(logo) Natural Genesis (logo text)
A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

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

2. The Origins of Life

Pascal, Robert, et al. Towards an Evolutionary Theory of the Origin of Life Based on Kinetics and Thermodynamics. Open Biology. Online November, 2013. In this new Royal Society web journal, prime theorists Pascal, Institut des Biomolecules, Montpellier, France, with Addy Pross, Ben-Gurion University of the Negev, and John Sutherland, MRC Laboratory of Molecular Biology, Cambridge, combine their prebiotic chemistry and energetic drive studies to achieve a unitary synthesis of regnant living systems with a conducive cosmos. On page 2, per the quote, the issue of whether life’s occasion is an improbable rarity, or arises due to intrinsic properties is put To wit, in addition to biochemical pathways, there must be some nonequilibrium creative force, which much evidence now implicates. See also The Nature and Mathematical Basis for Material Stability in the Chemical and Biological Worlds by Pascal and Pross in the Journal of Systems Chemistry, online March 2014. This work is a significant coalescence and contribution to explain a natural organic genesis.

A sudden transition in a system from an inanimate state to the living state — defined on the basis of present day living organisms — would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages — dynamic kinetic stability (DKS) — which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred. (Abstract)

We thus face a dilemma; either Monod was right, life emerged as a consequence of an event that had almost no chance to occur during the lifetime of the universe, or the emergence of life is not a mere question of the probability of a single event, but a driving force exists—and can thus be discovered—to drive this process through its various stages. So the second possibility — the existence of some driving force governing the evolutionary process—needs to be investigated. (2)

A true understanding of biology must include knowledge of its chemical origins, and comprehending the chemical events that gave biology its foundations – cellular format, the central dogma, the genetic code – is therefore a fundamental aspect of natural science. Furthermore, understanding the way in which extant biology arose can inform the design of 'synthetic' biologies. We are interested in uncovering prebiotically plausible syntheses of the informational, catalytic and compartment–forming molecules necessary for the emergence of life. We have previously demonstrated the constitutional self-assembly of pyrimidine ribonucleotides from mixtures of simple building blocks, and we are now exploring similar 'systems chemistry' approaches to the purine ribonucleotides, and ways of assembling RNA from these ribonucleotides with regiocontrol of the internucleotide phosphodiester linkage. (JS, Chemical Origins of Molecular Biology site)

Patel, Bhavesh, et al. Common Origins of RNA, Protein and Lipid Precursors in a Cyanosulfidic Protometabolism. Nature Chemistry. 7/4, 2015. A team from John Sutherland’s (coauthor) laboratory at the MRC Laboratory of Molecular Biology, Cambridge describe for the first time how the essential classes of nucleic acids, amino acids, and lipids could have all formed at once. The work is noted as a breakthrough in an editorial A Primordial Soup that Cooks Itself, and by the Nobel chemist and origin of life researcher Jack Szostak in the journal Science (347/1298). As a result of this advance, it is said a singular environment can be identified which gave rise to diverse molecules that could store information, administer metabolism, and form bounded units, the three prime traits of life.

A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others. Here we experimentally investigate the validity of this assumption by examining the assembly of various biomolecular building blocks from prebiotically plausible intermediates and one-carbon feedstock molecules. We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant and can be accelerated by Cu(I)–Cu(II) photoredox cycling. (Abstract)

Pearce, Ben, et al. Origin of the RNA World: The Fate of Nucleobases in Warm Little Ponds. Proceedings of the National Academy of Sciences. 114/11327, 2017. Origins Institute, McMaster University and MPI Astronomy astrophysicists expand considerations of how living systems came to form on Earth, quite akin to Charles Darwin’s imagination of conducive baths. A commentary by David Deamer, Darwin’s Prescient Guess, in this issue commends their 2010s insight into life’s watery, and astral occasion.

There are currently two competing hypotheses for the site at which an RNA world emerged: hydrothermal vents in the deep ocean and warm little ponds. Because the former lacks wet and dry cycles, which are well known to promote polymerization (in this case, of nucleotides into RNA), we construct a comprehensive model for the origin of RNA in the latter sites. Our model advances the story and timeline of the RNA world by constraining the source of biomolecules, the environmental conditions, the timescales of reaction, and the emergence of first RNA polymers. (Significance)

Pearce et al. (1) have made a bold and challenging attempt to provide a quantitative estimate for the accumulation of nucleobases, like adenine, on the Hadean Earth some 4 billion y ago, before life began. Why bold? There must have been a source of organic compounds for life to begin, and they chose an extraterrestrial source—carbonaceous meteorites—rather than the geochemical source more commonly assumed in origins of life research. Why challenging? The authors chose to model the origin of life in fresh-water ponds on volcanic land masses emerging from a global ocean, in direct contrast to the current paradigm that life originated in sea water using chemical energy associated with hydrothermal vents. (Deamer, 11264)

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.

Previous   1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10  Next  [More Pages]