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

1. The Origins of Life

López-Díaz, Amahury Jafet , et al. The Origin of Information Handling. arXiv:2404.04374. Binghamton University, New York theorists including Hiroki Sayama and Carlos Gershenson consider and finesse another algorithm-like component as life gets its well proscribed act altogether. In regard, core guidance is provided by Howard Pattee, Juan Perez-Mercader, Chiara Marletto and Matthew Egbert. Once again something and someone seems in gestation, as long foreseen.

A major challenge when describing the origin of life is to explain how instructional information systems emerge naturally from mere molecular dynamics. Based on recent experimental results showing that chemical computations does not require a biological basis, we elucidate the origin and evolution of information processes by automata, computation and storage and transmission. In contrast to theories that assume initial complex structures, our narrative starts from early interactive self-replicators. By way of describing these primordial transitions, our metaphor can be translated to other models to explore biological phenomena at multiple spatial and temporal scales. (Excerpt)

We can imagine our planet as a big parallel, quasi-universal Turing machine capable of simulating a huge variety of functions (programs). Of course, natural resources are finite, and this is a limitation for life to emerge. Under this perspective, the first organisms on the planet could be described as some kind of automata which were running in these primitive environments. As a result of the geophysical and geochemical constraints, which we could call the primeval ecosystem language, elementary bimolecular reactions emerged. These chemical reactions are capable of recognizing regular languages, a task that does not involve counting or memory. (1, 2)

Lu, Heng, et al. Small-molecule autocatalysis drives compartment growth, competition and reproduction. Nature Chemistry. August 7, 2023. Fifteen investigators mainly at the Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, and Université PSL, Paris, France, along with Eors Szathmary (Centre for Ecological Research, Budapest) post novel insights into how a network of small-molecule autocatalytic reactions, without genetic material and enzymes, can foster and grow into protocellular compartments. The result is said to be fundamental to the experimental verification of the principles of systems chemistry and points the way forward in the study of the origin of life. So once more in a major study nature’s propensity to boot itself up through auto-spontaneous means is well quantified.

Sustained autocatalysis coupled to compartment growth and division is a key step in the origin of life, but an experimental demonstration of this phenomenon in an artificial system has proven elusive. We show that autocatalytic reactions within compartments drive osmosis and diffusion resulting in vesicle growth. Our work indicates how a combination of properties of living systems (growth, division, variation, competition, rudimentary heredity and selection) can arise from simple physical–chemical processes and may have paved the way for the emergence of evolution by natural selection. (Excerpt)

Lynn, David, et al. Origins of Chemical Evolution. Accounts of Chemical Research. 45/12, 2012. This significant topical issue is reviewed much more in Organic Universe, where several articles are also noted separately.

Lyons, Timothy, et al. Co‐evolution of early Earth environments and microbial life. Nature Reviews Microbiology. May, 2024. Akin to many current studies herein, UC Riverside, University of Alberta, Dartmouth, MIT, and University of Washington researchers can now proceed, so it seems, to recover, quantify and fill in the entire continous course from the physical ecosmos to a prokaryote milieu as it forms a viable ecosphere.

Two records of Earth history evoke the ascent of life and its co-evolving ecosystems: the geobiological and geochemical traces preserved in rocks and the evolutionary histories within genomes. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. (Excerpts)

Malaterre, Christophe, et al. The Origin of Life: What is the Question? Astrobiology. May, 2022. Astroscholars in Montreal and Paris including Philip Nghe post a somewhat procedural review as a way to identify and integrate several schools of studies from early biochemistry to synthetic biology aspects.

Markovitch, Omer, et al. Chemical Heredity as Group Selection at the Molecular Level. arXiv:1802.08024. As many similar studies nowadays, systems biochemists OM, University of Groningen with Olaf Witkowski and Nathaniel Virgo, Earth-Life Science Institute, Tokyo, proceed to root life’s multilevel evolutionary phenomena such as selection, replication, autocatalysis, and especially cooperative groups deeply and firmly into fertile, active physical matter. In one more way, the extant natural cosmos is becoming wholly organic in kind.

