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

2. The Origins of Life

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)

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)

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.

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