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

1. The Origins of Life

Boiteau, Laurent and Robert Pascal. Energy Sources, Self-Organization and the Origin of Life. Origins of Life and Evolution of Biospheres. 41/1, 2011. French biochemists begin by contrasting the diametric views of Jacques Monod and Christian de Duve about whether life is an accident or inevitable. They go on to contend that a positive answer accrues if nature’s physical propensity for self-organizing systems is factored in, not so often done in origin studies, which reveals a novel, endemic source of increasing supramolecular complexity.

Brack, Andre, ed. The Molecular Basis of Life. New York: Cambridge University Press, 1998. A wide-ranging survey from prebiotic compounds, genetic molecules and processes, and autocatalysis to clues from Mars and the moons of Jupiter.

Bray, Marcus, et al. Multiple Prebiotic Metals Mediate Translation. Proceedings of the National Academy of Sciences. Online November 9, 2018. By way of a “bioinorganic chemistry” which studies the role of metals in biology, Georgia Tech biochemists including Nicholas Hud and Jennifer Glass explain the importance of ferrous elements during life’s animating origin and early evolution.

Ribosomes are found in every living organism, where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ∼4 billion years ago when ecosystems were anoxic and metal-rich. The ribosome is a model system for the study of bioinorganic chemistry, owing to the many highly coordinated divalent metal cations that are essential to its function. We studied the structure, function, and cation content of the ribosome under early Earth conditions. Our results expand the roles of Fe2+ and Mn2+ in ancient and extant biochemistry as cofactors for ribosomal structure and function. (Abstract)

Bunn, Hayley, et al. Laboratory Rotational Spectroscopy Leads to the First Interstellar Detection of Deuterated Methyl Mercaptan. Astrophysical Journal Letters. 980/L13, 2025. This entry by MPI Extraterrestrial Physics, Université Paris-Saclay, University of Saskatchewan and University of Copenhagen astroscientists is an example of mid-decade sophisticated instrumentation and techniques which are able to quantify critical precursors on the evident course to viable rudiments and replicant evolution.

We report an extensive rotational spectroscopic analysis of singly deuterated methyl mercaptan (CH2DSH) using both millimeter and far-infrared synchrotron spectra to achieve a global torsional analysis of the three lowest torsional substates of this species. This is the first interstellar detection of a deuterated sulfur-bearing complex organic molecule and an important step toward understanding the chemical origin of sulfur-based prebiotics.

Cafferty, Brian, et al. Robustness, Entrainment, and Hybridization in Dissipative Molecular Networks, and the Origin of Life. Journal of the American Chemical Society. 141/20, 2019. A seven person Harvard University team led by George Whitesides describe a prebiotic propensity to generate robust complex behaviors, instead of damping them out. More evidence thus accrues for a cosmic, vital inherency to bear, form and develop in an organic fashion. A commentary on this breakthrough is Rhythm before Life by Nathaniel Wagner and Gonen Ashkenasy in Nature Chemistry (11/680, 2019).

How simple chemical reactions self-assembled into complex, robust networks at the origin of life is unknown. This general problem—self-assembly of dissipative molecular networks—is also important in understanding the growth of complexity from simplicity in molecular and biomolecular systems. Here, we describe how heterogeneity in the composition of a small network of oscillatory organic reactions can sustain (rather than stop) these oscillations, when homogeneity in their composition does not. Remarkably, a mixture of two reactants of different structure—neither of which produces oscillations individually—oscillates when combined. These results demonstrate that molecular heterogeneity present in mixtures of reactants can promote rather than suppress complex behaviors. (Abstract)

Cairns-Smith, A. G. Chemistry and the Missing Era of Evolution. Chemistry: A European Journal. 14/13, 2008. The University of Glasgow chemist updates his theory that inorganic, clay-like materials of a pre-RNA period served via a Darwinian selection to generate increasingly replicative “complex molecular machinery.”

Camprubi, Eloi, et al. The Emergence of Life. Space Science Reviews. 215/56, 2019. Eight researchers posted in the Netherlands, France, and the USA including Frances Westall and Michael Russell provide a comprehensive illustrated survey to date of both Earthly and astronomic environs such as watery moons, along with candidate RNA, geologic surface, first prokaryote and other aspects as they may have served to foster our late sentience and present reconstructive vista.

The aim of this article is to provide an overview of possible scenarios for the emergence of life, to critically assess them and to analyze whether similar processes could have been conducive to independent origins of life on the several icy moons of the Solar System. Instead of proposing an unequivocal cradle of life on Earth, we describe the different requirements that seem to be needed for the transition between non-life to life from geological, biological, and chemical perspectives in an integrative manner. Based on the conclusions extracted, we address whether the conditions for abiogenesis are/were met in any of the oceanic moons. (Abstract excerpt)

Cardoso, Silvana, et al. Chemobrionics: From Self-Assembled Material Architectures to the Origin of Life. Artificial Life. 26/3, 2020. Eleven systems biochemists from the UK, Scotland, Spain, Czech Republic, Belgium, Portugal, Hungary, and Italy including Julyan Cartwright, Leroy Cronin, and Michael Russell (search each) contribute to ever-increasing realizations of an innately fertile, life-bearing ecosmic genesis due to such innate properties. As a result, a generative inherency and consequent vital development is being found at procreative effect wherever organically conducive.

