VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

2. The Origins of Life

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.

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)

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)

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)

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.”

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