V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

1. The Origins of Life

Deamer, David and Jack Szostak, eds. The Origins of Life. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2010. A premier, current collection with these five sections: Setting the Stage, Components of First Life, Primitive Systems, First Polymers, and Transition to a Microbial World. Its emphasis is more on overt entities, which are seen to arise from a prebiotic conducive chemistry. And even at this early outset, one can observe nature’s recurrent persistence to form distinct, bounded vesicles and protocells.

The advent of systems biology and synthetic biology also changed the way we think about the origin of life. At some point in the pathway leading to life, there must have been a process by which molecular systems were encapsulated in cellular compartments. This understanding is now driving serious efforts to assemble artificial cells using the tools of synthetic biology, in sense attempting to achieve a second origin of life that will tell us much about the first origin. (Editors, vii)

Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. (Schrum, Zhu, Szostak, 245)

Deamer, David, et al. The First Cell Membranes. Astrobiology. 2/4, 2003. On the tendency of organic macromolecules to self-assemble into and be encapsulated by closed membranous vesicles.

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.

Demoulin, Catherine, et al. Demoulin, Catherine, et al. Oldest thylakoids in fossil cells directly evidence oxygenic photosynthesis. Nature. 625/529, 2024. Early Life Traces & Evolution, University of Liège astrobiologists post a further example of the analytic depths that our late Earthuman intelligence can now achieve as our global genius proceeds with a whole scale retrospect description. One is moved to ask whom is this emergent personsphere prodigy ready and able to carry out this project for which our late transitory phase seems made to do. Why does an apparent self-making cocreation need to achieve its own retrospect, recorded description.

Today oxygenic photosynthesis is unique to cyanobacteria and their plastid relatives within eukaryotes. The accumulation of O2 profoundly modified the redox chemistry of the Earth and the evolution of the biosphere, with complex life. Here we report the oldest direct evidence of thylakoid membranes in a parallel-to-contorted arrangement within the cylindrical microfossils Navifusa majensis from Australia. This discovery allows the identification of early oxygenic photosynthesizers, and the importance of examining the ultrastructure of fossil cells to decipher their palaeobiology and early evolution.

Thylakoids are membrane-bound compartments inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis.

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 â€œpredispositionâ€ at work. Indeed, this ultimate â€œto be or not to beâ€ 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)

Douglas, Jordan, et al. Douglas, Jordan, et al. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Research. 52/2, 2024. Into this late year, University of Auckland and University of North Carolina paleobiologists including Peter Wills and Charles Carter (search each) are able todelve deeper to reach better quantified reasons of how and why prebiotic precursors and reactions formed biomolecular systems that could replicate themselves. And as one reads along, an impression grows that our Earthuman retrospective has indeed come upon a preordained ecosmic fertility as it proceeds to complexify, reproduce, develop and evolve.

How genetic information gained its control over chemical processes which build living cells remains to be understood. Today, the aminoacyl-tRNA synthetases (AARS) are known to foster the genetic codes in all living systems. A phylogenetic reconstruction of extant AARS genes, enhanced by modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that did not appear until later. A probable evolutionary route for an amino acid type to find a place in the code was by recruiting older, less specific AARS. (excerpt)

Edri, Rotem, et al. From Catalysis of Evolution to Evolution of Catalysis. Accounts of Chemical Research. October, 2024. Hebrew University, Jerusalem and Georgia Tech biochemists accomplish a strongest recognition to date of the integral presence of successive, self-promoting, reactive processes. As a further result (second quote), it can now be said that life’s course from chemical molecules to organic complexity and replicative evolution seems to be deeply ingrained and oriented in a procreative reality. This entry thus achieves a significant confirmation of an inherently self-making ecosmos. (In 1962 my first patent, with Ed Reisman, was for a battery/fuel cell catalyst. I have followed the literature for 62 hale years and am pleased to see this natural propensity attain its vital place.)

In this paper, we discuss a chemical framework that explores the very roots of catalysis by showing how standard catalytic activity based on chemical and physical principles can evolve into complex machineries. We provide several examples of how prebiotic catalysis can facilitate polymerization by which in biology evolved, and evolution was catalyzed. Here, we consider how prebiotic molecules such as hydroxy acids and mercaptoacids promote the formation of peptide bonds. Taken together, this account connects prebiotic catalysis and contemporary biocatalysis such that the evolution of catalysis was intertwined with chemical evolution from the very beginning. (Excerpt)

We suggest that environmental conditions on Early Earth provided the infrastructure for the straightforward evolution of chemical catalysis. Our approaches to understanding the origins of life are guided by the presumption that the transition from geo-chemistry to biology on the ancient Earth was driven by experimentally accessible processes in environments that were not exceptional or impenetrable. The origins of life did not involve inscrutable, idiosyncratic, or one-off innovations. We assume that the transition from chemistry to biology was remarkable in sum but unremarkable during any localized step or time period. (8, 9)

Egbert, Matthew, et al. Behavior and the Origin of Organisms. Origins of Life and Evolution of Biospheres. May, 2023. A nine person international effort by ME and Emily Parke, University of Auckland, Martin Hanczyc, University of Trento, Inman Harvey, University of Sussex, Nathaniel Virgo, Earth-Life Science Institute, Tokyo, Hiroki Sayama, SUNY Binghamton, Tom Froese, Okinawa Institute of Science and Technology, Alexandera Penn, University of Surrey, and Stuart Bartlett, Cal Tech (search each) draw on years of empirical and theoretic research, a good part their own, to quantify how prebiotic environs are suffused by an innately conducive viability. Typical sections include Behavior that Responds to Viability: A Common Structure Underlying the Self-Perserving Behaviors of Ante-Organisms; A Platform of Opportunity for Organismic Functional Diversity. Just as the JWST can hark back to the earliest galaxies, so a deeply rooted fertility can be found long before. Here is a prime 2023 advance as biology and physics come together within a phenomenal natural genesis. See also How Prebiotic Complexity Increases through Darwinian Evolution by Kohtoh Yukawa, et al in Current Opinion in Systems Biology (June 2023) for another deeper rooting.

It is common in origins of life research to view the first stages of life as the passive result of particular environmental conditions. This paper considers the alternative possibility: that the antecedents of life were already actively regulating their environment to maintain the conditions necessary for their own persistence. In support of this proposal, we describe ‘viability-based behaviour’: a way that simple entities can adaptively regulate their environment in response to their health, and in so doing, increase the likelihood of their survival. Drawing on empirical investigations of simple self-preserving abiological systems, we argue that these viability-based behaviours are simple enough to precede neo-Darwinian evolution. We also explain how their operation can reduce the demanding requirements that mainstream theories place upon the environment(s) in which life emerged. (Abstract)
Along the way, four ante-organism (ancestor) modes are reaction-diffusion spots, motile oil droplets, charge transportation networks, and Bénard convection cells which share a basic essential form: their activities occur in response to a systemic liveliness. To explain, each is a far-from-equilibrium dissipative structure (Nicolis and Prigogine 1989) whose ‘metabolism’ (i.e., energy-dissipating, structure-producing processes of self-construction) is distributed spatially. (10)

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)

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