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

1. The Origins of Life

Kempes, Christopher, et al. The Thermodynamic Efficiency of Computations Made in Cells Across the Range of Life. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. Kempes and Juan Perez-Mercader, Harvard University, David Wolpert, Santa Fe Institute, and Zachary Cohen, University of Illinois propose that living systems from amoebae to people ought to be seen as constantly performing computations. Such information processing involves genomes in translation making proteins, which is said to go on with inherent efficiency at a minimum energetic cost. Another way that cosmic nature seems made to foster evolutionary life can thus be entered. See also the November 2017 SFI Parallax Newsletter for a commentary on the paper.

Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer’s bound was proposed, it has been known that all computation has some thermodynamic cost. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting from the perspective of how close life has come to maximally efficient computation. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. (Abstract excerpts)

Kim, Kyung Mo and Gustavo Caetano-Anolles. Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data. Molecular Biology and Evolution. 27/7, 2009. A paper from the Evolutionary Bioinformatics Laboratory, University of Illinois, offers still another insight upon preexisting properties at work to impel life’s quickening metabolism. See also from this group: “The Origin, Evolution and Structure of the Protein World” in the Biochemical Journal (417/3, 2009).

Knoll, Andrew, et al. Life: The First Two Billion Years. Philosophical Transactions of the Royal Society B. Vol. 371/Iss. 1707, 2016. This lead paper in a New Bacteriology issue by Harvard, MIT, and Dartmouth scientists reconstructs how microbial phases successfully achieved oxygenation and photosynthesis as a crucial basis for and step to multicellular evolution.

Microfossils, stromatolites, preserved lipids and biologically informative isotopic ratios provide a substantial record of bacterial diversity and biogeochemical cycles in Proterozoic (2500–541 Ma) oceans that can be interpreted, at least broadly, in terms of present-day organisms and metabolic processes. Archean (more than 2500 Ma) sedimentary rocks add at least a billion years to the recorded history of life, with sedimentological and biogeochemical evidence for life at 3500 Ma, and possibly earlier; phylogenetic and functional details, however, are limited. Geochemistry provides a major constraint on early evolution, indicating that the first bacteria were shaped by anoxic environments, with distinct patterns of major and micronutrient availability.

Archean rocks appear to record the Earth's first iron age, with reduced Fe as the principal electron donor for photosynthesis, oxidized Fe the most abundant terminal electron acceptor for respiration, and Fe a key cofactor in proteins. With the permanent oxygenation of the atmosphere and surface ocean ca 2400 Ma, photic zone O2 limited the access of photosynthetic bacteria to electron donors other than water, while expanding the inventory of oxidants available for respiration and chemoautotrophy. Thus, halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape. (Abstract)

Kocher, Charles and Ken Dill.. The prebiotic emergence of biological evolution.. arXiv:2311.13650. Into 2023, SUNY Stony Brook biophysicists (search) post extensive theoretic and empirical quantifications which achieve a robust affirmation of natural life-bearing propensities as they seem to arise from an innate ecosmic fertility. See also a companion paper Origins of life: first came evolutionary dynamics, by the authors in QRB Discovery (March 2023, Cambridge Press open journal)

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise and from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any evolutionary dynamics. We find that cooperative autocatalysts whose reproductive rate grows as their population increases are able to cross a barrier from their initial degradation-dominated state to a growth-dominated state. (arXiv Excerpt)

The question we have raised in this paper is how prebiotic non-catalytic reactions could have transitioned to autocatalytic growth processes toward biology. Of necessity, this requires explaining the molecular bases of cooperativities and their bootstrapping origins. An explanation of origins requires a plausible microscopic model that has a basis in molecular physics and tenable grounding in prebiotic processes. The Foldcat hypothesis is found to satisfy these criteria. As random peptides grow longer, they fold, protecting their cores from degradation, and they catalyze the further growth of peptides as a plausible basis for the origins of biological evolution. (7)

When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than a molecule type, a dynamical evolutionary process is proposed which was rooted in the peptide folding process. Our models show how short random peptides can catalyse the elongation of others, powering increased folding stability and emergent autocatalysis through a disorder-to-order process. (QRD Discovery Abstract

Koonin, Eugene and William Martin. On the Origin of Genomes and Cells within Inorganic Compartments. Trends in Genetics. 21/12, 2005. The last universal common ancestor (LUCA) is proposed to be housed in iron sulfide matrices in the vicinity of warm submarine hydrothermal vents. Initial natural selection was for molecular self-replication, which favored increasingly complex ensembles. Even at this early stage, a reciprocity between competition and “altruism” is noted with the formation of “selfish cooperatives.” But what kind of a universe does such life arise from – is it innately fertile or basically “inorganic?”

