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

1. The Origins of Life

Trefil, James. How Life Began. Santa Fe Institute Bulletin. Winter, 2006. A substantial NSF grant has been awarded to SFI to systematically study how life first occurred, directed by Harold Morowitz. Two concurrent approaches are planned – bottom up from biomolecules and top down in a reverse-engineering fashion from cellular forms.

…what is exciting and new about this multi-pronged approach to the origin of life is its focus on the fundamental physical and chemical processes that we know were present early in the history of our planet – the processes we know must have given rise to life in the first place. It encourages us to see life not as some highly improbable accident but as a natural outcome of the workings of the physical universe. (7)

Trefil, James, et al. The Origin of Life. American Scientist. May-June, 2009. With co-authors Harold Morowitz and Eric Smith, a state of the art update noted more with quote in An Organic Universe.

Vaidya, Nilesh, et al. Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup. Chemistry & Biology. 20/2, 2013. Vaidya and Niles Lehman, Portland State University chemists, and Sara Walker, Arizona State University astrobiologist, propose that a biomolecular redundancy is at work to aid in life’s complex initiation.

Our studies take two complementary approaches, one computational and one empirical. In that regard, the results presented here are relatively uncommon. The computational approach allowed a thorough search of parameter space and concluded that catalytic recycling could lead to the selection of high-fitness genotypes, especially when rate constants were in an intermediate range. This result mirrors a common feature of biology: that reaction rates need to be attenuated to be neither too rapid nor too slow. The empirical approach, while unable to explore as many combinations as could be done on the computer, allowed an imposition of chemical reality to the recycling system. These studies show that recycling with a known recombinase of biological origin not only is facile but can lead to evolutionary self-selection. (250-251)

Vanchurin, Vitaly, et al. Thermodynamics of Evolution and the Origin of Life. arXiv:2110.15066. This is a companion paper by Vanchurin, Wolf, Koonin and Katsnelson to their Evolution as Multilevel Learning entry (2110.14602) so to provide a physical and chemical basis for life’s evident proclivity to progressively achieve an referential accumulated knowledge repository. Along the way a maximum entropy principle is seen to be involved. A Table compares thermodynamic qualities with machine learning methods and evolutionary biology, which are then fitted into a major transitions frame. Into the 2020s, these postings suggest that a composite explanatory synthesis which links many heretofore separate aspects into a single sweep from universe to us is newly possible.

We outline a phenomenological theory of evolution and the origin of life by combining classical thermodynamics with a statistical description of learning. The maximum entropy principle is employed to derive a canonical ensemble of organisms (population), their macroscopic fitness and free energy of additive fitness). We model evolution as a function of the biological temperature and potential development, This thermodynamics framework then allows major transitions in evolution such as from biomolecular stages to an ensemble organisms to be identified. As a further result, the origin of life, can be appreciated as a special case of physical phase transitions. (Abstract)

We employ the conceptual apparatus of thermodynamics to develop a phenomenological theory of evolution and of the origin of life that incorporates both equilibrium and non-equilibrium evolutionary processes within a mathematical framework of the theory of learning. The threefold correspondence is traced between the fundamental quantities of thermodynamics, the theory of learning and the theory of evolution. Under this theory, major transitions in evolution, including the origin of life, represent specific types of physical phase transitions. (Significance)

The key idea of our theoretical construction is the interplay between the entropy increase in the environment dictated by the second law of thermodynamics and the entropy decrease in evolving systems (such as organisms or populations) dictated by the second law of learning (19)

Vaneechoutte, Mario. The Scientific Origin of Life. Jerry Chandler and Gertrudis Van de Vijver, eds. Closure: Emergent Organizations and Their Dynamics. Annals of the New York Academy of Sciences, 2000. The author contends that early life and the scientific enterprise develop in the same way by corresponding molecular and linguistic codes.

