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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

Hud, Nicholas and David Lynn, eds. Model Systems From Life’s Origins to a Synthetic Biology. Current Opinion in Chemical Biology. 8/627, 2004. Of especial note is Benner, Steven, et al. Is There a Common Chemical Model for Life in the Universe?. Whenever there is a thermal disequilibrium and temperatures consistent with chemical bonding, living systems of some kind will appear. Further features of a habitable environment are a solvent bath, availability of carbon, hydrogen, oxygen and nitrogen, and relative isolation.

These inevitable developments will open the field of a new synthetic science, beyond defining the origins of living systems, where the powerful principles of biology can be extended and enriched in new ways, ways that both benefit mankind and deepen our understanding of the Universe. (628)

Humphries, Courtney. Life’s Beginnings. Harvard Magazine. September/October, 2013. A Boston science writer interviews major players in this field conveniently at Harvard and environs for a succinct update. Inspired by recent exo-planet findings and implications, astronomer Dimitar Sasselov, paleontologist Andrew Knoll, Nobel laureate chemist Jack Szostak, geneticist George Church, and mathematical biologist Martin Nowak, along with MIT astrobiologist Sara Seager, offer scientific intimations of a conducive cosmos that by way of “universal principles” is innately made for life to appear and evolve.

Life requires more than just getting the right molecules together—it’s an engine propelled by evolution. Martin Nowak, professor of mathematics and of biology and a member of the (Origins of Life) initiative, says that most biologists think of evolution as a process that takes place among organisms that reproduce; evolution at the level of molecules is unfamiliar. But Nowak looks at the problem from a mathematical perspective; to him, evolution “is a well defined process that can be described as precise mathematical equations.” Accordingly, he believes that the same principles governing complex life forms must have been present at the simplest levels—otherwise scenarios for the origins of life depend on a collection of random events. (74)

Ingber, Donald. The Origin of Cellular Life. BioEssays. 22/12, 2000. Nature’s employ of a tensegrity geometry forms hierarchical cell and skeletal structures facilitated by “self-renewing functional webs through the emergence of autocatalytic sets.”

My premise in this article is that evolution is the process by which matter self-organizes in space and, thus, that the origin of life is merely one aspect of the natural evolution of the cosmos. (1160)

Jortner, Joshua. Conditions for the Emergence of Life on the Early Earth. Philosophical Transactions of the Royal Society B. 361/1877, 2006. A reflective summary of a dedicated issue on this subject. One of the most complete and up-to-date sources on the origin and ramifications of life, but within a mechanistic frame. A noteworthy aspect is an accepted recognition of intrinsic self-organizing dynamics.

The arsenal of self-organization of complex biological matter driven by information acquisition, storage, retrieval and transfer, which allows selection, adaptation, self-reproduction, evolution and metabolism may constitute many of the missing links… (1879)

Kempes, Christopher, et al. The Thermodynamic Efficiency of Computations Made in Cells Across the Range of Life. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. Kempes and Juan Perez-Mercader, Harvard University, David Wolpert, Santa Fe Institute, and Zachary Cohen, University of Illinois propose that living systems from amoebae to people ought to be seen as constantly performing computations. Such information processing involves genomes in translation making proteins, which is said to go on with inherent efficiency at a minimum energetic cost. Another way that cosmic nature seems made to foster evolutionary life can thus be entered. See also the November 2017 SFI Parallax Newsletter for a commentary on the paper.

Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer’s bound was proposed, it has been known that all computation has some thermodynamic cost. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting from the perspective of how close life has come to maximally efficient computation. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. (Abstract excerpts)

Kim, Kyung Mo and Gustavo Caetano-Anolles. Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data. Molecular Biology and Evolution. 27/7, 2009. A paper from the Evolutionary Bioinformatics Laboratory, University of Illinois, offers still another insight upon preexisting properties at work to impel life’s quickening metabolism. See also from this group: “The Origin, Evolution and Structure of the Protein World” in the Biochemical Journal (417/3, 2009).

Knoll, Andrew, et al. Life: The First Two Billion Years. Philosophical Transactions of the Royal Society B. Vol. 371/Iss. 1707, 2016. This lead paper in a New Bacteriology issue by Harvard, MIT, and Dartmouth scientists reconstructs how microbial phases successfully achieved oxygenation and photosynthesis as a crucial basis for and step to multicellular evolution.

Microfossils, stromatolites, preserved lipids and biologically informative isotopic ratios provide a substantial record of bacterial diversity and biogeochemical cycles in Proterozoic (2500–541 Ma) oceans that can be interpreted, at least broadly, in terms of present-day organisms and metabolic processes. Archean (more than 2500 Ma) sedimentary rocks add at least a billion years to the recorded history of life, with sedimentological and biogeochemical evidence for life at 3500 Ma, and possibly earlier; phylogenetic and functional details, however, are limited. Geochemistry provides a major constraint on early evolution, indicating that the first bacteria were shaped by anoxic environments, with distinct patterns of major and micronutrient availability.

