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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 Origin of Life

Delaye, Luis and Antonio Lazcano. Prebiological Evolution and the Physics of the Origin of Life. Physics of Life Reviews. 2/1, 2005. This new journal is available online, via Google. The authors contend that understanding life’s origin requires a synthesis of geology, chemistry, biology, astrophysics, theoretical physics, paleontology and philosophy. In this broad context, their hypothesis combines the relatively rapid appearance of chemical replicating, gene-like molecules, possibly in the vicinity of deep-sea vents, along with a consideration of intrinsic self-organizing, emergent systems.

Derr, Julien, et al. Prebiotically Plausible Mechanisms Increase Compositional Diversity of Nucleic Acid Sequences. Nucleic Acids Research. 40/10, 2012. By way of sophisticated theory and experiment, Harvard University biosystem scientists including Irene Chen and Martin Nowak, engage the deepest issue of whether the appearance of such viable replicative biomolecules happened by capriciousness or was due to some innate, independent “predisposition” at work. Indeed, this ultimate “to be or not to be” question is just lately becoming answerable in actual favor of a primal propensity to cause and give rise to complexifying life and its evolutionary ascent.

During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme?

Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life. (Abstract)

Dokholyan, Nikolay, et al. Expanding Protein Universe and Its Origin from the Biological Big Bang. Proceedings of the National Academy of Sciences. 99/14132, 2002. The microcosm of macromolecular proteins is found to exhibit a universal similarity at different levels of complexity.

With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. (14132)

Egel, Richard. Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life. Life. Online January, 2012. For a special, on-going issue of this online journal on the Origin of Life, a University of Copenhagen Biocenter researcher provides a 50 page contribution that stresses an inherent proclivity of biomatter toward such social assemblies. One might imagine that prokaryotes, eukaryotes, and precursor vesicles are moved and guided by these independent, genetic-like forces. See also the author’s chapter “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth” in Egel, et al, eds. Origins of Life (Springer, 2011 herein).

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other. (Abstract, 170)

Egel, Richard. Origins and Emergent Evolution of Life. Origins of Life and Evolution of Biospheres. Online September, 2014. The emeritus University of Copenhagen systems biologist continues his project to integrate many diverse approaches, theories, and aspects of this early occasion of proto-organic molecules, assemblies, cellular complexities, and so on into a succinct synthesis. He has schooled himself, as a long bibliography reflects, in contributions from Alexander Oparin in the 1930s to Sidney Fox and Freeman Dyson in the 1970s and 1980s to everyone today. Here the “colloid microsphere hypothesis” is revisited. A companion paper as humankind now learns altogether is The Origin and Spread of a Cooperative Replicase in a Prebiotic Chemical System by Julie Shay, Chris Huynh and Paul Higgs in the Journal of Theoretical Biology (Online September 2014).

Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life’s complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative ‘protolife’ communities, in which ‘protoplasmic continuity’ was maintained throughout a graded series of ‘proto-biofilms’, ‘protoorganisms’ and ‘protocells’ toward modern life. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms. (Abstract excerpts)

Egel, Richard, et al, eds. Origins of Life: The Primal Self-Organization. Heidelberg: Springer, 2011. With coeditors Dirk-Henner Lankenau and Armen Mulkidjanian, a large volume with these sections: Energetics of the First Life, Primeval Syntheses, Facets of an Ancestral Peptide World, and RNA Worlds – Ancestral and Contemporary. And might one wonder what kind of cosmos strives by way of us late collaborative creatures over a noosphere world, many billion years on, to reconstruct how life and mind came to be. Could such an apparent self-learning, observing, and selecting universal emergence be meant to engender the beginning of a second, intentional genesis?

If theoretical physicists can seriously entertain canonical “standard models” even for the big-bang generation of the entire universe, why cannot life scientists reach a consensus on how life has emerged and settled on this planet? Scientists are hindered by conceptual gaps between bottom-up inferences (from early Earth geological conditions) and top-down extrapolations (from modern life forms to common ancestral states). This book challenges several widely held assumptions and argues for alternative approaches instead. Primal syntheses (literally or figuratively speaking) are called for in at least five major areas. (1) The first RNA-like molecules may have been selected by solar light as being exceptionally photostable. (2) Photosynthetically active minerals and reduced phosphorus compounds could have efficiently coupled the persistent natural energy flows to the primordial metabolism. (3) Stochastic, uncoded peptides may have kick-started an ever-tightening co-evolution of proteins and nucleic acids. (4) The living fossils from the primeval RNA World thrive within modern cells. (5) From the inherently complex protocellular associations preceding the consolidation of integral genomes, eukaryotic cell organization may have evolved more naturally than simple prokaryote-like life forms. – If this book can motivate dedicated researchers to further explore the alternative mechanisms presented, it will have served its purpose well. (Publisher)

Falck, Jessica. Coarse-Graining as a Downward Causation Mechanism. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. In this Origins issue, the Santa Fe Institute professor of Collective Computation continues her project (search) to discern and express life’s apparent ascent from earlier upward forces of some kind to later, emergent realms which can then proceed in an intentional, formative way to act upon lower levels so as to facilitate higher phases going forward. As the Abstract says, a salient feature seems to be regular, iterative motifs that a knowledge-gaining evolution consistently employs. Again neural networks are availed as an iconic model.

