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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

1. The Origins of Life

Davies, Paul. The Fifth Miracle. New York: Simon & Schuster, 1999. Research on the advent of life has lately matured to a point where an overall review can connect this event with the elemental properties of the universe. The phenomena of self-organization and informed complex systems are seen to imply emergent life is a natural, intended presence. Davies goes on to say that we seem on the verge of a grand shift from an older comatose cosmos to an organic universe presently giving birth to its sentient human phase.

The search for life elsewhere in the universe is therefore the testing ground for two diametrically opposed world-views. On one side is orthodox science, with its nihilistic philosophy of the pointless universe, of impersonal laws oblivious of ends, a cosmos in which life and mind, science and art, hope and fear are but fluky incidental embellishments on a tapestry of irreversible cosmic corruption. On the other, there is an alternative view, undeniably romantic but perhaps true nevertheless, the vision of a self-organizing and self-complexifying universe, governed by ingenious laws that encourage matter to evolve towards life and consciousness. A universe in which the emergence of thinking beings is a fundamental and integral part of the overall scheme of things. (272-73)

De Duve, Christian. Singularities: Landmarks on the Pathways of Life. New York: Columbia University Press, 2005. The Nobel laureate biochemist explains the latest findings on life’s origin, which are seen mostly as an inevitable result of “deterministic” physical-chemical propensities. Multicellular flora and fauna arose from singular phenomena such as a common ancestor for nucleated, eukaryotic cells, and as offshoots of a single founding organism

de Duve, Christian. Vital Dust. New York: Basic Books, 1995. Noted elsewhere, the book is an authoritative exposition of the sequential Ages of Chemistry, Information, Protocells, Single Cell, Multicellular Organisms from which arises Mind and Humankind. And all this is seen to occur due to ingrained laws and properties.

De la Escosura, Andres. The Informational Substrate of Chemical Evolution. Life. Online August 8, 2019. A Universidad Autonoma of Madrid chemist group leader (search) contributes to “abiogenesis” studies, aka how could living organisms have arisen from seemingly inanimate or inorganic substrates, via novel perceptions that precursor biochemistries can similarly be understood to possess a semantic communicative quality. In regard, this earlier material phase or stage can thus accrue an inherent, lively genetic-like content. See also Permeability-driven Selection in a Semi-empirical Protocell Model: The Roots of Prebiotic Systems Evolution by Gabriel Piedrafita, et al in Nature Scientific Reports (7/3141, 2017) for a companion Spanish study.

A key aspect of biological evolution is the capacity of living systems to process information coded in DNA. The overall picture indicates that information processing in cells occurs through a hierarchy of genes regulating other genes through metabolic networks. There is an implicit semiotic character based on functional molecules that act as signs to self-regulate the whole network. In contrast to cells, chemical systems not seen as able to process information, yet they have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could regulate their constituent reactions and supramolecular organization processes. This essay will consider distinctive features of information in living and non-living matter, and how the capacity of biological information processing might be rooted in an autonomous chemical system which could self-sustain and reproduce through organizational closure. (Abstract)

Deacon, Terrence. Reciprocal Linkage Between Self-organizing processes is Sufficient for Self-reproduction and Evolvability. Biological Theory. 1/2, 2006. (A new journal of theoretical biology from MIT Press.) A sophisticated organic dynamics are laid out whereof life complexifies to selectable stages in the minimum form of autocatalytical, bounded “autocells.” (or UR-cell if you wish.) These primal units are further distinguished by properties of information transfer, metabolism, and bounded containment.

Deamer, David. Assembling Life: How Can Life Begin on Earth and Other Habitable Planets? New York: Oxford University Press, 2019. The veteran UC Santa Cruz origins researches continues his lifelong flow of frontier volumes with ever better retrospective explanations. See also his Origin of Life: What Everyone Needs to Know (Oxford, 2020) for even more insights.

In Assembling Life, David Deamer continues to address how did non-living organic compounds assemble into the first forms of primitive cellular life? What was the source of those compounds and the energy that produced the nucleic acids? Did life begin in the ocean or in fresh water on terrestrial land masses? Deamer describes organic chemicals that were likely to be available in the prebiotic environment and the volcanic conditions that could drive their complexity. In a wider view the goal is to understand how life can begin on any habitable planet.

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)

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