Villarreal, Luis and Guenther Witzany. That is Life: Communicating RNA Networks from Viruses and Cells in Continuous Interaction. Annals of the New York Academy of Sciences. Online March, 2019. A UC Irvine biologist and a Telos–Philosophische Praxis, Austria philosopher (search each) continue their project to better explain how life’s biomolecular origins came to be. Herein a novel finesse of ribonucleic and deoxyribonucleic acids, along with viral–like modes, is seen to provide a fuller, more accurate reconstruction.

The conserved results of evolution stored in DNA must be read, transcribed, and translated via an RNA‐mediated process for the development and growth of each individual cell. Thus, all living organisms depend on these RNA‐mediated processes. The precellular evolution of RNAs was crucial to the emergence of cellular life. Here we argue that RNA networks and RNA communication can interconnect precellular and cellular levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (Abstract excerpts)

Wachtershauser, Gunter. Chemoautotrophic Origin of Life: The Iron-Sulfur World Hypothesis. Barton, Barry, et al. Geomicrobiology: Molecular and Environmental Perspectives. Dordrecht: Springer, 2010. I once heard the author, a Munich patent attorney and Ph.D. chemist, speak on the subject at a 1984 AAAS meeting in New York City. He has stayed on the case, and is now recognized for crafting a unique integration which this lead chapter summarizes. In so doing, as the quotes express, dichotomous methods of close analysis or overall synthesis, discrete molecule or relational metabolism, can be resolved. In support of an organic cosmos, significant aspects can be gleaned. By way of our human “retrodiction” some twenty “bio-elements” such as Sulfur, Magnesium, Phosphorous, Zinc, and Vanadium are found well suited, as if “preordained,” which seem to act in concert for life to arise and evolve.

But, in a mix of some terms, it begs notice that while said “mechanisms” do not augur for a deeper reality, a perceived animate “teleology” across life’s long history would imply a greater, conducive milieu, something rather than nothing. A “bio-anthropic principle” could accrue if the periodic table is appreciated as a fertile materiality for creatures and planet. In this latter regard, as other book chapters add, if a “geologic-chemical-biology” truly graces the earth, a biological universe would be inferred as well.

At the philosophical level we still are faced with the conflict between mechanistic explanations and teleological judgments. Biochemistry is providing ever more refined mechanistic explanations of the chemistry of life, down to the finest molecular details. A theory of biology, by contrast, would have to treat organisms, i.e., organized beings, as integrated wholes. Biochemistry is reductionistic and mechanistic while biology is holistic and teleological. (1) This then is our problem: to postulate a primordial organism – here termed “pioneer organism,” which is at the same time mechanistic and organizational. Central to this effort will be the notion of a “synthetic autocatalysis,” the chemical equivalent of biological reproduction, which is a chemical reaction mechanism and at the same time a functional whole, and by being synthetic it is endowed from the start with the primary vector of complexity increase. (2)

The theory of Wallace and Darwin is based on the assumption of stochastic micromutations, which suggests to most biologists that there is no inner directionality in the process of evolution. The prebiotic broth theories and notably the RNA world theories extend this stochasticity down to the very beginning of life. By contrast, the theory of a chemoautotrophic origin of live forces us to view the overall process of evolution in a fundamentally novel manner, recognizing aspects of both directionality and uniqueness in the early process of evolution. (31) These factors jointly amount to a “chemical determinism” that is bound to hold in the farthest reaches of the Universe as on Earth. (31)

Wagner, Andreas. The Large-scale Structure of Metabolic Networks: A Glimpse of Life’s Origin? Complexity. 8/1, 2003. As the ‘universal character’ of network dynamics becomes known, their activity in organizing biomolecules and protocells into organic systems brings a novel feature to explain how life began and became increasingly complex.

