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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

Phillips, Melissa Lee. The Origins Divide: Reconciling Views on How Life Began. BioScience. October, 2010. A science writer seeks to report upon and review pathways toward a synthesis of various scientists and schools that, for example, favor metabolism or replication first, come from a systems chemistry, emphasize autocatalytic processes, and so on.

Pratt, Andrew. Prebiological Evolution and the Metabolic Origins of Life. Artificial Life. 17/3, 2011. As this section reports, researchers of life’s origins tend to emphasize a certain aspect, often due to education or experience, which then beg assembly into a composite theory. In this extensive paper, a University of Canterbury biochemist cites Tibor Ganti’s chemoton to propose an early rudimentary phase driven by complex, self-organizing, autocatalytic networks. From this basis, key components such as phosphates, iron and sulfur and the “RNA-first” approach can be linked through a sorting out of when each chemical came into play.

The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. (203)

Life depends on a continuous input of energy that can fuel redox chemistry. (Redox: a reversible chemical reaction in which one reaction is an oxidation and the reverse is a reduction.) This proposal follows the hypothesis….that life emerged to exploit the intrinsic redox gradient of the earth that has existed since its origin. (205) The driving force for the emergence of life was the so-called fourth law of thermodynamics, which proposes that systems with sufficient degrees of freedom self-organize to maximize the rate of entropy production. This feature of life continues to this day….with evidence pointing to the fact that ecosystems act in an analogous fashion to maximize the rate of entropy production. (205) It is proposed that life, as we know it, emerged when a digital information subsystem evolved that transcended the information limits of simple chemical networks and allowed open-ended Darwinian evolution with natural selection. (205)

Preiner, Martina, et al. The Future of Origin of Life Research: Bridging Decades Old-Divisions. Life. 10/3, 2020. This is a conference summary by twenty five “early career” scientists as a unique retrospect of this field over its past decades, so that an integrative resolve going forward can be scoped out. The overview allows prior aspects such as prebiotic catalysis, thermal sea vents, mineral surfaces, first replicators, encapsulations, some 21 in all, to be gathered into a graphic display. A further issue has been a broad split between an RNA replicator or bounded metabolism preference, see Iris Fry 2011 herein. New synoptic pathways will involve better theories, common trends, and clever experiment. In this regard, this intentional project is a good example of an intentional shift to a coordinated, worldwide scientific pursuit.

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories—e.g. bottom-up and top-down, RNA world vs. metabolism-first—have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research. (Abstract)

Prosdocimi, Francisco, et al. The Theory of Chemical Symbiosis: A Margulian View for the Original Emergence of Biological Systems. Acta Biotheoretica. August, 2020. Universidade Federal do Rio de Janeiro, Universidad Nacional Autónoma de México, and Universidade Federal da Paraíba theoretical biologists proceed to expand the occurrence of mutually beneficial symbiotic unions, as long advocated by Lynn Margulis (1938-2011) and now well proven, deeply into life’s prior biochemical beginnings. So into 2020, along with self-organization and networking phenomena, still another innately procreative agency can be found at constant effect at each and every lively stage.

The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable of binding amino acids together. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Further, we suggest that life evolved into progenotes and cells due to new layers of symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. TCS aims to apply the Margulian view of biology into the origins of life field. (Abstract excerpt)

Current works and views about the origins of life can be understood under two great epistemological grounds: the top-down and the bottom-up approaches. In a biological driven top-down approach, researchers have been looking into living organisms in order to search for features that could be observed in Bacteria, Archaea and Eukarya cells. In a chemical driven bottom-up approach, researchers have been looking into simple molecules capable to bind together and form the main biological polymers, to wit: proteins, nucleic acids, carbohydrates and lipids. (2)

Selfishness and Altruism: In everyday life, altruism and egoism are commonly used terminologies suggesting intentionality of acts, whether of collaboration or self-preservation to the detriment of others. When taking this terminology to the molecular level, we must keep in mind not the intentionality but the effect of the action. Thus, molecular altruism must be understood as the symbiotic process of interaction between molecules, creating a self-referring process. In terms of evolutionary processes, cooperation often allows greater system stability, a selective force that facilitates continuity via replication before degradation. (6)

Ranjan, Sukrit, et al. Atmospheric Constraints on the Surface UV Environment of Mars at 3.9 Ga Relevant to Prebiotic Chemistry. arXiv:1701.01373. Harvard University astrobiologists including Dimitar Sasselov quantify how billions of years ago, organic precursors could have formed on a Mars, which was back then a conducive planet, which raises the possibility that this fertility served to seed the presence of living systems on an early Earth.