Archean rocks appear to record the Earth's first iron age, with reduced Fe as the principal electron donor for photosynthesis, oxidized Fe the most abundant terminal electron acceptor for respiration, and Fe a key cofactor in proteins. With the permanent oxygenation of the atmosphere and surface ocean ca 2400 Ma, photic zone O2 limited the access of photosynthetic bacteria to electron donors other than water, while expanding the inventory of oxidants available for respiration and chemoautotrophy. Thus, halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape. (Abstract)

Koonin, Eugene and William Martin. On the Origin of Genomes and Cells within Inorganic Compartments. Trends in Genetics. 21/12, 2005. The last universal common ancestor (LUCA) is proposed to be housed in iron sulfide matrices in the vicinity of warm submarine hydrothermal vents. Initial natural selection was for molecular self-replication, which favored increasingly complex ensembles. Even at this early stage, a reciprocity between competition and “altruism” is noted with the formation of “selfish cooperatives.” But what kind of a universe does such life arise from – is it innately fertile or basically “inorganic?”

Kuhn, Hans. Is the Transition from Chemistry to Biology a Mystery? Journal of Systems Chemistry. 1/3, 2010. The emeritus director of the Max Planck Institute for Biophysical Chemistry, renowned chemist, author, and nonagenarian, in this new online edition strongly states that evolutionary life appears to be inexorably written into the physical universe, yet couches this in such machine terminology as per the long Abstract.

Today most chemists think that the answer to how life on earth emerged is still unknown. They assume a gap between chemistry and biology that is still unbridged. For chemists, understanding the origin of life requires the experimental modeling of a process that bridges this gap. They will not consider the problem solved before they are able to perform such tasks. No gap appears when we are pursuing a less ambitious goal, namely, to present a sequence of hypothetical processes that lead to an apparatus with the basic structure and fundamental feature of the genetic apparatus of biosystems but strongly simplified. The modeled apparatus has the basic machinery of living entities. Its fundamental feature is Darwinian behavior. Living individuals have the power to evolve toward ever increasing complexity and intricacy if appropriate conditions are given. The task to understand life’s origin as a rational process is closely related to the earlier attempts of the present author to design and construct supra-molecular machines.

The essence of what happens is inevitable, not accidental. Thus the emergence of life is assumed to be described by a distinct theory. Today’s great challenge is experimentally investigating chemical systems with the goal of creating artificial chemical life and the given theory provides a powerful stimulus. Life, from the perspective of physics, is the living state of matter and this view calls for a theory describing the fundamental requirements for the appearance of such a living state of matter (on the early earth and in the universe). The approach given here is an attempt in this direction. According to that approach the appearance of an entity with Darwinian behavior is instantaneous and linked with the creation of matter that carries information. Thus, Information (measured in bits according to Shannon) takes a meaning with that instant, the appearance of the first entity that evolves by multiplication, variation, selection and keeps that meaning during the entire evolution of the living (Information carrying) state of matter. (1)

Lahav, Noam. Biogenesis. New York: Oxford University Press, 1999. A proficient technical survey of the state of life’s biomolecular, genetic and protocellular origin.

Larson, Brian, et al. The Chemical Origin of Behavior is Rooted in Abiogenesis. Life. Online November, 2012. An online definition of Abiogenesis is “a natural organic phenomenon by which living organisms spontaneously arose from nonliving matter.” Coauthor Niles Lehman, Portland State University Chemistry Chair, with grad students Larson and Paul Jensen, join the mission to extend life’s regnant activity ever deeper into a conducive fertile ground. In regard, as a precursor “informational” source becomes more evident, suitable molecules then seem to make relative “choices” such as better “folding pathways” within a variable environment. Such an appreciation of an “anthropomorphic” biochemical materiality then contributes to a deep, true continuity between human and universe. Might one surmise that a dynamic cosmos of contingency and choice, a self-creating and selecting procreative genesis, could soon be in the offing?

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of choice. RNA polymers of sufficient length meet the criteria for behavioral chemistry and therefore are capable of making a choice. (Abstract)

Once Nature had the capacity to synthesize information-bearing macromolecules though, the stochasticity of the system became embodied into the “behavior” of the molecules because now there was the possibility that a molecule was the system! In essence, a system requires both a genotype and a phenotype to be able to display behavior. The “self” is now clearly defined; however, it can be a single self-replicating molecule or a network of related cooperators. Here we are using the example of RNA as the informational polymer, but the same conclusions were to apply if other polymers, or even inorganic lattices or compositional sets of macromolecules such as lipids, were the ancestral genotypes. Clearly, the advent of compartmentalization (protocellular life) would further enhance the establishment of a bounded genotype, thereby firmly entrenching behavior. (315)

Lazcano, Antonio. The Origins of Life. Natural History. February, 2006. A popular glimpse of the “heterotrophic” theory whereby “the first living entities evolved “abiotically” from nonliving organic molecules on the primitive Earth.” In this primal phase, a prebiotic soup cooked complex molecules such as amino acids. Although self-catalyzing systems are mentioned, this approach seems to labor within an inorganic, inanimate universe. Protein synthesis is seen as “machinery” leading to an RNA world.

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