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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

Shenhav, Barak and Doron Lancet. Prospects of a Computational Origin of Life Endeavor. Origins of Life and Evolution of the Biosphere. 34/1-2, 2004. A proposal to apply bioinformatic methods to emphasize the independent activity of “mutually catalytic networks” which served to complexify entities such as biopolymer replicator molecules.

Siebert, Charles. The Genesis Project. New York Times Sunday Magazine. September 26, 2004. The author notes that at the same time earth is beset by violent fundamentalisms, a concerted global effort, especially by NASA’s Astrobiology Institute, is revealing the true creation of life both here and in the universe. A good current summary of the collaborative enterprise.

Stankiewicz, Johanna and Lars Henning Eckardt. Chemobiogenesis 2005 and Systems Chemistry Workshop. Angewandte Chemie. 45/342, 2006. Frontier insights into an innately dynamic materiality which leads on to biological precursors are arising in central Europe as evidenced by this conference report. Leading researchers such as Peter Schuster, Eors Szathmary, Antonia Lazcano, Reza Ghadiri, and Steen Rasmussen were in attendance. A “prebiotic robustness” via the spontaneous coevolution of peptides and chemical energetics is seen to cause the emergence of homochirality (molecules of similar handedness) and nucleotides. Self-organizing catalytic networks will spawn non-Brownian self-reproducing vesicles. Such protocells can then be seen as a “supersystem” phase of a complex nonlinear chemistry. Chembiogenesis 2007 is to be held in Dubrovnik, Croatia in May.

Subramanian, Hemachander and Robert Gatenby. Evolutionary Advantage of a Broken Symmetry in Autocatalytic Polymers Explains Fundamental Properties of DNA. arXiv:1605.00748. Moffitt Cancer Center and Research Institute, Tampa, FL physicians appear to describe an inherent, primordial propensity for a fertile nature to live, evolve, and learn so that one fine day cognizant peoples might be able to self-realize, heal, save, select, and enhance.

The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and 3'-5' directionality, that are invariant across all life forms. Here we construct a simple model of hypothetical self-replicating polymers to show that asymmetric autocatalytic polymers are more successful in self-replication compared to their symmetric counterparts in the Darwinian competition for space and common substrates. This broken-symmetry property, called asymmetric cooperativity, arises when the catalytic influence of inter-strand bonds on their left and right neighbors is unequal. Asymmetric cooperativity also leads to simple evolution-based explanations for a number of other properties of DNA that include four nucleotide alphabet, three nucleotide codons, circular genomes, helicity, anti-parallel double-strand orientation, heteromolecular base-pairing, asymmetric base compositions, and palindromic instability, apart from the structural asymmetries mentioned above. (Abstract excerpts)

Living systems, uniquely in nature, acquire, store and use information autonomously. The molecular carriers of information, DNA and RNA, exhibit a number of distinctive physico-chemical properties that are optimal for information storage and transfer. This suggests that significant prebiotic evolutionary optimization preceded and resulted in RNA and DNA, and that the nucleotide properties are not simply random. (1)

Szathmary, Eors. Coevolution of Metabolic Networks and Membranes: the Scenario of Progressive Sequestration. Philosophical Transactions of the Royal Society B. 362/1781, 2007. As the extended Abstract notes, the Eotvos University, Budapest, biologist presses the view that enclosed proto-vesicles was a crucial feature of life’s original advance. Evolution is then a story of their sequential ramification via hierarchies of wholes nested within wholes, lately a worldwide humankind. See also in the same issue Tristan Rocheleau, et al. Emergence of Protocellular Growth Laws.

Many regard metabolism as one of the central phenomena (or criteria) of life. Yet, the earliest infrabiological systems may have been devoid of metabolism: such systems would have been extreme heterotrophs. We do not know what level of complexity is attainable for chemical systems without enzymatic aid. Lack of template-instructed enzymatic catalysis may put a ceiling on complexity owing to inevitable spontaneous decay and wear and tear of chemodynamical machines. Views on the origin of metabolism critically depend on the assumptions concerning the sites of synthesis and consumption of organic compounds. If these sites are different, non-enzymatic origin of autotrophy is excluded. Whether autotrophy is secondary or not, it seems that protocell boundaries may have become more selective with time, concurrent with the enzymatization of the metabolic network. Primary heterotrophy and autotrophy imply pathway innovation and retention, respectively. The idea of metabolism–membrane coevolution leads to a scenario of progressive sequestration of the emerging living system from its exterior milieu. Comparative data on current protein enzymes may shed some light on such a primeval process by analogy, since two main ideas about enzymatization (the retroevolution and the patchwork scenarios) may not necessarily be mutually exclusive and the earliest enzymatic system may have used ribozymes rather than proteins. (1781)

Szostak, Jack. Systems Chemistry on Early Earth. Nature. 459/171, 2009. A commentary on the paper “Synthesis of Activated Pyrimidine Ribonucleotides in Prebiotically Plausible Conditions” in the same issue by University of Manchester chemists Matthew Powner, Beatrice Gerland and John Sutherland which is seen as a breakthrough in being able to explain how RNA “informational polymers” first formed via phosphate reactants and catalysts. Its importance was also noted by Nicholas Wade in “Chemist Shows How RNA Can Be the Starting Point for Life” in the N. Y. Times for May 14, 2009. But even more significance might accrue because nature’s primordial chemistry then seems primed for such “spontaneous assembly,” as the quote avers with British understatement. See also a later article by Wade in the NYT for June 16, 2009 on this and other Origin of Life advances.