Recent findings suggest Mars may have been a clement environment for the emergence of life, and may even have compared favorably to Earth in this regard. These findings have revived interest in the hypothesis that prebiotically important molecules or even nascent life may have formed on Mars and been transferred to Earth. UV light plays a key role in prebiotic chemistry. Characterizing the early Martian surface UV environment is key to understanding how Mars compares to Earth as a venue for prebiotic chemistry. (Abstract)

Rasmussen, Steen, et al. Transitions from Nonliving to Living Matter. Science. 303/963, 2004. A report on two international workshops at the Santa Fe Institute and Los Alamos National Laboratory to review the status of artificial life and protocell research.

Although the definition of life is notoriously controversial, there is general agreement that a localized molecular assemblage should be considered alive if it continually regenerates itself, replicates itself, and is capable of evolving. (963)
Universal scaling in biological systems was discussed by Geoff West (SFI) and Woody Woodruff (LANL), who explained why regular patterns can be found, for example, between an organism’s weight and metabolic rate, regardless of whether the organism is a bacterium or an elephant. (964)

Rasmussen, Steen, et al, eds. Protocells: Bridging Nonliving and Living Matter. Cambridge: MIT Press, 2009. After years in quest of a scientific ability to create a synthetic, animate, minimal cell in a laboratory, a confluence of researchers felt the project was sufficiently robust for a book treatment. Co-editors Mark Bedau, Liaohai Chen, David Deamer, David Krakauer, Norman Packard, and Peter Stadler, along with 83 authors, flesh out its broad, fluid progress and international venue. A basic definition of life in its archetypal cellular form is closed upon, as the quote avers. In addition to the triade of physiology, genotype, and a bounded vesicle, ancillary attributes are said to be self-organization, relative autonomy, cognitive sensitivity, and a modicum of purposeful behavior. But a penchant for machine metaphors persists, since it is not addressed as to what kind of universe would engender increasingly complex and conscious entities, whom at some late, revolutionary stage might take up and over such organic creation. See also Eric Smith, et al for a typical paper that notes an endemic viability, but again in mechanical terms.

In this book a living system is operationally defined as a system that integrates three critical functionalities. First, it maintains an identity over time by localizing all its components. Second, it uses free energy from its environment to digest environmental resources in order to maintain itself, grow, and ultimately reproduce. Third, these processes are under the control of inheritable information that can be modified during reproduction. (xiii) The book generally reflects the perspective that chemical instances of such forms of life much embody the three operational functionalities in three integrated chemical systems: a metabolism that extracts usable energy and resources from the environment, genes that chemically realize informational control of living functionalities, and a container that keeps them all together. (xiii)

Ricardo, Alonso and Jack Szostak. Life on Earth. Scientific American. September, 2009. A popular article on the RNA first school, recently boosted by John Sutherland’s lab at the University of Manchester which figured out how such precursors could have initially arisen from “inanimate” substrates. But we wish to highlight an excessive use of machine metaphors to describe cellular life. This deep flaw burdens our thinking today, for the model gets everything wrong.

Every living cell, even the simplest bacterium, teems with molecular contraptions that would be the envy of any nanotechnologist. As they incessantly shake or spin or crawl around the cell, these machines cut, paste and copy genetic molecules, shuttle nutrients around or turn them into energy, build and repair cellular membranes, relay mechanical, chemical or electrical messages—the list goes on and on, and new discoveries add to it all the time. It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago. (54)

Rizzotti, Martino, ed. Defining Life. Padova, Italy: University of Padova Press, 1996. In this collection many origin of life researchers attempt to convey its essence by noting various energetic, dynamical, autopoietic, reproductive, self-organizing, and informative qualities.

Robinson, William, et al. Environmental Conditions Drive Self-Organization of Reaction Pathways in a Prebiotic Reaction Network. Nature Chemistry. 14/6, 2022. As this research field proceeds, Radboud University biochemists led by Wilhelm Huck can find and quantify novel ways that innate dynamical agencies can be seen to can generate life’s advancing, stirring intricacies. In respect, once again a robust process of a fertile mileu which organizing itself seems to be in effect. (And as peoples may now act as “ecosmic catalysts,” ought we all get a move on to “organize ourselves.”) See a note Complex Networks at Life’s Origin by Quentin Dherbassy and Kamila Muchowska in the same issue for a review.

The evolution of life from a prebiotic environment required a process of chemical evolution towards more molecular complexity. However, it is unclear how functional chemical systems evolved using only the interaction between inherent chemical reactivity and the abiotic milieu. Here we demonstrate how complex systems of chemical reactions exhibit well-defined self-organization in response to varying environmental conditions. This self-organization allows the compositional complexity of the reaction products to be controlled as a function of feedstock and catalyst availability. This certain emergence of organized systems of chemical reactions offers a potential mechanism bridge the gap between prebiotic chemicals and the origin of life. (WR Abstract)

Explaining the controlled emergence and growth of molecular complexity at life’s origins is one of prebiotic chemistry’s grand challenges. Now, it has been shown that we can observe how the self-organization of a complex carbohydrate network can be modulated by its environment. (QD & KM)

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)

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