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

1. The Origins of Life

Barge, Laura, et al. Thermodynamics, Disequilibrium, Evolution: Far from Equilibrium Geological and Chemical Considerations for Origin of Life Research. Origins of Life and Evolution of Biospheres. Online June, 2016. A 14 person team with several members from the Chemical Gardens group such as Julyan Cartwright and Michael Russell (search Barge) report on this NASA Astrobiology Institute conference, as the Abstract notes. Whereas other efforts may study biomolecular and environmental aspects, here nature’s energies which drive life’s evolutionary emergence are given their essential due. See also Leroy Cronin 2016 for another endeavor to also include intrinsic network dynamics.

The 8th meeting of the NASA Astrobiology Institute’s Thermodynamics, Disequilibrium, Evolution (TDE) Focus Group took place in November 2014 at the Earth-Life Science Institute, at the Tokyo Institute of Technology, Japan. The principal aim of this workshop was to discuss the conditions for early Earth conducive for the emergence of life, with particular regard to far-from-equilibrium geochemical systems and the thermodynamic and
chemical phenomena that are driven into being by these disequilibria. The TDE focus group seeks to understand how disequilibria are generated in geological, chemical and biological
systems, and how these disequilibria can lead to emergent phenomena, such as self-organization in bounded conditions eventuating in metabolism. Some planetary water-rock interfaces generate electrochemical disequilibria (e.g. electron, proton and/or ion gradients), and life itself is an out-of-equilibrium system that operates by harnessing such gradients across membranes. Understanding geochemical far-from-equilibrium systems and bounded self-organizing processes may be instructive in revealing some of the processes behind life’s origin. (Abstract)

Baross, John, et al. The Environmental Roots of the Origin of Life. Meadows, Victoria, et al, eds. Planetary Astrobiology. Tempe: University of Arizona Press, 2020. University of Washington, Carleton College and University of St. Andrews Earth system scientists first review of origin studies from J. B. Haldane and A. Oparin to current bottom up prebiotic chemistry and top down paleogenetics along with RNA and metabolism first views. The paper then digs deep into Hadean geologic, thermal and elemental conditions and on to early organic activities such as polymerization, compartments and cellularity. Again within the book paradigm of a whole biospherical active process, a global chemical and catalytic reactor is described. With this retrospect survey in place, the relative likelihood and biosignature detection of astrocosmic life occurrences is previewed.

The ongoing quest to understand how Earth life emerged and evolved converges on four aspects: the earliest evidence of life, geochemical properties of the environmental setting, and the life forms based on molecular and biochemical data. The fourth is how life got started which involves complex chemical and biochemical reactions that led to metabolism, genetics, and evolving organisms. One of the goals of this review is to identify the interrelationship of the Hadean environmental and geochemical conditions with critical biochemical determinants involved in the origin of life that could be helpful in our search for Earth-like life elsewhere. (Abstract excerpt)

Bartlett, Stuart and Michael Wong. Defining Lyfe in the Universe. Life. 10/4, 2020. CalTech and University of Washington astrobiologists scope out an expansive definition of living systems across a wide cosmic span so as to aid understandings of what they are and how vitality began at all. In regard, “four pillars” of autocatalysis, dissipation, homeostasis and learning are cited along with “three privileged functions” of replication, metabolism, and compartments. These features are seen to resolve the RNA first and other issues while broadening the presence of universal animation. See also Searching for Life, Mindful of Lyfe's Possibilities by the authors in the MDPI Life journal (12/6, 2022).

Life represents life as we know it; it uses the specific disequilibria and classes of components of earthly life. Life is an autocatalytic network of organometallic chemicals in aqueous solution that records and processes information about its environment and achieves dynamical order by dissipating any disequilibria. Lyfe represents any hypothetical phenomenon in the universe that fulfills these processes of the living state, regardless or components that it harnesses or uses. Lyfe maintains a low-entropy state via dissipation and disequilibria conversions, utilizes autocatalytic networks to achieve nonlinear growth and proliferation, employs homeostatic regulation to maintain stability and acquires information about its environment. (6)

Autocatalysis: The ability of a system to exhibit exponential growth of representative measures of size or population in ideal conditions. The property of autocatalysis can appear as self-catalysis, cross-catalysis, and network autocatalysis. Learning: The ability of a system to record information about its external and internal environment, process it, and carry out actions that feed back positively on its probability of surviving/proliferating. (7)

Bartlett, Stuart and Patrick Beckett. Probing Complexity: Thermodynamics and Computational Mechanics Approaches to Origins Studies. Interface Focus. October, 2019. University of Illinois and NASA Astrobiology Institute biophysicists contend that a prior emphasis on biomolecules and/or metabolism will not fully explain and that a further dimension of innate mathematical and geometric programs at work is needed. The paper courses across the titles domains, along with statistical physics and especially a regnant informational quality. Altogether in this way life’s emergent development gains an open-ended futurity. Akin to other efforts in this section, B & B’s course leads them to view the whole universe to human course as primarily a relative knowledge-gaining process. Prebiological settings can then be seen engaged in a “chemical associative learning” endeavor. Once again, as Ghosh and Kiparsky cite in Systems Chemistry, the grand scenario becomes textual in nature, seemingly made and meant for we peoples to read and write anew.

