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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 Origins of Life

Deamer, David. First Life and Next Life. Technology Review. May/June, 2009. The University of California, Santa Cruz “research professor of biomolecular engineering” muses that life’s earthly origin might have involved five steps: a source of organic monomers; self-assembly of compartments and protocells; polymer synthesis; evolution of catalysts; and combinatorial chemistry of cellular vesicles. As regnant life, actually its informational capacity, lately reaches self-awareness so as to pass to human agency, a radical new phase can begin of the intentional design of synthetic genomes, cells, and organic forms.

The requirement of variation within a population means that the first life forms capable of evolution could not be random mixtures of replication molecules unable to assemble into discrete entities; instead, they would be systems of interacting molecules encapsulated in something like a cell. (68)

Deamer, David. First Life: Discovering the Connections between Stars, Cells, and How Life Began. Berkeley: University of California Press, 2011. The veteran University of California at Santa Cruz biochemist offers a current survey upon an area that when I began readings some fifty years ago was an inaccessible void. Today organism and cosmos move ever closer together as a unified continuum. Typical chapters include When Did Life Begin?, Energy and Life’s Origins, Self-Assembly and Emergence, Achieving Complexity, and A Grand Simulation of Prebiotic Earth.

This pathbreaking book explores how life can begin, taking us from cosmic clouds of stardust, to volcanoes on Earth, to the modern chemistry laboratory. Seeking to understand life’s connection to the stars, David Deamer introduces astrobiology, a new scientific discipline that studies the origin and evolution of life on Earth and relates it to the birth and death of stars, planet formation, interfaces between minerals, water, and atmosphere, and the physics and chemistry of carbon compounds. Deamer argues that life began as systems of molecules that assembled into membrane-bound packages. These in turn provided an essential compartment in which more complex molecules assumed new functions required for the origin of life and the beginning of evolution. (Publisher)

What I will propose in this book is an integrated set of ideas and themes that suggest a new way to think about the origins of life. The primary themes are cycles (wet and dry), compartments (self-assembled protocells), and combinatorial chemistry(how vesicles became complex). Taken together, these themes suggest a novel approach that is guided by the principle of sufficient complexity, in which the origin of life is understood as an emergent phenomenon that occurs when water, mineral surfaces, and atmospheric gases interact with organic compounds and a source of energy. (4)

Deamer, David and Jack Szostak, eds. The Origins of Life. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2010. A premier, current collection with these five sections: Setting the Stage, Components of First Life, Primitive Systems, First Polymers, and Transition to a Microbial World. Its emphasis is more on overt entities, which are seen to arise from a prebiotic conducive chemistry. And even at this early outset, one can observe nature’s recurrent persistence to form distinct, bounded vesicles and protocells.

The advent of systems biology and synthetic biology also changed the way we think about the origin of life. At some point in the pathway leading to life, there must have been a process by which molecular systems were encapsulated in cellular compartments. This understanding is now driving serious efforts to assemble artificial cells using the tools of synthetic biology, in sense attempting to achieve a second origin of life that will tell us much about the first origin. (Editors, vii)

Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. (Schrum, Zhu, Szostak, 245)

Deamer, David, et al. The First Cell Membranes. Astrobiology. 2/4, 2003. On the tendency of organic macromolecules to self-assemble into and be encapsulated by closed membranous vesicles.

Delaye, Luis and Antonio Lazcano. Prebiological Evolution and the Physics of the Origin of Life. Physics of Life Reviews. 2/1, 2005. This new journal is available online, via Google. The authors contend that understanding life’s origin requires a synthesis of geology, chemistry, biology, astrophysics, theoretical physics, paleontology and philosophy. In this broad context, their hypothesis combines the relatively rapid appearance of chemical replicating, gene-like molecules, possibly in the vicinity of deep-sea vents, along with a consideration of intrinsic self-organizing, emergent systems.

Derr, Julien, et al. Prebiotically Plausible Mechanisms Increase Compositional Diversity of Nucleic Acid Sequences. Nucleic Acids Research. 40/10, 2012. By way of sophisticated theory and experiment, Harvard University biosystem scientists including Irene Chen and Martin Nowak, engage the deepest issue of whether the appearance of such viable replicative biomolecules happened by capriciousness or was due to some innate, independent “predisposition” at work. Indeed, this ultimate “to be or not to be” question is just lately becoming answerable in actual favor of a primal propensity to cause and give rise to complexifying life and its evolutionary ascent.

During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme?

Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life. (Abstract)

Dokholyan, Nikolay, et al. Expanding Protein Universe and Its Origin from the Biological Big Bang. Proceedings of the National Academy of Sciences. 99/14132, 2002. The microcosm of macromolecular proteins is found to exhibit a universal similarity at different levels of complexity.

