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

1. The Origins of Life

Rasmussen, Steen, et al. Transitions from Nonliving to Living Matter. Science. 303/963, 2004. A report on two international workshops at the Santa Fe Institute and Los Alamos National Laboratory to review the status of artificial life and protocell research.

Although the definition of life is notoriously controversial, there is general agreement that a localized molecular assemblage should be considered alive if it continually regenerates itself, replicates itself, and is capable of evolving. (963)
Universal scaling in biological systems was discussed by Geoff West (SFI) and Woody Woodruff (LANL), who explained why regular patterns can be found, for example, between an organism’s weight and metabolic rate, regardless of whether the organism is a bacterium or an elephant. (964)

Rasmussen, Steen, et al, eds. Protocells: Bridging Nonliving and Living Matter. Cambridge: MIT Press, 2009. After years in quest of a scientific ability to create a synthetic, animate, minimal cell in a laboratory, a confluence of researchers felt the project was sufficiently robust for a book treatment. Co-editors Mark Bedau, Liaohai Chen, David Deamer, David Krakauer, Norman Packard, and Peter Stadler, along with 83 authors, flesh out its broad, fluid progress and international venue. A basic definition of life in its archetypal cellular form is closed upon, as the quote avers. In addition to the triade of physiology, genotype, and a bounded vesicle, ancillary attributes are said to be self-organization, relative autonomy, cognitive sensitivity, and a modicum of purposeful behavior. But a penchant for machine metaphors persists, since it is not addressed as to what kind of universe would engender increasingly complex and conscious entities, whom at some late, revolutionary stage might take up and over such organic creation. See also Eric Smith, et al for a typical paper that notes an endemic viability, but again in mechanical terms.

In this book a living system is operationally defined as a system that integrates three critical functionalities. First, it maintains an identity over time by localizing all its components. Second, it uses free energy from its environment to digest environmental resources in order to maintain itself, grow, and ultimately reproduce. Third, these processes are under the control of inheritable information that can be modified during reproduction. (xiii) The book generally reflects the perspective that chemical instances of such forms of life much embody the three operational functionalities in three integrated chemical systems: a metabolism that extracts usable energy and resources from the environment, genes that chemically realize informational control of living functionalities, and a container that keeps them all together. (xiii)

Ricardo, Alonso and Jack Szostak. Life on Earth. Scientific American. September, 2009. A popular article on the RNA first school, recently boosted by John Sutherland’s lab at the University of Manchester which figured out how such precursors could have initially arisen from “inanimate” substrates. But we wish to highlight an excessive use of machine metaphors to describe cellular life. This deep flaw burdens our thinking today, for the model gets everything wrong.

Every living cell, even the simplest bacterium, teems with molecular contraptions that would be the envy of any nanotechnologist. As they incessantly shake or spin or crawl around the cell, these machines cut, paste and copy genetic molecules, shuttle nutrients around or turn them into energy, build and repair cellular membranes, relay mechanical, chemical or electrical messages—the list goes on and on, and new discoveries add to it all the time. It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago. (54)

Rimmer, Paul and Oliver Shorttle. A Surface Hydrothermal Source of Nitriles and Isonitriles. Life. 14/4, 2024. Cavendish Laboratory and University of Cambridge astrobiologists cite even more apparent biomaterial occasions and reasons for life’s inexorable coming together int increasingly complex, ascendant vitalities. See also Symmetry breaking and chiral amplification in prebiotic ligation reactions Min Deng, et al in Nature (626/1019, 2024).

Giant impacts can generate transient hydrogen-rich but carbon poor atmospheres. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences for a prebiotic surface hydrothermal vent scenario. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles and isonitriles relevant for biochemical precursors. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm which can participate in the non-enzymatic activation of the monomeric building blocks of life. (Excerpt)

Rizzotti, Martino, ed. Defining Life. Padova, Italy: University of Padova Press, 1996. In this collection many origin of life researchers attempt to convey its essence by noting various energetic, dynamical, autopoietic, reproductive, self-organizing, and informative qualities.

Robinson, William, et al. Environmental Conditions Drive Self-Organization of Reaction Pathways in a Prebiotic Reaction Network. Nature Chemistry. 14/6, 2022. As this research field proceeds, Radboud University biochemists led by Wilhelm Huck can find and quantify novel ways that innate dynamical agencies can be seen to can generate life’s advancing, stirring intricacies. In respect, once again a robust process of a fertile mileu which organizing itself seems to be in effect. (And as peoples may now act as “ecosmic catalysts,” ought we all get a move on to “organize ourselves.”) See a note Complex Networks at Life’s Origin by Quentin Dherbassy and Kamila Muchowska in the same issue for a review.