Bartolucci, Giacomo,, Giacomo, et al. Sequence self-selection by cyclic phase separation.. PNAS 120/43. 120/43, 2023. Into this year, MPI Physics of Complex Systems and Ludwigs-Maximilian-University, München researchers new describe findings about an apparent tendency for original biomolecules to form replicators by way of autocatalytic processes. As these many studies proceed, we wonder just what sufficient confluence will it take for to allow our worldwise collaborations to come to realize that an ecosmic procreativity can be seen going on by itself.

A central mystery of the molecular origin of life is the emergence of oligonucleotides, such as RNA, that can self-replicate. In our work, we theoretically study and experimentally verify a minimal capability which favored specific oligonucleotide sequences. This approach relies mainly on two physical conditions of the early Earth: cycles of phase separation into oligonucleotide-dense and dilute phases and cyclic oligonucleotide exchange with a surrounding pool. This non-equilibrium occasion could be the missing link in short-chained peptides, RNA, and DNA were recruited from a prebiotic milieu for their replicate self-assembly. Our findings may thus imply a natural way that a vital screening for auto-catalytic self-replicating oligonucleotides proceeded forth. (Significance)

Baum, David and Niles Lehman. Life’s Late Digital Revolution and Why It Matters for the Study of the Origins of Life. Life. 7/3, 2017. University of Wisconsin and Portland State University biochemists make a good case for dual computational phases in effect as they inform and propel organic evolution. Notably it is said that “life began in an analog mode” (akin our initial right brain?) from which a later digital mode could arise. An integral analog cast leads to an autocatalysis of to novel cellular forms, to be later facilitated by digital components. As a final result, a whole genome system can be better specified.

The information contained in life exists in two forms, analog and digital. Analog information is manifest mainly in the differing concentrations of chemicals that get passed from generation to generation and can vary from cell to cell. Digital information is encoded in linear polymers such as DNA and RNA, whose side chains come in discrete chemical forms. Here, we argue that the analog form of information preceded the digital. Acceptance of this dichotomy, and this progression, can help direct future studies on how life originated and initially complexified on the primordial Earth, as well as expected trajectories for other, independent origins of complex life. (Abstract)

The origin of life itself has typically been viewed as requiring at least one major transition of very low probability. Yet to explain the simultaneous origin of growing and dividing cellular compartments and a digital genetic encoding system would require two such events to occur concomitantly. Recognizing that life almost certainly went digital much after it was already evolving adaptively helps lessen the extreme improbability of its origin. Evolvable analog systems could self-organize with high probability and then permit the gradual acquisition of digital genetic encoding, first at the molecular and then at the cellular levels. We believe that separating the analog and digital steps represents a significant change of focus that can help scientists sharpen their understanding of origins of life and develop new, productive empirical research programs. (6)

Becerra, Arturo and Aaron Goldman. Introduction to the Special Issue on Early Evolution and the Last Common Ancestor. Journal of Molecular Evolution. 92/5, 2024. UNAM, Mexico and Oberlin College introduce a Special Issue: Early Evolution and the Last Common Ancestor as a latest survey of life’s ramifying procession of proto-cells and processes on their way, so it seems, to our Earthuman amazement and record. Typical entries are Protocells and the Path to Minimal Life by David Deamer, Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition by Gregory Fournier, Evolution of Cellular Organization Along the First Branches of the Tree of Life by Freya Kailing, et al and On Protein Loops, Prior Molecular States and Common Ancestors of Life by Kelsey Caetano-Anollés, et al.

The early evolution of life spans an extensive period preceding the emergence of the first eukaryotic cell. This epoch from 4.5 to 2.5 billion years ago marked the advent of many cellular attributes and the Last Common Ancestor (LCA) of all life forms. Uncovering and reconstructing elusive LCA's characteristics and genetic makeup represents a formidable pursuit in early evolution. While most scientific accounts concur that the LCA resembles contemporary prokaryotes, its precise definition, genome composition, metabolic capabilities, and ecological niche remain subjects of contentious debate. (Abstract)

Bedau, Mark and Emily Parke, eds. The Ethics of Protocells. Cambridge: MIT Press, 2009. A companion volume to Protocells: Bridging Nonliving and Living Matter whose chapters consider “Moral and Social Implications of Creating Life in the Laboratory” in an effort to get in front of, or in step with, where such probable advances, which will occur for this very reason, might take us. But without a conducive cosmology to guide why human beings should now be invited and empowered to take over, continue, and enhance animate creation, indeed to “play God,” many fraught issue persist.