Our findings suggest that the prebiotic synthesis of activated pyrimidine nucleotides should be viewed as predisposed. This predisposition would have allowed the synthesis to operate on the early Earth under geochemical conditions suitable for the assembly sequence. (Powner, et al 242)

Szostak, Jack. The Narrow Road to the Deep Past: In Search of the Chemistry of the Origin of Life. Angewandte Chemie International. 56/37, 2017. The Nobel chemist (2009) at the Howard Hughes Medical Institute, Center for Computational and Integrative Biology, Boston writes a popular update on his own work and on the long project to recover and quantify how living, evolving systems came to be. A salient aspect is the appearance of membrane-bounded protocell vesicles, which then play a role in forming vital RNA polymerase replicators. Once life got going, other catalytic biochemicals could complexify toward enzymes, metabolisms all the way to we curious curators.

The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly beyond our reach. Understanding the processes that led to the chemical building blocks of biology and how these molecules self‐assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems insurmountably difficult. And yet, to my own surprise, simple experiments have revealed robust processes that could have driven the growth and division of primitive cell membranes. Even our efforts to combine replicating compartments and genetic materials into a full protocell model have moved forward in unexpected ways. Fortunately, many challenges remain, so the future in this field is brighter than ever! (Abstract)

Takeuchi, Nobuto and Paulien Hogeweg. Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization. PLoS Computational Biology. 5/10, 2010. In a follow up to their 2003 paper herein, Utrecht University bioinformaticians offer new pathways to help perceive and factor in these real, prior, endemic dynamics and resultant nested emergences for the welling evolutionary revision to complement and augment post selection.

Takeuchi, Nobuto, et al. On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems. PLoS Computational Biology. Online March 24, 2011. As the extensive Abstract explains, bioinformatic researchers Nobuto, NIH, Paulien Hogeweg, Utrecht University, and Eugene Koonin, NIH, achieve notable insights into how life’s replication process initially got its evolving act together. We resultant people are just beginning to learn the rest of the story. And might one imagine that since material nature innately appears to develop this way, it might in fact be made for this purpose?

At the core of all biological systems lies the division of labor between the storage of genetic information and its phenotypic implementation, in other words, the functional differentiation between templates (DNA) and catalysts (proteins). This fundamental property of life is believed to have been absent at the earliest stages of evolution. The RNA world hypothesis, the most realistic current scenario for the origin of life, posits that, in primordial replicating systems, RNA functioned both as template and as catalyst. How would such division of labor emerge through Darwinian evolution? We investigated the evolution of DNA-like molecules in minimal computational models of RNA replicator systems. Two models were considered: one where molecules are adsorbed on surfaces and another one where molecules are compartmentalized by dividing cellular boundaries. Both models exhibit the evolution of DNA and the ensuing division of labor, revealing the simple governing principle of these processes: DNA releases RNA from the trade-off between template and catalyst that is inevitable in the RNA world and thereby enhances the system's resistance against parasitic templates. Hence, this study offers a novel insight into the evolutionary origin of the division of labor between templates and catalysts in the RNA world. (Abstract)

Takeuchi, Nobuto, et al. The Origin of a Primordial Genome through Spontaneous Symmetry Breaking. Nature Communications. 8/250, 2017. Veteran theoretical and experimental biologists NT and Kunihiko Kaneko, University of Tokyo and Paulien Hogeweg, Utrecht University go on to perceive a whole genomic complementarity amongst replicative nucleotides in rudimentary bounded cells and autocatalytic processes. As the Abstract notes, an efficient self-organized critical poise between these dual functional stages is then becoming apparent.

The paper is included in an Early Earth Collection on this site which has Nucleoside and Nucleotide, Early Cells, and Early Earth Conditions segments. See, e.g., Considering Planetary Environments in Origin of Life Studies by Laura Barge, Life as a Guide to Prebiotic Nucleotide Synthesis by Stuart Harrison and Nick Lane, and Prebiotic Plausibility and Networks of Paradox-Resolving Independent Models by Stephen Benner.

The heredity of a cell is provided by a small number of non-catalytic templates. How did these genomes originate? We demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness.

These conflicting tendencies induce the symmetry breaking, whereby one strand of the molecules remains catalytic and increases its copy number (enzyme-like molecules), whereas the other becomes non-catalytic and decreases its copy number (genome-like molecules). This asymmetry increases the equilibrium cellular fitness by decreasing mutation pressure and increasing intracellular genetic drift. These results implicate conflicting multilevel evolution as a key cause of the origin of genetic complexity. (Abstract)

Trefil, James. How Life Began. Santa Fe Institute Bulletin. Winter, 2006. A substantial NSF grant has been awarded to SFI to systematically study how life first occurred, directed by Harold Morowitz. Two concurrent approaches are planned – bottom up from biomolecules and top down in a reverse-engineering fashion from cellular forms.

…what is exciting and new about this multi-pronged approach to the origin of life is its focus on the fundamental physical and chemical processes that we know were present early in the history of our planet – the processes we know must have given rise to life in the first place. It encourages us to see life not as some highly improbable accident but as a natural outcome of the workings of the physical universe. (7)

Trefil, James, et al. The Origin of Life. American Scientist. May-June, 2009. With co-authors Harold Morowitz and Eric Smith, a state of the art update noted more with quote in An Organic Universe.

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