Many examples of cooperation exist in biology. In chemical systems however we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. The biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology. (Abstract excerpts)

Arguing that it is possible to apply biology tools on chemical systems, together with the present example help portray a route to further deepen the connections between chemistry
and biology, as much as such connections exist. For the origins of life, this supports a view of a continuous transition from the prebiotic chemistry towards present-day biology. The picture we imagine is that selection on ensembles of molecules gives rise to cooperative processes between molecules; this provides a starting point from which the complexity of biology can develop. (15)

Mathis, Cole, et al. Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation. Life. Online October, 2017. Mathis, Sanjay Ramprasad, and Sara Imari Walker, Arizona State University, with Niles Lehman, Portland State University, find that nature’s network topologies and dynamics are in effect even at this early nucleotide phase because they provide cooperative benefits. The entry is for The RNA World and the Origin of Life issue, see also Evolutionary Conflict Leads to Innovation (Paulien Hogeweg) and The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture (Paul Higgs). In further regard, see Topological and Thermodynamic Factors that Influence the Evolution of Small Networks of Catalytic RNA Species by Niles Lehman, et al in the journal RNA (23/7, 2017).

Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life. (Abstract)

Mathis, Cole, et al. Self-Organization in Computation & Chemistry: A Return to AlChemy. arXiv:2408.12137. Arizona State University, University of Michigan, and Santa Fe Institute complexity theorists including Stephanie Forrest provide a 30 year update to an original attempt to inform reaction networks with novel computational aspects. As the Abstract says, the approach can presently yield new insights into nature’s seemingly innate propensity to engender complex, viable, evolving entities.

How do complex adaptive systems such as life emerge from constituent parts? In the 1990s Walter Fontana and Leo Buss proposed an approach based on a computation model known as λ calculus whereby simple rules within in large space of possibilities could yield complex, dynamic stable biochemical reaction networks. Here, we revisit this classic model, called AlChemy, to study those results using current computing resources. Our analysis now reveals that complex, stable organizations emerge more frequently than expected, and are robust against collapse. We conclude with applications of AlChemy to self-organization in programming languages and to the origin of life.

Mathis, Cole, et al. The Emergence of Life as a First Order Phase Transition.. arXiv:1503.02776. Astrophysicists Mathis, ASU, Tanmoy Bhattacharya, SFI, and Sara Imari Walker, ASU, assume an inherently organic cosmos whereof “life is a phase of matter.” By this frontier scientific view, a non-equilibrium universe is seen to spontaneously evolve and develop by way of information and replication. Again in 2015, we move closer to a revolutionary natural genesis as its genetic narrative begins to breakthrough unto its own recognition.

We demonstrate a phase transition from non-life to life, defined as non-replicating and replicating systems respectively, and characterize some of its dynamical properties. The transition is first order and demonstrates many characteristics one might expect from a newly emergent biosphere. During the phase transition the system experiences an explosive growth in diversity, with restructuring of both the extant replicator population and the environment. The observed dynamics have a natural information-theoretic interpretation, where the probability for the transition to occur depends on the mutual information shared between replicators and environment. Through the transition, the system undergoes a series of symmetry breaking transitions whereby the information content of replicators becomes increasingly distinct from that of their environment. Thus, the replicators that nucleate the transition in the non-life phase are often not those which are ultimately selected in the life phase. We discuss the implications of these results for understanding the emergence of life, and natural selection more broadly. (Abstract)

Matsumara, Shigeyoshi, et al. Transient Compartmentalization of RNA Replicators Prevents Extinction Due to Parasites. Science. 354/1293, 2016. Ten researchers from Japan, France, Germany, and Hungary, including Eors Szathmary, Faith Coldren, and Phillippe Nghe, explain how original living systems were able to evolve in spite of contrary conditions, which the quotes detail. A natural propensity seem to be the formation of bounded cellular forms, which as primordial communities fostered their survival. See also, for example, How Life Can Arise from Chemistry by Michael Gross in Current Biology (26/R1247, 2016). A philosophical view of these many reports implies an innately conducive biocosmos from which our late collaborative quantification is meant to appear, discovery and affirm.

