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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

A. UniVerse Alive: An Organic, Self-Made, Encoded, Familial Procreativity

Boeyens, Jan. Chemical Cosmology. Berlin: Springer, 2010. A South African chemist, in the 1990s University of Witwatersrand dean of science, now at the University of Pretoria, proposes akin to quantum cosmology, a deep affinity between chemical and celestial realms and geometries, but with a major difference. While the (Ptolemaic) physics paradigm denies any intrinsic reality or constancy of pattern, if such a presence might be admitted, as tradition well knows, then a “universal self-similarity” can again be observed and discovered. From atoms to organisms to galaxies, nature employs and recycles the same topologies, which necessarily arise from a common mathematical source. If we might lately turn our gaze from hadron depths to real affinities from molecule to communities to nebulae, an edifying micro/macro reiteration can indeed be revealed.

We conclude that the organization of atomic matter is self-similar with the arrangement of planetary systems and conditioned by the same design principles recognized in biological growth and in galaxies. (163)

Brandenburg, Axel and David Hochberg. Introduction to Origins of Biological Homochirality. Origins of Life and Evolution of Biospheres. 52/1-3, 2022. Stockholm University and Center for Astrobiology, Madrid editors open a special issue for the latest research on life’s deep tendency to branch into relative left or right topological phases See, for example, Symmetry Breaking by Consecutive Amplification by Laura Huber and Oliver Trapp (view his website), Biological Homochirality and the Search for Extraterrestrial Biosignatures by Marcelo Gleiser, et al, Molecular Self-Assembly as a Trigger of Life Origin and Development by Dmitry Zlenko, et al, and Frontiers in Prebiotic Chemistry and Early Earth Environments by Ulrich Muller, et al.

The chemistry of terrestrial life is based on a spatial molecular asymmetry whose three dimensional geometrical structure or conformation is not identical to that of their mirror image or spatial reflections though a mirror. The parity P, or space inversion, is a discrete symmetry transformation in physics, and is broken at the molecular level. Such molecules thus possess homochirality or handedness. Amino acids, the building blocks of proteins, and the sugar backbones present in DNA and RNA are chiral molecules. Chirality constitutes a unifying feature of the living world and is a prime driving force for genetic evolution and biologic selection. (First paragraph)

Most amino acids and sugar molecules occur in mirror, or chiral, images of each other, knowns as enantiomers. However, life on Earth is mostly homochiral: proteins contain almost exclusively L-amino acids, while only D-sugars appear in RNA and DNA. We review potential mechanisms for biological homochirality on primal Earth an their implications for astrobiology: that it is a stochastic process driven by local environmental fluctuations; second, that it is driven by circularly-polarized ultraviolet radiation in star-forming regions; and that it is driven by parity violation at the elementary particle level. (Gleiser, et al)

Homochirality is a uniformity of chirality, or handedness. Objects are chiral when they cannot be superposed on their mirror images. For example, the left and right hands of a human are approximately mirror images of each other but are not their own mirror images, so they are chiral. In biology, 19 of the 20 natural amino acids are homochiral, being L-chiral (left-handed), while sugars are D-chiral (right-handed). (Wikipedia)

Branscomb, Elbert and Michael Russell. On the Beneficent Thickness of Water. Interface Focus. October, 2019. In an 80th birthday festschrift for the NASA astrobiologist Michael Russell, he and the University of Illinois biochemist (search) wax over how amazing is it that life’s fluid bath seems to inherently possess extraordinarily ideal properties so as simple and complex cells and peoples can come into being.

In the 1930s, Lars Onsager published his famous ‘reciprocal relations’ describing free energy conversion processes, which assumed that the fluxes involved in the conversion were proportional to the forces driving them. For chemical reactions, this condition holds only for systems close to equilibrium. Soon thereafter, it was observed that in some biological conversions both the reciprocal relations and linear flux–force dependency appeared to be obeyed no matter how far from equilibrium the system was being driven. No explanation for this ‘paradoxical’ behaviour has emerged and it has remained a mystery. We here argue, however, that this anomalous behaviour is simply a gift of water, of its viscosity in particular; a gift, moreover, without which life almost certainly could not have emerged. (Abstract excerpt)

Buchanan, Mark. Birds of a Feather. Nature Physics. 9/7, 2013. In this month’s column, the physicist writer reports on the work of Cristina Marchetti, et al, and Andrea Cavagna, et al (search each) about how “scale-free collectives of interacting, self-propelling elements” from microbes to flocks and every animal assembly are becoming known as a natural form of “active matter.” Casting back, the term is akin to Vladimir Vernadsky’s 1920s citation of “living matter.” In our worldwide midst, a revolution thus seems in process from material substance as stone-cold passive to an increasing reanimation, taking flight on its own. “Deep analogs” indeed appear between growth and ground, a conducive spacescape, as a 21st century genesis uniVerse dawns.