With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. (14132)

Egel, Richard. Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life. Life. Online January, 2012. For a special, on-going issue of this online journal on the Origin of Life, a University of Copenhagen Biocenter researcher provides a 50 page contribution that stresses an inherent proclivity of biomatter toward such social assemblies. One might imagine that prokaryotes, eukaryotes, and precursor vesicles are moved and guided by these independent, genetic-like forces. See also the author’s chapter “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth” in Egel, et al, eds. Origins of Life (Springer, 2011 herein).

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other. (Abstract, 170)

Egel, Richard. Origins and Emergent Evolution of Life. Origins of Life and Evolution of Biospheres. Online September, 2014. The emeritus University of Copenhagen systems biologist continues his project to integrate many diverse approaches, theories, and aspects of this early occasion of proto-organic molecules, assemblies, cellular complexities, and so on into a succinct synthesis. He has schooled himself, as a long bibliography reflects, in contributions from Alexander Oparin in the 1930s to Sidney Fox and Freeman Dyson in the 1970s and 1980s to everyone today. Here the “colloid microsphere hypothesis” is revisited. A companion paper as humankind now learns altogether is The Origin and Spread of a Cooperative Replicase in a Prebiotic Chemical System by Julie Shay, Chris Huynh and Paul Higgs in the Journal of Theoretical Biology (Online September 2014).

Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life’s complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative ‘protolife’ communities, in which ‘protoplasmic continuity’ was maintained throughout a graded series of ‘proto-biofilms’, ‘protoorganisms’ and ‘protocells’ toward modern life. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms. (Abstract excerpts)

Egel, Richard, et al, eds. Origins of Life: The Primal Self-Organization. Heidelberg: Springer, 2011. With coeditors Dirk-Henner Lankenau and Armen Mulkidjanian, a large volume with these sections: Energetics of the First Life, Primeval Syntheses, Facets of an Ancestral Peptide World, and RNA Worlds – Ancestral and Contemporary. And might one wonder what kind of cosmos strives by way of us late collaborative creatures over a noosphere world, many billion years on, to reconstruct how life and mind came to be. Could such an apparent self-learning, observing, and selecting universal emergence be meant to engender the beginning of a second, intentional genesis?

If theoretical physicists can seriously entertain canonical “standard models” even for the big-bang generation of the entire universe, why cannot life scientists reach a consensus on how life has emerged and settled on this planet? Scientists are hindered by conceptual gaps between bottom-up inferences (from early Earth geological conditions) and top-down extrapolations (from modern life forms to common ancestral states). This book challenges several widely held assumptions and argues for alternative approaches instead. Primal syntheses (literally or figuratively speaking) are called for in at least five major areas. (1) The first RNA-like molecules may have been selected by solar light as being exceptionally photostable. (2) Photosynthetically active minerals and reduced phosphorus compounds could have efficiently coupled the persistent natural energy flows to the primordial metabolism. (3) Stochastic, uncoded peptides may have kick-started an ever-tightening co-evolution of proteins and nucleic acids. (4) The living fossils from the primeval RNA World thrive within modern cells. (5) From the inherently complex protocellular associations preceding the consolidation of integral genomes, eukaryotic cell organization may have evolved more naturally than simple prokaryote-like life forms. – If this book can motivate dedicated researchers to further explore the alternative mechanisms presented, it will have served its purpose well. (Publisher)

Falck, Jessica. Coarse-Graining as a Downward Causation Mechanism. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. In this Origins issue, the Santa Fe Institute professor of Collective Computation continues her project (search) to discern and express life’s apparent ascent from earlier upward forces of some kind to later, emergent realms which can then proceed in an intentional, formative way to act upon lower levels so as to facilitate higher phases going forward. As the Abstract says, a salient feature seems to be regular, iterative motifs that a knowledge-gaining evolution consistently employs. Again neural networks are availed as an iconic model.

Downward causation is the controversial idea that ‘higher’ levels of organization can causally influence behaviour at ‘lower’ levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties. I introduce a weak and strong notion of downward causation and discuss the role the strong form plays in the origins of new organizational levels. I illustrate these points with examples from the study of biological and social systems and deep neural networks. (Abstract)

Fishkis, Maya. Emergence of Self-Reproduction in Cooperative Chemical Evolution of Prebiological Molecules. Origins of Life and Evolution of Biospheres. Online September, 2010. A Canadian systems biologist proposes that the complexity sciences via agent-based modeling, aka artificial chemistry, can be extended to prebiotic material realms. The implication then arises that primordial matter appears so composed that life’s origin is a non-random probability.

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