucleate the transition in the non-life phase are often not those which are ultimately selected in the life phase. We discuss the implications of these results for understanding the emergence of life, and natural selection more broadly. (Abstract)

Matsumara, Shigeyoshi, et al. Transient Compartmentalization of RNA Replicators Prevents Extinction Due to Parasites. Science. 354/1293, 2016. Ten researchers from Japan, France, Germany, and Hungary, including Eors Szathmary, Faith Coldren, and Phillippe Nghe, explain how original living systems were able to evolve in spite of contrary conditions, which the quotes detail. A natural propensity seem to be the formation of bounded cellular forms, which as primordial communities fostered their survival. See also, for example, How Life Can Arise from Chemistry by Michael Gross in Current Biology (26/R1247, 2016). A philosophical view of these many reports implies an innately conducive biocosmos from which our late collaborative quantification is meant to appear, discovery and affirm.

The evolution of molecular replicators was a critical step in the origin of life. Such replicators would have suffered from faster-replicating “molecular parasites” outcompeting the parental replicator. Compartmentalization of replicators inside protocells would have helped ameliorate the effect of parasites. Matsumura et al. show that transient compartmentalization in nonbiological materials is sufficient to tame the problem of parasite takeover. They analyzed viral replication in a droplet-based microfluidic system, which revealed that as long as there is selection for a functional replicator, the population is not overwhelmed by the faster-replicating parasite genomes. (Editorial Summary)

The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin of life. However, parasitic replicators would take over and would have prevented life from taking off unless the replicators were compartmentalized in reproducing protocells. Paradoxically, control of protocell reproduction would seem to require evolved replicators. We show here that a simpler population structure, based on cycles of transient compartmentalization (TC) and mixing of RNA replicators, is sufficient to prevent takeover by parasitic mutants. TC tends to select for ensembles of replicators that replicate at a similar rate, including a diversity of parasites that could serve as a source of opportunistic functionality. Thus, TC in natural, abiological compartments could have allowed life to take hold. (Abstract)

McFarland, Ben. A World From Dust: How the Periodic Table Shaped Life. New York: Oxford University Press, 2016. In the main lecture hall of the new Integrated Sciences Building at UM Amherst hangs an iconic, 12’X16’ periodic table. By any stretch the millions of compounds which those 100 elements can form so that we peoples can write and observe it cannot be an accident. In this volume, a Seattle Pacific University biochemist draws on the latest advances to trace and document an oriented evolutionary universe to human scenario. Surely contingencies abound, with dead ends along the way, but it is not a random, blind passage. Akin to a physical basis, chemical structures and reactions serve to constrain and guide the course of complex organisms. By these lights, it is pointedly put that Stephen Jay Gould’s 1980s claim that earth life’s tape is so chancy it would not run again can be refuted. Here is another glimpse that a Ptolemaic pointless, accidental, nature from nothing is seriously wrong, and need be set aside for intimations of a phenomenal genesis cosmos from which entailed, intended persons can so witness, and creatively continue.

Therefore, the story of chemical life must start, as chemists do, with the periodic table itself. If life is built from the periodic table, then what is the periodic table built from? Like physics itself (and to tell the truth, this is physics itself), the answer would make Plato proud. The rows and columns of the periodic table are built from Platonic ideals, from the abstract combinations and logical consistencies of mathematics. (39) If we do find conditions that could have built life on the early Earth, say with (John) Sutherland’s light driven reactions, then that would argue against (Stephen Jay) Gould’s “tape of life” thought experiment at the molecular level. Such a result would mean that, despite a vast distance of time, early-Earth chemistry could be deduced and repeated in a modern lab. This first song on the tape of life would be rewound, replayed, and recapitulated, even 4 billion years later. Life’s most fundamental biochemistry would be explained by and predicted from the chemistry of the periodic table. (109)

Gould’s tape of life was a story that was too simple. It assumed that genetic changes were largely independent of other events, when in fact they were hemmed in by the biology of other species in the ecological network, by the chemistry available in the environment, and by the physics of energy efficiency. Gould’s assertion that the tape of life is unrepeatable requires a type of evolution that can solve hard problems only once, rather than a tape that converges on repeated and efficient solutions. Gould’s evolution is weak tea compared to a chemically driven and convergent evolution. (264)

Melendez-Hevia, Enrique, et al. From Prebiotic Chemistry to Cellular Metabolism: The Chemical Evolution of Metabolism before Darwinian Natural Selection. Journal of Theoretical Biology. 252/505, 2008. Biologists at the Institute of Cell Metabolism, Canary Islands, and the Universidad Complutense de Madrid, Spain present a detailed case for life’s inexorable occasion, for which we cite the full article abstract.

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin. (505)

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