The evolution of molecular replicators was a critical step in the origin of life. Such replicators would have suffered from faster-replicating “molecular parasites” outcompeting the parental replicator. Compartmentalization of replicators inside protocells would have helped ameliorate the effect of parasites. Matsumura et al. show that transient compartmentalization in nonbiological materials is sufficient to tame the problem of parasite takeover. They analyzed viral replication in a droplet-based microfluidic system, which revealed that as long as there is selection for a functional replicator, the population is not overwhelmed by the faster-replicating parasite genomes. (Editorial Summary)

The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin of life. However, parasitic replicators would take over and would have prevented life from taking off unless the replicators were compartmentalized in reproducing protocells. Paradoxically, control of protocell reproduction would seem to require evolved replicators. We show here that a simpler population structure, based on cycles of transient compartmentalization (TC) and mixing of RNA replicators, is sufficient to prevent takeover by parasitic mutants. TC tends to select for ensembles of replicators that replicate at a similar rate, including a diversity of parasites that could serve as a source of opportunistic functionality. Thus, TC in natural, abiological compartments could have allowed life to take hold. (Abstract)

Mauro, Ernesto, ed.. The First Steps of Life. Wiley Online, 2023. This edited, authoritative collection is published as an ebook edition. Typical chapters are The Emergence of Life-Nurturing Conditions in the Universe by Juan Vladilo, The Role of Formamide in Prebiotic Chemistry (Raffaele Saladino), A Praise of Imperfection: Emergence and Evolution of Metabolism (Juli Pereto), and Making Biochemistry-Free Life in a Test Tube by Juan Perez-Mercader (see review). Here again, a dozen diverse chapters convey and integrate strong evidence that a veritable proof an in fact confirm a revolutionary ecosmic procreation.

Origin of Life studies have a retrospective goal: understanding nature through the comprehension of its origins and its complexities. This book proposes both an overview of this large area and an in-depth look at the opinions and results obtained by some of the active contributors. The topics occur a bottom-up order from the habitability of the universe to a meaningful prebiotic chemistry, the problem of chirality, and on through the role of minerals in biogenesis, fertile environments, cellular vesicles, replicative codes, the structure of LUCA and on their way to the evolution of information and complexity. (EDM)

Ernesto Di Mauro is a Molecular Biology professor and vice-president of the Académie Européenne Interdisciplinaire des Sciences, France. His research focuses on structural codes for complex molecular interactions in DNA topology, RNA-polymerases and DNA-topoisomerases.

McFarland, Ben. A World From Dust: How the Periodic Table Shaped Life. New York: Oxford University Press, 2016. In the main lecture hall of the new Integrated Sciences Building at UM Amherst hangs an iconic, 12’X16’ periodic table. By any stretch the millions of compounds which those 100 elements can form so that we peoples can write and observe it cannot be an accident. In this volume, a Seattle Pacific University biochemist draws on the latest advances to trace and document an oriented evolutionary universe to human scenario. Surely contingencies abound, with dead ends along the way, but it is not a random, blind passage. Akin to a physical basis, chemical structures and reactions serve to constrain and guide the course of complex organisms. By these lights, it is pointedly put that Stephen Jay Gould’s 1980s claim that earth life’s tape is so chancy it would not run again can be refuted. Here is another glimpse that a Ptolemaic pointless, accidental, nature from nothing is seriously wrong, and need be set aside for intimations of a phenomenal genesis cosmos from which entailed, intended persons can so witness, and creatively continue.

Therefore, the story of chemical life must start, as chemists do, with the periodic table itself. If life is built from the periodic table, then what is the periodic table built from? Like physics itself (and to tell the truth, this is physics itself), the answer would make Plato proud. The rows and columns of the periodic table are built from Platonic ideals, from the abstract combinations and logical consistencies of mathematics. (39) If we do find conditions that could have built life on the early Earth, say with (John) Sutherland’s light driven reactions, then that would argue against (Stephen Jay) Gould’s “tape of life” thought experiment at the molecular level. Such a result would mean that, despite a vast distance of time, early-Earth chemistry could be deduced and repeated in a modern lab. This first song on the tape of life would be rewound, replayed, and recapitulated, even 4 billion years later. Life’s most fundamental biochemistry would be explained by and predicted from the chemistry of the periodic table. (109)

Gould’s tape of life was a story that was too simple. It assumed that genetic changes were largely independent of other events, when in fact they were hemmed in by the biology of other species in the ecological network, by the chemistry available in the environment, and by the physics of energy efficiency. Gould’s assertion that the tape of life is unrepeatable requires a type of evolution that can solve hard problems only once, rather than a tape that converges on repeated and efficient solutions. Gould’s evolution is weak tea compared to a chemically driven and convergent evolution. (264)

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