Walde, Peter, ed. Prebiotic Chemistry. Berlin: Springer, 2005. Volume 259 in the Topics in Current Chemistry. series. Much recent progress via theory and experiment is reported about the procession from simple amphiphilic molecules, which combine both hydrophilic and hydrophobic (water affinity or aversion) properties, to the self-assembly of membrane-bounded minimum protocells. Typical papers discuss rudimentary cell structures, chirality, and amino acid synthesis, whose authors include David Deamer and Eors Szathmary. The tacit implication is a fertile cosmos which innately complexifies to its current human reconstruction and self-witness.

Walker, Sara Imari. Origin of Life: A Problem for Physics. arXiv:1705.08073. The Arizona State University, School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science polyscholar continues her insightful syntheses. In this case a succinct entry to this active frontier which expands to a vital reunion with, and grounding in a conducive cosmos. Her project involves gathering many research strands such as RNA world, genetics first, cooperative networks, autocatalysis, self-organization, homochirality, metabolism, biochemistry, information, thermodynamics, criticality, programmable constructors, universality, and more into a composite scenario. This is an achievement in itself, but a translation to an actual “cosmic elephant” these abstractions are trying to express still awaits us.

The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins. (Abstract)

Walker, Sara Imari and Cole Mathis. Network Theory in Prebiotic Evolution. Menor-Salvan, Cesar, ed. Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. International: Springer, 2018. In a final chapter, Arizona State University astrobiology theorists expand the theoretical basis of this aboriginal advent with an intrinsic interconnective quality that joins discrete biochemicals and nucleotides into a whole dynamic living system. These node/link lineaments are also seen to foster and carry generative information. As many other fields, the “universal properties” of multiplex nets provides a formative physiology as a natural fertile materiality came to life and evolution. A further section extends the composite system onto Planetary Biospheres by way of a “network theory of biogeochemistry.”

A most challenging aspect of origins of life research is that we do not know precisely what life is. In recent years, the use of network theory has revolutionized our understanding of living systems by permitting a mathematical framework for understanding life as an emergent, collective property of many interacting entities. So far, complex systems science has seen little direct application to the origins of life, particularly in laboratory science. Yet, networks are important mathematical descriptors where the structure of interactions matters more than individual component parts – which is what we envision happens as matter transitions to life. We review notable examples of the use of network theory in prebiotic evolution, and discuss the promise of systems approaches to life’s origin. Our end goal is to develop a statistical mechanics that deals with interactions of system components (rather than parts alone) and is thus equipped to model life as an emergent phenomena. (Abstract)

Walker, Sara Imari and Paul Davies. The Algorithmic Origins of Life. Journal of the Royal Society Interface. 10/Art. 79, 2012. In this noted paper, as the extended quotes convey, Sara Walker, NASA Astrobiology Institute, and Paul Davies, cosmologist and author now at the Beyond Center for Fundamental Concepts in Science, Arizona State University, articulate how an episodic evolutionary emergence seems to be driven and tracked by way of an native informational source. A perceptive, closer to actuality, reading results but constrained by abstract computational terms used to explain. In brief, from a prior “inorganic” materiality with “trivial” forms of information then arises by degrees a replicative, instructional phase that serves to spawn animate biomolecules and vesicles. As life evolves and complexifies over eras, broadly by the major transitions scale, this informational essence attains an increasing efficacy by way of “top-down causation.” So put, the dual options of an RNA-first, “digital” onset, and “analogue” metabolic aspects, can be combined in a general software-hardware scenario. See also by Walker, Davies, and Luis Cisneros, “Evolutionary Transitions and Top-Down Causation” herein. For further takes, check the Foundational Questions Institute www.fqxi.org where winning 2012 essays by Sara Walker “Is Life Fundamental?” and “Recognizing Top-Down Causation” by George Ellis can be found. An Abstract for each is appended below.

Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation—where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies—may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. (Abstract)

In this paper, we postulate that it is the transition to context-dependent causation—mediated by the onset of information control—that is the key defining characteristic of life. We therefore identify the transition from non-life to life with a fundamental shift in the causal structure of the system, specifically a transition to a state in which algorithmic information gains direct, context-dependent, causal efficacy over matter. (2) A longstanding debate—often dubbed the chicken or the egg problem—is which came first, genetic heredity or metabolism? A conundrum arises because neither can operate without the other in contemporary life, where the duality is manifested via the genome–proteome systems. The origin of life community has therefore tended to split into two camps, loosely labelled as ‘genetics-first’ and ‘metabolism first’. In informational language, genetics and metabolism may be unified under a common conceptual framework by regarding metabolism as a form of analogue information processing, to be contrasted with the digital information of genetics. In approaching this debate, a common source of confusion stems from the fact that molecules play three distinct roles: structural, informational and chemical. In terms of computer language, in living systems chemistry corresponds to hardware and information (e.g. genetic and epigenetic) to software. The chicken-or-egg problem, as traditionally posed, thus amounts to a debate of whether analogue or digital hardware came first. (2)

An Analogue Origin for Life: In contrast to models that rely on extrapolating backward in time from extant biology, approaches that move forward from what is known of the geochemical conditions on the primitive Earth typically favour an analogue format for the first living systems. In analogue chemical systems, information is contained in a continuously variable composition of an assembly of molecules rather than in a discrete string of digital bits. ‘Metabolism-first’ scenarios for the origin of life fall within this analogue framework, positing that early life was based on autocatalytic metabolic cycles that would have been constructed in a manner akin to how analogue computer systems are cabled together to execute a specific problem-solving task. (3)

Both the traditional digital-first and analogue-first viewpoints neglect the active (algorithmic or instructional) and distributed nature of biological information. In our view, an explanation of life’s origin is fundamentally incomplete in the absence of an account of how the unique causal role played by information in living systems first emerged. In other words, we need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. (4) Characterizing the emergence of life as a shift in causal structure due to information gaining causal efficacy over matter marks the origin of life as a unique transition in the physical realm. It distinguishes non-living dynamical systems, which display trivial information processing only, from living systems which display non-trivial information processing as two logically and organizationally distinct kinds of dynamical systems. (Conclusion, 7)

A central challenge in studies of the origin of life is that we don’t know whether life is 'just' very complex chemistry, or if there is something fundamentally distinct about living matter. What’s at stake here is not merely an issue of complexification; the question of whether life is fully reducible to just the rules chemistry and physics (albeit in a very complicated manner) or is perhaps something different, forces us to assess precisely what it is that we mean by the very nature of the question of the emergence of life. I argue that if we are going to treat the origin of life as a solvable scientific inquiry (which we certainly can and should), we must assume, at least on phenomenological grounds, that life is nontrivially different from nonlife. As such, a fully reductionist picture may be inadequate to address the emergence of life. The essay focuses on how treating the unique informational narrative of living systems as more than just complex chemistry may open up new avenues for research in investigations of the origin of life. I conclude with a discussion of the potential implications of such a phenomenological framework – if successful in elucidating the emergence of life as a well-defined transition – on our interpretation of life as a fundamental natural phenomenon. (Walker FQXi Abstract)

One of the basic assumptions implicit in the way physics is usually done is that all causation flows in a bottom up fashion, from micro to macro scales. However this is wrong in many cases in biology, and in particular in the way the brain functions. Here I make the case that it is also wrong in the case of digital computers – the paradigm of mechanistic algorithmic causation - and in many cases in physics, ranging from the origin of the arrow of time to the process of quantum state preparation. I consider some examples from classical physics; from quantum physics; and the case of digital computers, and then explain why it this possible without contradicting the causal powers of the underlying micro physics. Understanding the emergence of genuine complexity out of the underlying physics depends on recognizing this kind of causation. It is a missing ingredient in present day theory; and taking it into account may help understand such mysteries as the measurement problem in quantum mechanics. (Ellis FQXi Abstract)

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