V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis
1. The Origins of Life
In the 1960s when I began my readings, an opaque discontinuity stood between the presence of organic Earth life and the extant physical cosmos. In the years since and especially the last decade this disconnect has been bridged by deep biological rootings in a conducive materiality, whence by turns condensed matter has come to have innate, active spontanities. Researchers have reconstructed many primordial components and sequential steps such as replicator biomolecules and protocell vesicles. Origin studies have often divided into two schools as to whether RNA replicators or metabolisms came first (Iris Fry). Three main features are now said to define living systems – a vital metabolism, bounded compartments, and informational programs. In the later 2010s as a unified understanding is being worked out, nature’s self-organizing network dynamics have additionally been factored in (Sara Walker, et al) in a guise of autocatalysis, hypercycles, autopoiesis, and so on.
Re-Conceptualizing the Origin of Life. carnegiescience.edu/events/lectures/re-conceptualizing-origin-life. A November 2015 event to be held at the Carnegie Institution for Science in Baltimore. Sara Imari Walker, as chairperson, is joined by co-organizers Chris Adami, Lee Cronin, Douglas Erwin, Piet Hut, Nathaniel Virgo, and others. The list of twenty-five speakers includes main players such as Robert Hazen, Nigel Goldenfeld, Laurie Barge, Simon DeDeo, Jessica Flack, Manfred Laubichler, and Tetsuya Yomo. Some early papers are Life as a State of Matter by Lee Cronin, and A Unified View of Emergence and Evolution by Douglas Erwin.
Physics and chemistry have arrived at a deep understanding of the non-living world. Can we expect to reach similar insights, integrating concepts and quantitative explanation, in biology? Life at its origin should be particularly amenable to discovery of scientific laws governing biology, since it marks the point of departure from a predictable physical/chemical world to the novel and history-dependent living world. The origin of life problem is difficult because even the simplest living cell is highly evolved from the first steps toward life, of which little direct evidence remains. The conference aims to explore ways to build a deeper understanding of the nature of biology, by modeling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets. The conference will examine the origin of life as part of a larger concern with the origins of organization, including major transitions in the living state and structure formation in complex systems science.
Systems Chemistry. www.esf.org/conferences/08267. An October 2008 meeting held at Maratea, Italy by the European Science Foundation as part of its Action CM0703: Systems Chemistry initiative. Noted more in the SC section, many signs are noted of life’s origins rooting into an organic nature.
Adami, Christoph. Information-Theoretic Considerations Concerning the Origin of Life. arXiv:1409.0590. The Michigan State University scientist makes an important point that in addition to the usual metabolic and/or replicative aspects, the presence of innate autocatalytic programs ought to be factored in for a complete scenario.
Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show that (under certain simplifying assumptions) the probability to discover a self-replicator by chance depends exponentially on the rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. (Abstract)
Adami, Christoph and Thomas LaBar. From Entropy to Information: Biased Typewriters and the Origin of Life. arXiv:1506.06988. A chapter in From Matter to Life: Information and Causality, edited by Sara Walker, Paul Davies and George Ellis, from Cambridge University Press in late 2015. The posting updates Adami’s 2014 paper at arXiv:1409.0590 (search) about the necessity and presence beyond metabolic components of a prescriptive source driving the occasion of early organisms. But as many entries, a tacit conflation persists about greater nature. While it is proposed that an inherent exigency toward complex life seems to exist, per the second quote, this still occurs “by chance.” In our revolutionary moment, many authors remain on the fence often mixing both sides. While “information” is seen as “the defining characteristic of life,” this quality may yet occur by statistical excesses.