The evolution of life from a prebiotic environment required a process of chemical evolution towards more molecular complexity. However, it is unclear how functional chemical systems evolved using only the interaction between inherent chemical reactivity and the abiotic milieu. Here we demonstrate how complex systems of chemical reactions exhibit well-defined self-organization in response to varying environmental conditions. This self-organization allows the compositional complexity of the reaction products to be controlled as a function of feedstock and catalyst availability. This certain emergence of organized systems of chemical reactions offers a potential mechanism bridge the gap between prebiotic chemicals and the origin of life. (WR Abstract)

Explaining the controlled emergence and growth of molecular complexity at life’s origins is one of prebiotic chemistry’s grand challenges. Now, it has been shown that we can observe how the self-organization of a complex carbohydrate network can be modulated by its environment. (QD & KM)

Ross, David and David Deamer. Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis. Life. Online July, 2016. We cite this entry by an SRI International researcher and the senior UC Santa Cruz biochemist for itself, and to record the Emergence of Life: From Chemical Origins to Synthetic Biology issue, edited by Pier Luigi Luisi, which it is included in. See also therein The Role of Lipid Membranes in Life’s Origin by Deamer and Coevolution Theory of the Genetic Code by Tze-Fei Wong, et al. Some other special collections on this open site are The Landscape of the Emergence of Life, The Origin and Evolution of the Genetic Code, and The Origins and Early Evolution of RNA.

Rout, Saroj, et al. An Analysis of Nucleotide–Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.. J. Am. Chem. Soc.. 145/21915, 2023. This recent posting by fourteen ETH Zurich and Aachen University biochemists including Roland Riek contends that rather than a single prebiotic path, several companion, catalytic reactivities and replicators were merging altogether toward a long vivid traverse to our retrospective curiosity. Into these 2020s then, by virtue of ever stronger evidence like this, a sufficient veracity may have been reached so as to confirm a phenomenal presence of an ecosmic procreativity.

Interactions between RNA and proteins form the basis of many biological processes from transcription and translation to gene regulation, yet little is known about their ancient origins. We hypothesize that peptide amyloids played a role whose repetitive structure lends itself to building interfaces with other polymers. Here, we report that short RNA binds in a sequence-dependent manner to peptide amyloids. Sequence-specific RNA–peptide interactions of this kind may then provide a path to understand how genetic code replication came to be. (Excerpt)

Ruelle, David. The Origin of Life Seen From the Point of View of Non-Equilibrium Statistical Mechanics. arXiv:1701.08388. The Rutgers University mathematician has been a pioneer systems theorist since the 1960s and was co-coiner with Floris Takens (1940-2010) of the widely used phrase strange attractor. This latest note seeks to clarify earlier thermodynamic versions of this approach by noting new work by Gavin Crooks, Christopher Jarzynski and Jeremy England (search each). It then proposes a series of steps by which living systems may arise from this conducive, natural environment. An evident surmise, if to admit, is an innately conducive, life entailing, genesis cosmos.

The purpose of the present note is to attempt a more precise discussion of the above remarks by using basic ideas of non-equilibrium statistical mechanics. In view of this we have just presented some accepted or acceptable ideas on pre-biological or pre-metabolic systems. Note that one such system may occupy several distinct regions of space (just as biological species may consist of different individuals). But pre-metabolic systems have a discrete structure: we are not thinking of a homogeneous pre-biological soup. (4)

Ruiz-Mirazo, Kepa and Alvaro Moreno. Reflections on the Origin of Life: More than an “Evolutionary” Problem. Metode Science Studies. Volume 6, 2016. In this University of Valencia online journal, University of the Basque Country researchers in the Science Philosophy and Logic group and Biology Philosophy Cognition group (which AM founded) pick up on Thomas Nagel’s 2012 work Mind and Cosmos which contends that a mechanist evolution by selection alone misses a key mental, generative feature. In regard, an evident need for a prior source force is specified as nature’s physical (lawful) propensity to organize into emergent, self-sustained scales of complexity and consciousness. As a result, the article achieves one of the clearest and most strident inclusions of (essentially) a natural genetic code. See also Chemical Roots of Biological Evolution by K. Ruiz-Mirazo, et al in Open Biology (April 2017, herein).

This paper argues that the question of the origin of life cannot be explained by appealing exclusively to Darwinian evolutionary mechanisms, as many experts tend to assume, but requires a profound change in perspective. Accordingly, we highlight the fact that, in order to operate as a diversification force (and indirectly, a force for a potential increase in complexity), natural selection requires a number of conditions to be met in order for it to be possible: specifically, self-sustained and self-(re-)productive chemical organisation within a sufficiently large phenotypic space (that is, a wide range of functions). Therefore, we suggest an extension of the self-organising paradigm towards a self-(re-)productive one as an alternative to the main proposals regarding the origin of life, based on molecular populations subject to Darwinian evolution. Such a paradigm would adequately portray the specificity of the biological phenomenon (metabolic and cellular dimensions) and would be relevant before, during, and after natural selection started to operate. (Abstract)

Ruiz-Mirazo, Kepa, et al. Chemical Roots of Biological Evolution: The Origins of Life as a Process of Development of Autonomous Functional Systems. Open Biology. April, 2017. In this Royal Society journal, Spanish astrobiologists K R-M, Carlos Briones and Andres de la Escosura exercise a meld of “systems chemistry with evolutionary theory” along with innate organizational agencies to reach a complete, plausible explanation. A main theme of this extended collegial endeavor is to view life’s oriented development as facilitated by a biochemical autocatalysis toward an enhanced free individuality. As a result, an increasing self control of kinetic, energetic, creative, and spatial dimensions leads to a finesse of the major evolutionary transition scales.

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided.

Ruiz-Mirazo, Kepa, et al. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chemical Reviews. 114/1, 2014. Reviewed more Systems Chemistry, Spanish scientists extensively presage a revolutionary genesis cosmos.

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