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

1. The Origins of Life

Walker, Sara Imari, et al. Evolutionary Transitions and Top-Down Causation. Adami, Christoph, et al, eds. Proceedings of Artificial Life XIII. Cambridge: MIT Press, 2012. A companion chapter by Walker, Paul Davies, with Luis Cisneros, to the “Algorithmic Origins of Life” paper above wherein “Major Transitions in Causal Structure” at the rise of organic life and of multicellularity receive further elucidation.

Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down causation -- mediated by a reversal in the flow of information from lower to higher levels of organization, to that from higher to lower levels of organization -- is a driving force for most major evolutionary transitions. We suggest that many major evolutionary transitions might therefore be marked by a transition in causal structure. We use logistic growth as a toy model for demonstrating how such a transition can drive the emergence of collective behavior in replicative systems. We then outline how this scenario may have played out in those major evolutionary transitions in which new, higher levels of organization emerged, and propose possible methods via which our hypothesis might be tested. (Abstract)

If there are in fact any universal principles common to all such major jumps in biological complexity, we should expect there to be a common mechanism driving each such transition that is not dependent on a precise series of historical (evolutionary) events. In this paper, we focus on those major evolutionary transitions leading to the emergence of new, higher level entities, which are composed of units that previously reproduced autonomously. We propose that these major transitions, corresponding to major jumps in biological complexity, are associated with information gaining causal efficacy over higher levels of organization. (284)

Walker, Sara, et al. Re-conceptualizing the Origins of Life. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. In a special issue, Sara W., Norman Packard and George Cody introduce edited proceedings from a conference by this title held at the Carnegie Institute of Science, Washington, DC in November 2015. The meeting joined a number of earlier efforts, see Conference website, to formally consider, at long last, an obvious, vital reintegration of living, evolving, biological systems with nature’s physics and chemistry. The best place would seem to be at this initial juncture. Prime aspects in need of synthesis are information, self-organization, computation, astrobiology, complexity, bioprecursors, individuality, and so on. An array of leading theorists such as Larissa Albantakis, Giulio Tononi, Christoph Adami, Leroy Cronin, Jessica Flack, David Wolpert, Caleb Scharf, James Cleaves, Paulien Hogeweg, Douglas Erwin and Robert Hazen spoke, view contents for pithy papers. The general motive is a unified explanation of a fertile inherency and ascent, a 21st century revolution indeed. But we are not there yet, the cosmos is referred to as non-living, proteins are machinery, and the like. And phenomenal peoples able to retrospectively learn all this are not factored in.

Over the last several hundred years of scientific progress, we have arrived at a deep understanding of the non-living world. We have not yet achieved an analogous, deep understanding of the living world. The origins of life is our best chance at discovering scientific laws governing life, because it marks the point of departure from the predictable physical and chemical world to the novel, history-dependent living world. This theme issue aims to explore ways to build a deeper understanding of the nature of biology, by modelling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets and bridging quantitative frameworks approaching universal aspects of life. (Abstract)

Physics and chemistry have arrived at a deep understanding of the non-living world. Can we expect to reach similar insights, integrating concepts and quantitative explanation, in biology? Life at its origin should be particularly amenable to discovery of scientific laws governing biology, since it marks the point of departure from a predictable physical/chemical world to the novel and history-dependent living world. The origin of life problem is difficult because even the simplest living cell is highly evolved from the first steps toward life, of which little direct evidence remains. The conference aims to explore ways to build a deeper understanding of the nature of biology, by modeling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets. The conference will examine the origin of life as part of a larger concern with the origins of organization, including major transitions in the living state and structure formation in complex systems science. (2015 Conference)

Walton, Craig, et al. Cosmic dust fertilization of glacial prebiotic chemistry on early Earth. arXiv:2402.12310. ETH Zurich. Cambridge University, Oxford University, University of Bergen and Open University, UK including Oliver Shorttle make a latest case that an interstellar medium suffused with biomaterials shed from exoplanets may well have showered our own planet with vital missing reagents,

Earth's surface lacks many elements considered necessary for prebiotic chemistry. In contrast, extraterrestrial rocky objects are rich in these ingredients and may have delivered them as exogenous material. Today, the flux of extraterrestrial matter to Earth is made up of fine-grained cosmic dust deposits due to the action of sedimentary processes. We study dust formation and planetary accretion to show that localized deposits could have accumulated in arid environments on early Earth. Our results challenge the widely held assumption that cosmic dust is incapable of fertilizing prebiotic chemistry. (Abstract)

Ward, Peter. Life as We Do Not Know It: The NASA Search for (and Synthesis of) Alien Life. New York: Viking, 2005. The University of Washington astrobiologist surveys first hand the current thought and findings about life’s definitions and diverse origins.