Downward causation is the controversial idea that ‘higher’ levels of organization can causally influence behaviour at ‘lower’ levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties. I introduce a weak and strong notion of downward causation and discuss the role the strong form plays in the origins of new organizational levels. I illustrate these points with examples from the study of biological and social systems and deep neural networks. (Abstract)

Fishkis, Maya. Emergence of Self-Reproduction in Cooperative Chemical Evolution of Prebiological Molecules. Origins of Life and Evolution of Biospheres. Online September, 2010. A Canadian systems biologist proposes that the complexity sciences via agent-based modeling, aka artificial chemistry, can be extended to prebiotic material realms. The implication then arises that primordial matter appears so composed that life’s origin is a non-random probability.

Froese, Tom, et al. Horizontal Transfer of Code Fragments between Protocells can Explain the Origins of the Genetic Code without Vertical Descent. Nature Scientific Reports. 8/3532, 2018. As the Abstract notes, TF and Jorge Campos, National Autonomous University of Mexico, Kosuke Fujishima and Nathaniel Virgo, Earth-Life Science Institute, Tokyo Institute of Technology, and Daisuke Kiga, Waseda University, Tokyo achieve a robust proof of Carl Woese’s integral evolutionary synthesis (search CW, Sarkar) about how early dynamic genome cross-transmissions served life’s initial development.

Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. (Carl) Woese’s solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells, rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese’s conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone. (Abstract)

Froese, Tom, et al. Motility at the Origin of Life: Its Characterization and a Model. Artificial Life. Online February, 2013. As the Abstract notes, at our present mature stage of origins research, Tom Froese and Takashi Ikegami, University of Tokyo, and Nathaniel Virgo, Max Planck Institute for Biogeochemistry, propose to join vying replicator and metabolism options by way of an “information-compartment-metabolism first” consensus. This triad has variously arisen as a preferred definition for living systems, search this section. In regard, an organism’s propensity for movement is seen to unfold through a sequence of “being, doing, developing, and evolving” phases. It is then broached that by virtue of such a reconstructed quantification, a new animate creation may commence via human intentional continuance.

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an impoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively. (Abstract)

Fry, Iris. Are the Different Hypotheses on the Emergence of Life as Different as They Seem? Biology & Philosophy. 10/4, 1995. The Tel Aviv University philosopher and author of The Emergence of Life on Earth (Rutgers, 2000), achieves in this earlier piece, cited by Richard Egel (2012) as akin to Jeffery Wicken’s prescience, a synoptic entry into the pantheon of 20th century views. Two prime schools or persuasions can be identified. An “almost miracle camp” allows a mechanical nature wherein life is so radical as to be either divinely sparked or a capricious accident. On the other hand, a “continuity thesis or law camp” avers that biology and physics must somehow be seamlessly unified. This preferred path is seen to hold from Alexander Oparin and J. B. S. Haldane to Manfred Eigen, Marcel Florkin (biochemical orthogenesis), Sidney Fox, Harold Morowitz, Christian de Duve, onto Stuart Kauffman and others. Circa the mid 1990s, the growing evidence for non-equilibrium thermodynamics and self-organizing systems is seen to bode for this organic resolve, a synthesis beyond only lumpen mechanism or vitalism due to a special principle.

This paper was devoted to the discussion of, what I have coined, the continuity thesis. This thesis states that the development of life from matter is a gradual process to be explained on the basis of physical principles. The thesis rejects the “chance camp” notion, expressed by several scientists, that the gap between inanimate matter and life was bridged by a unique, miraculous event. I described the continuity thesis as a philosophical presupposition that unites researchers of the origin of life, and that forms the basis for the “law damp.” Surveying several models suggested in the field, e.g., replication-first and cell-first theories, I pointed out the presence of the continuity thesis in all of them, despite their differences. The assumption that life emerged from matter based on physical mechanisms of self-organization is, I claimed, not a “passive ingredient” of all these theories. When acknowledged, this assumption can serve as a guidance to devise more probable scenarios. (414)

Fry, Iris. The Emergence of Life on Earth. New Brunswick, NJ: Rutgers University Press, 2000. The Technion – Israel Institute of Technology historian of science achieves a most complete, incisive statement at the time of this broad endeavor across centuries and continents. Please then see her 2011 concise update next. The work runs from antiquity to Immanuel Kant, Louis Pasteur, Alexander Oparin, onto Manfred Eigen and Freeman Dyson, and everyone else along the way who has made a contribution. She picks up early on the field’s sorting into replication or metabolism camps, now a main divide as the 2011 paper reports. But it is her initial statement, per the quote, as a natural philosopher that poses a rarest attempt to make a stand and frame a conclusion, which academia so avoids, to admit realize an inherently organic genesis universe.

It is the claim of some biologists – fewer today than in the past – that due to the enormous complexity of even the most primitive living system, chances of its emergence are extremely small. Some of these scientists view the origin of life as a rare “happy accident,” as “almost a miracle.” Relying on a similar argument but drawing from it very different conclusions, creationists deny the natural emergence of life and uphold the necessity of a divine intervention. This book will provide scientific and philosophical arguments denying such claims. In agreement with most researchers in the origin-of-life field today, it is my contention that within the realistic confines of space and time of our universe, the emergence could not have been the result of chance. Rather it involved the working of physical and chemical mechanisms responsible for the self-organization of matter into living systems. (7)

This position, though based on several empirical considerations, is first and foremost an expression of a philosophical worldview that denies the separation of living systems and inanimate matter into two unbridgeable categories and provides an implicit guideline for origin-of-life research. (7-8)

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