Kuhn, Hans. Is the Transition from Chemistry to Biology a Mystery? Journal of Systems Chemistry. 1/3, 2010. The emeritus director of the Max Planck Institute for Biophysical Chemistry, renowned chemist, author, and nonagenarian, in this new online edition strongly states that evolutionary life appears to be inexorably written into the physical universe, yet couches this in such machine terminology as per the long Abstract.

Today most chemists think that the answer to how life on earth emerged is still unknown. They assume a gap between chemistry and biology that is still unbridged. For chemists, understanding the origin of life requires the experimental modeling of a process that bridges this gap. They will not consider the problem solved before they are able to perform such tasks. No gap appears when we are pursuing a less ambitious goal, namely, to present a sequence of hypothetical processes that lead to an apparatus with the basic structure and fundamental feature of the genetic apparatus of biosystems but strongly simplified. The modeled apparatus has the basic machinery of living entities. Its fundamental feature is Darwinian behavior. Living individuals have the power to evolve toward ever increasing complexity and intricacy if appropriate conditions are given. The task to understand life’s origin as a rational process is closely related to the earlier attempts of the present author to design and construct supra-molecular machines.

The essence of what happens is inevitable, not accidental. Thus the emergence of life is assumed to be described by a distinct theory. Today’s great challenge is experimentally investigating chemical systems with the goal of creating artificial chemical life and the given theory provides a powerful stimulus. Life, from the perspective of physics, is the living state of matter and this view calls for a theory describing the fundamental requirements for the appearance of such a living state of matter (on the early earth and in the universe). The approach given here is an attempt in this direction. According to that approach the appearance of an entity with Darwinian behavior is instantaneous and linked with the creation of matter that carries information. Thus, Information (measured in bits according to Shannon) takes a meaning with that instant, the appearance of the first entity that evolves by multiplication, variation, selection and keeps that meaning during the entire evolution of the living (Information carrying) state of matter. (1)

Kuppers, Bernd-Olaf. The Nucleation of Semantic Information in Prebiotic Matter. Current Topics in Microbiology and Immunology. Volume 392, 2016. The University of Jena natural philosopher continues his endeavor (search) to explain how a newly fertile physics, vital biochemicals, an informed, encoded biology and more can engender life’s emergent evolution. Into the mid 2010s, the presence of nonlinear, complex, “structural systems,” along with a deep propensity for an informative, genetic-like basis, are being factored into the discussion.

The analysis of the inherent context-dependence of genetic information suggests that there are evolutionary mechanisms which are independent of environmental adaptation and yet are able to push prebiotic matter towards functional complexity. In regard, the extension of information space by random prolongation of biological macromolecules must have played a decisive role in the origin of life. The extension of information space can lead to an increase in the syntactic complexity of potential information carriers, and in turn to the evolution of semantic information. The increase in the dimensionality of information space expands the number of pathways for evolutionary optimisation and thereby improves the choices that can be made by progressive evolution. In addition, there are principles of evolutionary dynamics that direct the formation of functional order in prebiotic matter. Since these principles are constitutive for the proto-semantics of genetic information, they may be regarded as the elements of the semantic code of evolution. (Abstract)

Lahav, Noam. Biogenesis. New York: Oxford University Press, 1999. A proficient technical survey of the state of life’s biomolecular, genetic and protocellular origin.