Weber, Bruce. Complex Systems Dynamics and the Emergence of Life and Natural Selection. International Conference on Complex Systems. May 16-21, 2004. The problem of life’s origin is not intractable if the independent existence of “deep natural laws and process” that drive the autocatalytic self-organization of biomolecules toward increasingly complex, replicative systems is admitted. An extended abstract can be found at www.necsi.org, click on ICCS 2004.

Weber, Bruce. Emergence of Life. Zygon. 42/4, 2007. The emeritus biochemist at California State University, following up on previous writings, contends that if a ‘complex systems view’ as an expression of nature’s innate creativity is taken, then life’s occasion and course can be appreciated as inherently teleological in kind. If fully appreciated, Weber argues, such a finding can inform a vital natural theology.

If the problem (life’s origin) is recast as one of a process of emergence of biochemistry from protobiochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to life. In such a view the emergence of life is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. (837) The emergence of life may thus be seen as an instance of the broader innate creativity of nature and consistent with a possible natural teleology. (837)

Weber, Bruce. On the Emergence of Living Systems. Biosemiotics. 2/3, 2009. Further insights by the emeritus biochemist in this new Springer journal from the International Society for Biosemiotic Studies. In addition to precursor RNA molecules and vesicular protocells, a prime factor in life’s origin is the influence of far-from-equilibrium, possibly “4th law,” thermodynamics and along with self-organizing complex dynamics. This real domain has not been fully appreciated. As a result, living systems can appear as an innate consequence of a fertile nature. Such generative propensities, in this case, are thirdly to be seen as distinguished by a meaningful, constantly communicated information.

If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. (Abstract, 343)

Weberndorfer, Gunter, et al. On the Evolution of Primitive Genetic Codes. Origins of Life and Evolution of the Biosphere. 33/4-5, 2003. The search for a simpler, primordial code that became present day genomes.

Weiss, Madeline, et al. The Last Universal Common Ancestor between Ancient Earth Chemistry and the Onset of Genetics. PLoS Genetics. August, 2018. As the collective intelligence and knowledge of anthropo sapiens grows in ability and expanse, Heinrich Heine University, Dusseldorf evolutionary molecular biologists reconstruct a deep ancestry all the way to an assumed original proto-organism critter. From this out of LUCA source, a continuous path can be drawn from earliest bio/nucleotide chemicals to multi-cellular entities and onto our global retrospective. See also Physiology, Phylogeny, and LUCA by this group (William Martin, et al) in Microbial Cell (3/12. 2016).

All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.

Williams, Tom, et al. Integrative Modeling of Gene and Genome Evolution Roots the Archaeal Tree of Life. Proceedings of the National Academy of Sciences. Online May 22, 2017. An eight member team from the UK, Hungary, Sweden, and France including Anja Spang and Martin Embley trace and discriminate a deeper, firmer grounding for living systems from earliest microbes to our collective faculty which can proceed to learn this.

The Archaea represent a primary domain of cellular life, play major roles in modern-day biogeochemical cycles, and are central to debates about the origin of eukaryotic cells. However, understanding their origins and evolutionary history is challenging because of the immense time spans involved. Here we apply a new approach that harnesses the information in patterns of gene family evolution to find the root of the archaeal tree and to resolve the metabolism of the earliest archaeal cells. Our approach robustly distinguishes between published rooting hypotheses, suggests that the first Archaea were anaerobes that may have fixed carbon via the Wood–Ljungdahl pathway, and quantifies the cumulative impact of horizontal transfer on archaeal genome evolution. (Significance)

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer. (Abstract excerpt)

Wills, Christopher and Jeffery Bada. The Spark of Life. Cambridge, MA: Perseus Books, 2000. A missing element in attempts to explain precellular life is the presence of natural selection even amongst biochemical precursors.

Wills, Peter and Charles Carter. Insuperable Problems of the Genetic Code Initially Emerging in an RNA World. Biosystems. Online September 7, 2017. The University of Auckland and UNC Chapel Hill biochemist team weighs in to say that a current origin of life fix on this primordial nucleotide is misplaced. While they are a factor, in a integral view many more facets and forces are in play such as dynamical self-assemblies. Once again, to comment, every project seems to divide into a particulate view (large colliders) and relational dynamics (neural nets) as equally in effect. An evident solution would be to join all the approaches, aspects, models into a composite synthesis as humankinder may reconstruct how Earth life came to form, arise, evolve unto our seemingly intended, worldwide retrospect. See also their concurrent paper Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding in Molecular Biology and Evolution (Online October 2017), along with a news review The End of the RNA World is Near, Biochemists Argue by Jordana Cepelewicz in Quanta Magazine (Online December 2017).

Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide•RNA world. (Abstract)

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