Self-organizing precipitation processes, such as chemical gardens forming biomimetic micro- and nanotubular forms, offer much potential to help explore, quantify, and understand nonequilibrium physicochemical systems with regard to life's original emergence. Advances in this area require a combination of expertise in physics, chemistry, mathematical modeling, biology, and nanoengineering, as well as in nonlinear complex systems and materials sciences, giving rise to this new synergistic discipline of chemobrionics. (Abstract excerpt)

It is today commonly accepted that self-assembly is an excellent way to form complex structures in an evolving series of small steps. Indeed, it is the foundation for much of modern nanoscience. Yet nature applies not only self-assembly, but also self-organization, which allows the stepwise building of complex patterns ultimately from simple building blocks. (316)

Cho, Christy, et al. Protocells by spontaneous reaction of cysteine with short-chain thioesters.. Nature Reviews Chemistry. October, 2024. Eight University of California, San Diego and UCLA biochemists including Irene Chen describe previously unknown procedures by which the vital appearance of distinct, multiple function cellular entities may have actually taken place.

While all forms of life are composed of cells with boundaries defined by lipid membranes, it is not known how the earliest life became compartmentalized. Here we show that the amino acid cysteine can readily react with two short-chain (C8) thioesters to form diacyl lipids, generating protocell-like membrane vesicles.. The protocells formed are compatible with functional ribozymes, suggesting that coupling of multiple short-chain precursors may have provided membrane building blocks during the early evolution of cells. (Excerpt)

Cornish-Bowden, Athel and Maria Luz Cardenas. Contrasting Theories of Life: Historical Context, Current Theories. Biosystems. November, 2019. CRNS, University of Marseilles biochemists post a 64 page synoptic review of prior conceptions about how life came to be, evolve and develop. The integral (all male) survey runs from Aristotle to Stuart Kauffman and Karl Friston, with extra time given to Manfred Eigen, Robert Rosen, and Francisco Varela. A steady implication is that some manner of autocatalytic, self-making optimization process is going on.

Most attempts to define life have been individual opinions, but here we compare all of the major current theories. We begin by asking how we know that an entity is alive, and continue by way of the contributions of La Mettrie, Burke, Leduc, Herrera, Bahadur, D’Arcy Thompson and, especially Schrödinger, whose book What is Life? is a vital starting point. All of these incorporate the idea of circularity, but fail to take account of metabolic regulation. In a final section we study the extent to which each of the current theories can aid the search for a more complete theory of life, and explain the characteristics of metabolic control analysis essential for an adequate understanding of organisms. (Abstract)

Cornish-Bowden, Athol and Maria Luz Cardenas. Self-Organization at the Origin of Life. Journal of Theoretical Biology. 252/411, 2008. Researchers at the Institut de Biologie Structurale et Microbiologie, Marseilles, France expand upon Robert Rosen’s 1990s advocacy of “invariant metabolic closure” or “metabolism-replacement systems,” akin to Maturana and Varela’s autopoiesis, to both set aside machine metaphors and stress how life can be seen to organize itself from an earliest occasion. By way of an update, the authors add that a sense of cellular and organismic “identity” ought to be included. (Autopoietic living systems likewise cite an “individuality.”)

Coveney, Peter, et al. Theory, Modelling and Simulation in Origin of Life Studies. Chemical Society Reviews. 41/5430, 2012. In a special section on “Prebiotic Chemistry,” Coveney, and Jacob Swadling, University College London computational chemists, Jonathan Wattis, University of Nottingham mathematician, and Christopher Greenwell, Durham University earth scientist review past and further orientations for this broad, significant field. Beyond vying schools of replication or metabolism, it is advised that an intrinsic self-organization ought to be equally factored in as an original driving source. By virtue of their nonlinear iterative dynamics, a novel, improved understanding of how living systems got going can accrue. Having followed this field since the 1970s, one gets a sense of a new integral phase at last coming together with these theoretical lineaments. See also in this issue, for example, Out of Fuzzy Chemistry: From Prebiotic Chemistry to Metabolic Networks by Juli Pereto.

Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the “systems chemistry” level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life. (Abstract)

It is important to begin by scotching a nugatory argument that has been articulated surprisingly often by members of the origins of life community. This argument goes along the lines that the probability of synthesizing a mere gram of the ‘one’ (or a few) particular self-reproducing sequences by a random assembly process would need more mass of substance than exists in its totality on Earth, so cannot have happened. This argument is based on the naïve notion that RNA sequences in a soup form by random synthesis (i.e. as if at equilibrium) and entirely ignores the nonlinear nature of their dynamical self-assembly. (5431) Life is indeed driven by a set of chemical processes taking place from equilibrium. (Coveney cites his prior books and articles, search) To maintain these processes, all organisms are open systems; their complexity is founded on feedback involving autocatalytic and cross catalytic molecules that assist reactions without being destroyed in the process. One metabolic or regulatory pathway may produce a molecule that accelerates other pathways which through a vast among of interlinked chemistry, may end up indirectly catalyzing the original pathway. (5431)

In this review, we have discussed chemical kinetic and molecular modeling approaches that are now throwing very considerable light on numerous challenging issues associated with the origin of life on Earth (and probably elsewhere in the Universe). The methods….span a host of length and time scales, from the quantum mechanical description of electron dynamics, through the atomistic and molecular levels which are described most often by classical mechanics, to more mesoscopic and macroscopic levels which represent the collective kinetic behavior of much larger assemblies of reacting and self-reproducing molecules. (5344)

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