Protocells are microscopic, self-organizing, evolving entities that spontaneously assemble from simple organic and inorganic materials. (1) Because protocells are living matter created from nonliving matter, they will be unlike any previous technology humans have created, and their development will take society into uncharted waters. (1-2) Protocell research strategies can fall into one of two categories: the “top down” and “bottom-up” approaches. The top-down approach involves creating new kinds of life forms by modifying existing ones. The bottom-up approach involves creating living systems from nonliving materials, or “from scratch.” (2)

Benner, Steven, et al. Setting the Stage: The History, Chemistry, and Geobiology behind RNA. Atkins, John, et al, eds. RNA Worlds: From Life’s Origins to Diversity in Gene Regulation. Cold Spring Harbor: CSH Laboratory Press, 2011. Foundation for Applied Molecular Evolution, Gainesville, FL, biochemists introduce this collection about new respect for and understanding of this ribonucleic acid macromolecule so crucial to life. Four approaches are enlisted: “paleogenetics” the gaining of inferences about past life from present structures; “prebiotic chemistry” via studies of organic and inorganic species thought to populate the early earth; “exploration” with hopes to find extraterrestrial biosamples; and “synthetic biology” experiments to create new bioversions. We quote a synopsis for the edition.

Once thought to be just a messenger that allows genetic information encoded in DNA to direct the formation of proteins, RNA (ribonucleic acid) is now known to be a highly versatile molecule that has multiple roles in cells. It can function as an enzyme, scaffold various subcellular structures, and regulate gene expression through a variety of mechanisms, as well as act as a key component of the protein synthesis and splicing machinery. Perhaps most interestingly, increasing evidence indicates that RNA preceded DNA as the hereditary material and played a crucial role in the early evolution of life on Earth. This volume reviews our understanding of two RNA worlds: the primordial RNA world before DNA, in which RNA was both information store and biocatalyst; and the contemporary RNA world, in which mRNA, tRNA, rRNA, siRNA, miRNA, and a host of other RNAs operate.

Benner, Steven, et al. When did Life Likely Emerge on Earth in an RNA-First Process?. arXiv:1908.11327. A ten person team from the Foundation for Applied Molecular Evolution, Florida (SB), UCLA, Tokyo Institute of Technology, Ludwig-Maximilians University, Munich, University of Colorado, University of South Florida and University of Rochester prepare a plausible scenario via recreations of an original biochemical and nucleotide milieu under Hadean geological to atmospheric environs some 4.6 to 4.0 billion years ago. Graphic visualizations illustrate our incredible global capability as the universe’s way of converting itself into consciously perceived description.

The widespread presence of ribonucleic acid catalysts and cofactors in Earth's biosphere today suggests that RNA was the first biopolymer to support Darwinian evolution. However, most "path-hypotheses" to generate RNA precursors require reduced nitrogen-containing compounds not made in useful amounts in the CO2-N2-H2O atmospheres of the Hadean. We review models for Earth's impact history that invoke a ~10^23 kg meteor to account for measured amounts of platinum, gold, and other siderophilic elements on the Earth and Moon. A sterilizing impactor would have reduced the atmosphere but not its mantle, opening a "window of opportunity" for RNA synthesis, a period with surface oxidized minerals that stabilize advanced RNA precursors and RNA. Surprisingly, this combination of physics, geology, and chemistry suggests a time when RNA formation was most probable, ~120 +/- 100 million years after a meteor, or ~4.36 +/- 0.1 billion years ago. (Abstract edits)

Berlinski, David. On the Origins of Life. Commentary. February, 2006. The mathematician and senior fellow at the Discovery Institute succinctly surveys the latest theories and findings. But the standard reliance on statistical chance or Darwinian explanations alone is found wanting. Rather, Harold Morowitz’s insights into “a quiet revolution in biology” to “a much more scientific law-regulated emergence of life” are advanced as a better case.

Bich, Leonardo and Luisa Damiano. Life, Autonomy and Cognition: An Organizational Approach to the Definition of the Universal Properties of Life. Origins of Life and Evolution of Biospheres. 42/5, 2012. University of the Basque Country, and University of Bergamo, Italy, biophilosophers propose that the quest for life’s elusive essence can be served by an integrative emphasis on “the traditions of Self-organization, Relational Biology, Systems Biology, Synthetic Biology, Autopoiesis and Artificial Life.” In regard, “the specific properties of life lie not in its physicochemical components, which can be found also in non living systems, but in the specific way in which these components are functionally correlated — organized — within living systems.” Four recurrent, universally organizing principles are then cited: their circular, autopoietic character, a hierarchical scale, adaptive interaction, and an increasing autonomous “self-distinction.”

This article addresses the issue of defining the universal properties of living systems through an organizational approach, according to which the distinctive properties of life lie in the functional organization which correlates its physicochemical components in living systems, and not in these components taken separately. Drawing on arguments grounded in this approach, this article identifies autonomy, with a set of related organizational properties, as universal properties of life, and includes cognition within this set. (Abstract)

In this article we address one of the most debated open questions about life and its origins on the basis of an emerging theoretical approach. We propose to call it “the organizational approach”, since it arises from a multiplicity of research trends in contemporary theoretical and experimental biology which focus their inquiries about life on the organization of living systems. Indeed, these 20th century research trends, among which we include for example the traditions of Self-organization, Relational Biology, Systems Biology, Synthetic Biology, Autopoiesis and Artificial Life, converge in a general basic research hypothesis. Synthetically: the specific properties of life lie not in its physicochemical components, which can be found also in non living systems, but in the specific way in which these components are functionally correlated — organized — within living systems. (1-2)

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