Larson, Brian, et al. The Chemical Origin of Behavior is Rooted in Abiogenesis. Life. Online November, 2012. An online definition of Abiogenesis is “a natural organic phenomenon by which living organisms spontaneously arose from nonliving matter.” Coauthor Niles Lehman, Portland State University Chemistry Chair, with grad students Larson and Paul Jensen, join the mission to extend life’s regnant activity ever deeper into a conducive fertile ground. In regard, as a precursor “informational” source becomes more evident, suitable molecules then seem to make relative “choices” such as better “folding pathways” within a variable environment. Such an appreciation of an “anthropomorphic” biochemical materiality then contributes to a deep, true continuity between human and universe. Might one surmise that a dynamic cosmos of contingency and choice, a self-creating and selecting procreative genesis, could soon be in the offing?

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of choice. RNA polymers of sufficient length meet the criteria for behavioral chemistry and therefore are capable of making a choice. (Abstract)

Once Nature had the capacity to synthesize information-bearing macromolecules though, the stochasticity of the system became embodied into the “behavior” of the molecules because now there was the possibility that a molecule was the system! In essence, a system requires both a genotype and a phenotype to be able to display behavior. The “self” is now clearly defined; however, it can be a single self-replicating molecule or a network of related cooperators. Here we are using the example of RNA as the informational polymer, but the same conclusions were to apply if other polymers, or even inorganic lattices or compositional sets of macromolecules such as lipids, were the ancestral genotypes. Clearly, the advent of compartmentalization (protocellular life) would further enhance the establishment of a bounded genotype, thereby firmly entrenching behavior. (315)

Lazcano, Antonio. The Origins of Life. Natural History. February, 2006. A popular glimpse of the “heterotrophic” theory whereby “the first living entities evolved “abiotically” from nonliving organic molecules on the primitive Earth.” In this primal phase, a prebiotic soup cooked complex molecules such as amino acids. Although self-catalyzing systems are mentioned, this approach seems to labor within an inorganic, inanimate universe. Protein synthesis is seen as “machinery” leading to an RNA world.

Letelier, Juan-Carlos, et al. From L'Homme Machine to Metabolic Closure: Steps Toward Understanding Life. Journal of Theoretical Biology. Online July, 2011. For a 50th Anniversary Review of this journal’s tenure, Universidad de Chile (Letelier), and CRNS, France (Maria Cardenas and Athel Cornish-Bowden), biologists provide a unique history of many efforts to define the phenomenon of life. Julien Offray de La Mettrie’s (1707-1751) title mechanical manifesto leads to Nicolas Rashevshy’s (1899-1972) relational biology, Robert Rosen’s (1934-1998) M,R systems, and onto cybernetics, chemotons, hypercycles, autocatalysis, autopoiesis, systems biology. From our late vantage, by a re-evaluation and synthesis of these precursors, the essence of life appears much to be a bounded metabolic organization, with a penchant for self-construction. The article wraps up with the quoted paragraph, for a definitive discovery still eludes.

As for whether biology really needs a theory of the living state, we conclude by quoting (Carl) Woese (2004, search), who wrote that “without an adequate technological advance (sequencers, etc.) the pathway of progress is blocked, and without an adequate guiding vision there is no pathway, there is no way ahead.” Of course we need the technological advances that we have seen in the past 60 years, bu we also need a guiding vision.

Lilley, David and John Sutherland. The Chemical Origins of Life and its Early Evolution. Philosophical Transactions of the Royal Society B. 366/2853, 2011. University of Dundee and MRC Laboratory of Molecular Biology researchers introduce a full issue on increasing accessible primeval seedings and stirrings of life’s earthly emergence, lately bent on reconstructing itself via our human phenomenon. In addition to Hanczyc above, “Prebiotic Chemistry: A New Modus Operandi” by Matthew Powner and John Sutherland cites an original “systems chemistry” that forms vesicular membranes, while Robert Pascal and Laurent Boiteau in “Energy Flows, Metabolism and Translation” continue their work on a thermodynamic basis for cellular compartments, information, and metabolism. And many authors and articles seem by inference to be on the verge of admitting an inherent cosmic and earthly predisposition for life to get going from nature’s deepest material recesses and ancient ages.

Can we look at contemporary biology and couple this with chemical insight to propose some plausible mechanisms for the origin of life on the planet? In what follows, we examine some promising chemical reactions by which the building blocks for nucleic acids might have been created about a billion years after the Earth formed. This could have led to self-assembling systems that were based on an all-RNA metabolism, where RNA is both catalytic and informational. (Abstract, 2853)

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