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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

2. The Origin of Life

    This image of a generic original protocell is from a NASA site: www.nas.nasa.gov/Main/Features/2000/Spring/Astro_protocells_image.html. Following the accompanying definition, “protocells” presage the formation of cellular life. This image depicts its basic functions; yellow represents the capture and utilization of environmental energy, blue represents the transport of nutrients, and green represents the transport of ions.

 
     

Around 1960 when I began my readings, an opaque discontinuity stood between the presence of evolving earth life and the extant physical cosmos. In the years since and especially the last decade the dissonance has been mostly bridged. Researchers have reconstructed many of the primordial components and steps such as rudimentary genetic molecules and protocell vesicles. Three main features are now seen to define living systems – a vital metabolism, bounded compartments, and information programs. A significant advance has been to identify the universal self-organizing dynamics at work in the guise of autocatalytic networks, hypercycles, autopoiesis, and so on. By these lights the occasion of emergent life, mind and selves can be ever more deeply rooted in an increasingly fertile, amniotic universe.

Emergence in Chemical Systems 2.0. www.math.uaa.alaska.edu/~afkjm/chemicalemergence/index.php. An announcement for a conference to be held at the University of Alaska Anchorage, June 22-26, 2009 to consider the growing sense of a fertile natural materiality whose innate propensities develop into intricate and intelligent life. Leading researchers such as Robert Hazen, David Deamer, Jennifer Dunne, Steen Rasmussen, and others are confirmed speakers. The second quote for a Chemical Complexity section makes an engaging analogy with grammatical language.

The spontaneous increase of complexity, from nucleons to atoms to compounds to cells to organisms to society, is a basic property of nature. It involves the continuous creation of new entities and processes. The subject of this conference is to try to understand this drive to increasing complexity, and to creatively participate in the process. (Conference Mission)

In emergence we may deal with complex systems made of few parts that can be connected in different ways forming large number of entities that have never been fully explored. One example is the formation of chemical elements from electrons, protons and neutrons. This results in 117 elements and more than 3000 isotopes. From these, the large number of inorganic compounds is spontaneously generated in nature. From only 4 elements, C, O, N, and H, the infinite number of organic compounds may be created. These systems have much in common with languages. There, 25 letter are used to create thousands of words and from these words we may create infinite number of sentences (determined by grammar) and from these sentences and infinite number of ideas may be communicated. The common thread of emergence of complex structures may be seen in many systems. (Chemical Complexity)

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)

If the one invariant in life is information, it becomes imperative to understand the general principles by which information could arise by chance. It is generally understood that evolution, viewed as a computational process leads to an increase in information on average. (2)

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)

What is the cultural significance of the study of the origin of life? Physics as an empirical science depends on observations by us, macroeukaryotes. On the other hand, physicists wish to deduce everything we can observe from physics. Thus, a naturalistic Weltanschauung demands consistent understanding of physics and biology. Consequently, the origin study is its key ingredient. (1)

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. 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)

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.

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