The origin of life can be understood mathematically to be the origin of information that can replicate. The likelihood that entropy spontaneously becomes information can be calculated from first principles, and depends exponentially on the amount of information that is necessary for replication. Here we present evidence from numerical simulations (using the digital life chemistry "Avida") that using a biased probability distribution for the creation of monomers (the "biased typewriter") can exponentially increase the likelihood of spontaneous emergence of information from entropy. We show that this likelihood may depend on the length of the sequence that the information is embedded in, but in a non-trivial manner: there may be an optimum sequence length that maximizes the likelihood. We conclude that the likelihood of spontaneous emergence of self-replication is much more malleable than previously thought, and that the biased probability distributions of monomers that are the norm in biochemistry may significantly enhance these likelihoods. (Abstract)
Allwood, Abigail. Evidence of Life in Earth’s Oldest Rocks. Nature. 537/500, 2016. A commentary by an JPL CalTech astrobiologist on Rapid Emergence of Life Shown by Discovery of 3,700 Million Year Old Microbial Structures by Allen Nutman, et al in the same issue (537/535). Ancient rocky Greenland strata were found to have microbial fossils even in this earliest period not long after Earth’s calculated formation about 4 billion years ago. The inference is that given any minimum milieu, organic semblances will readily occur. Give life half an opportunity and it’ll will run with it.
Aono, Masashi, et al. A Principled Approach to the Origin Problem. Origins of Life and Evolution of the Biosphere. Online July, 2015. A presentation at the 2014 Earth-Life Science Symposium by Japanese astrobiologists which contends, in so many words, that in addition to a current emphasis on replicator molecules and protocell metabolisms, a further independent domain of dynamic complex self-organization, as a “fundamental requisite,” need be factored in for a complete scenario and explanation
The key issue of the origin of life is the origin of a complex system rather than the abiotic formation of various organic substances, small and large. To consider this origin problem, it is advantageous to abstract some principles from biology and statistical physics to guide our approach. Referring to these principles, we aim to construct a chemical system called protometabolism, which would be a precursor of metabolism. (Abstract)
Asche, Silke, et al. What it takes to solve the Origin(s) of Life: An integrated review of techniques. arXiv:2308.11665. We post this frontier 109 page entry by a worldwise array of OoLEN (Origin of Life Early-career Network) researchers to have it already on line. A longer review will ensue in turn.
Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number of different scientific perspectives relevant to the problem has resulted in the coexistence of diverse tools, techniques, data, and software in OoL studies. This has made communication between the disciplines relevant to the OoL extremely difficult because the interpretation of data, analyses, or standards of evidence can vary dramatically. Here, we hope to bridge this wide field of study by providing common ground via the consolidation of tools and techniques rather than positing a unifying view on how life emerges. We review the common tools and techniques that have been used significantly in OoL studies in recent years. In particular, we aim to identify which information is most relevant for comparing and integrating the results of experimental analyses into mathematical and computational models. This review aims to provide a baseline expectation and understanding of technical aspects of origins research, rather than being a primer on any particular topic. As such, it spans broadly -- from analytical chemistry to mathematical models -- and highlights areas of future work that will benefit from a multidisciplinary approach to tackling the mystery of life's origin. Ultimately, we hope to empower a new generation of OoL scientists by reviewing how they can investigate life's origin, rather than dictating how to think about the problem. (Abstract)
Ashkenasy, Gonen, et al. Emergence of Animate Behavior in Peptide-Based Ecosystems. Astrobiology. 2/4, 2003. A conference abstract notes the deep propensity of nature to give rise to increasingly complex, evolving organic systems and societies.
Living systems are comprised of autonomous self-reproducing ‘molecular ecosystems,’ defined as a collective of self-organized communities of dynamic interacting molecular species. (599)
Bada, Jeffery. How Life Began on Earth: A Status Report. Earth and Planetary Science Letters. 226/1-2, 2004. Two complementary views are joined to explain the transition from abiotic compounds to autonomous self-replicating molecules. The prebiotic soup theory proposes organic chemicals in primordial seas which underwent polymerization to produce increasingly complex macromolecules. The metabolist version brings in the impetus of autocatalytic self-sustaining reactions which foster this evolution to form information-bearing polynucleotides. In so doing, life arises from an initial RNA chemistry to its DNA/protein biochemistry phase and on to cells and organisms.
Barge, Laura, et al. Redox and pH Gradients Drive Amino Acid Synthesis in Iron Oxyhydroxide Mineral Systemss. Proceedings of the National Academy of Sciences. 116/4828, 2019. Cal Tech researchers including Michael Russell detail a probable pathway by which biochemical precursors were able to energetically come together and complexify.
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
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)