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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

1. The Origins of Life

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)

Fahrenbach, Albert and Quoc Phuong Tran. Prebiotic Metabolism gets a Boost. Nature Chemsitry. 12/11, 2020. University of New South Wales biochemists introduce a special issue on the latest research with entries such as: A Metal-free Ancestral Analogue of the Krebs cycle Composed of Alpha-ketoacids by Trent Stubbs, et al. and Harnessing Chemical Free Energy for Activation and Joining of Prebiotic Building Block by Ziwei Liu, et al.

It’s generally assumed that primitive forms of cellular life arose from nucleic acids and peptides compartmentalized within vesicles, along with a non-enzymatic protometabolism. So then how could this complex chemistry arise in the first place? To address this question, prebiotic chemists have explored non-enzymatic pathways for production of these biomolecules under conditions that are consistent with an early-Earth environment, and represent various stages along the progression from non-life to protolife amd to life as we recognize it today. In this issue of Nature Chemistry, three studies demonstrate such non-enzymatic chemistry that can point towards possible mechanisms,at life’s progressive emergence. (982)

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.

Flack, 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)

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)

Fry, Iris. The Role of Natural Selection in the Origin of Life. Origins of Life and Evolution of Biospheres. 41/1, 2011. The author of a 2000 review, The Emergence of Life on Earth, noted above, can a decade on report significant advances as researchers now mostly divide into two camps or persuasions. As the quote avers, an iconic sorting has arisen between an emphasis on discrete nucleotide molecules – ‘gene-first’, or in favor of primal autocatalytic, self-organizational processes – ‘metabolism first.’ A necessity for the gene group is the formation of membrane enclosed compartments or proto-cells to house such RNA informants. This feature, posed early on by Alexander Oparin and Sidney Fox, is seen to bridge into the equally real and vital realm of dynamic “metabolic” hypercycles.

Working back then from evolutionary selection, a further sorting occurs over “digital genetic polymers” and a (prebiotic) “analog metabolic system.” From here Preparatory Metabolism gets into the act, much due to Christian de Duve, as a “protometabolic chemistry” that led to enzyme and ribozyme gene precursors. Iris Fry surveys the major players and aspects, such as Michael Russell’s hydrothermal vents, Gunther Wachtershauser’s ferrous substrates, along with the work of Leslie Orgel, Robert Shapiro, and many others. So from any worldwide vista today, viewing this common project over the years and schools, it begs a synthesis of both modes, which could then be readily seen as the paternal and maternal evidences of a cosmos to child genetic code.

It is commonly accepted among origin-of-life scientists that the emergence of life was an evolutionary process involving at one stage or other the working of natural selection. Researchers disagree, however, on the nature of the chemical infrastructure that could have formed prebiotically, enabling the evolutionary process. The division of the origin-of-life research community into `geneticists' and `metabolists' usually revolves around the issue whether the first to arise prebiotically was a genetic polymer or a primitive metabolic system. In this paper I offer an alternative classification based on the attitude to the onset of natural selection. From this perspective I add to the conventional division between gene-first and metabolism-first groups a position I call "preparatory metabolism". (Abstract, 3)

To recapitulate, according to the prevailing thesis the emergence of life, entailing the development of complex organization, depended on a process of evolution by natural selection. Fro such a gradual process to succeed, any advantage feature achieved at one state had to be handed over, or memorized from one generation to the next. This is why the unique chemical properties of nucleic acids: their ability to form specific hydrogen bonds between their bases that enable their faithful copying, are so attractive and so difficult of give up even as the earliest genetic systems. A central debate in the context of evolution and development is the question of digital versus analog information. (9)

Garcia, Adrien, et al. The Astrophysical Formation of Asymmetric Molecules and the Emergence of a Chiral Bias. Life. 9/1, 2019. Université Côte d’Azur, CNRS, France, and Aarhus University, Denmark scientists report a persistent proclivity of cosmic nature to form a rich variety of precursor complex biochemicals.

The biomolecular homochirality in living organisms has been investigated for decades, but its origin remains poorly understood. It has been shown that circular polarized light and other energy sources are capable of inducing small enantiomeric excesses in primary biomolecules such as amino acids or sugars. Since the first findings of amino acids in carbonaceous meteorites, a scenario in which essential chiral biomolecules originate in space and are delivered by celestial bodies has arisen. In this review we summarize the discoveries in amino acids, sugars, and organophosphorus compounds in meteorites, comets, and laboratory-simulated interstellar ices. (Abstract excerpt)

Goldenfeld, Nigel, et al. Universal Biology and the Statistical Mechanics of Early Life. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. A paper by University of Illinois systems biophysicists for this Origins of Life issue which delves into the rootings and continuity that organic/genetic entities ought to have with an abiding physical cosmos. As the Abstract cites, an array of material tendencies (see second quote) seem to portend precursor biomolecular forms. Again, as living systems become known to inhere natural, dynamic principles, they can better merge with a physical ground which is in turn becoming more animate and fecund.

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. (Abstract)

Homochirality describes a geometric property of some materials that are composed of chiral units. Chiral bodies are objects which are non-superposable on their mirror images. For example, left and right hands are chiral. A substance is said to be homochiral if all the constituent units have the same chiral form (enantiomer). In biology, homochirality is a common property of amino acids and sugars; almost all biologically produced chiral amino acids are L-chiral, while sugars are D-chiral. (Wikipedia)

Greenwell, Chris and Peter Coveney. Layered Double Hydroxide Minerals as Possible Prebiotic Information Storage and Transfer Compounds. Origins of Life and Evolution of Biospheres. 36/1, 2006. This substrate is suggested as the necessary suitable matrix which not only had the capacity to replicate, but could undergo discrete inherited mutations.

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