Even more active is a colony of bacteria, each member of which can carry out sustained motion as well as complex signaling and coordination with others. Or think of a flock of birds or herd of migratory animals. Despite obvious differences, these systems all share a similar character as collectives of interacting and self-propelling elements with internal sources of energy. It’s natural to think of all of these as examples of a more general kind of “active” matter – a new frontier where ideas from physics on the principles of order and organization are proving very useful. (387)

This is interesting as it suggests some kind of evolutionary tuning of interactions to produce optimal sensitivity in the group’s ability to respond to signals gathered by any one member. But there’s a deep analogy to physics too. Indeed, the interactions between birds seem to be organized in a ‘scale-free’ way, with the flock’s sensitive dynamics closely linked to the behavior of a physical substance held near a critical point between an organized and disorganized phase. (387)

Caetano-Anolles, Gustavo, ed. Evolutionary Genomics and Systems Biology. New York: Wiley-Blackwell, 2010. The editor is a University of Illinois Professor of Bioinformatics and Agricultural Sciences who has put together an extraordinary collection by leading practitioners on the breadth, robustness and maturity of a 21st century science of systems genetics. Typical, notable papers are “The Role of Information in Evolutionary Genomics of Bacteria” by Antoine Danchin and Agnieszka Sekowska (search), “Genotypes and Phenotypes in the Evolution of Molecules” by Peter Schuster, “Evolution of Metabolic Networks” Eivind Almaas, and “Modularity and Dissipation in Evolution of Macromolecular Structures, Functions, and Networks” by Caetano-Anolles, Liudmila Yafremava and Jay Mittenthal which, as the quote below, situates living systems within and as the result of a cosmic thermodynamic drive.

We have been considering biological evolution. Now we broaden evolution’s meaning by considering it in a cosmological sense. Several central questions can be posed. What are the fundamental evolutionary drivers of EDS (emergent dissipative systems) organization and complexity? How does dissipation of energy and matter contribute to EDS formation? We contend the answer lies in information. (Caetano-Anolles, 435)

Cantine, Marjorie and Gregory Fournier. Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor. Origins of Life and Evolution of Biospheres. Online July, 2017. Earth, Atmospheric, and Planetary Sciences, MIT researchers analytically and graphically display this initial two billion year span when living proto-cellular formations began to arise and evolve. Again, by the tripartite union of replicative modes, closed compartments, and rudimentary metabolism, life’s nested cellularity was on its course all the way to our late reconstruction. For this section, the presence of an innately organic, conducive, habitable cosmos becomes robustly evident.

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life’s earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life’s persistence on a changing planet. (Abstract)

Capra, Fritjof. The Web of Life. New York: Anchor Books, 1995. The nonlinear sciences of self-organization, chaos theory, thermodynamics and fractal complexity are artfully integrated as a basis for an ecological philosophy. An entire chapter is devoted to the “self-making” role of autopoietic systems.

Carter, Brandon. Hominid Evolution: Genetics versus Memetics. International Journal of Astrobiology. 11/1, 2011. The CNRS Paris Observatory theorist, a prime conceiver of the Anthropic Principle, offers another take on how human beings might be considered as cosmically meant to be. See also Carter, 2011 in Anthropic and Biotropic Principle. Albeit technical excursions, we seem to be closing to something but not yet there whence people are a functional phenomenon of a greater reality and genesis.

The last few million years on planet Earth have witnessed two remarkable phases of hominid development, starting with a phase of biological evolution characterized by rather rapid increase of the size of the brain. This has been followed by a phase of even more rapid technological evolution and concomitant expansion of the size of the population that began when our own particular ‘sapiens’ species emerged, just a few hundred thousand years ago. The present investigation exploits the analogy between the neo-Darwinian genetic evolution mechanism governing the first phase, and the memetic evolution mechanism governing the second phase. From the outset of the latter until very recently – about the year 2000 – the growth of the global population N was roughly governed by an equation of the form dN/Ndt=N/T*, in which T* is a coefficient introduced by von Foerster, (1960) who evaluated it empirically as about 200,000 million years. It is shown here how the value of this hitherto mysterious timescale governing the memetic phase is explicable in terms of what happened in the preceding genetic phase. The outcome is that the order of magnitude of the Foerster timescale can be accounted for as the product of the relevant (human) generation timescale, about 20 years, with the number of bits of information in the genome, of the order of 10,000 million. Whereas the origin of our ‘homo’ genus may well have involved an evolutionary hard step, it transpires that the emergence of our particular ‘sapiens’ species was rather an automatic process. (Abstract)

Chen, Irene and Martin Nowak. From Prelife to Life: How Chemical Kinetics Become Evolutionary Dynamics. Accounts of Chemical Research. 45/12, 2012. Premier scientists at Harvard University join their Origins laboratory and Behavioral studies to consider and evoke an apparent natural genesis which seamlessly develops by the same impetus and vital forms from cosmos to children. Irene Chen, a biophysicist, is Bauer Fellow at the FAS Center for Systems Biology. Martin Nowak, a mathematical biologist and author (search), directs the Program for Evolutionary Dynamics. Once again an active material ground is no longer “inorganic” but in some way expectant, gravid with life’s infinitely repetitive, emergent patterns, processes, and stirring sentience.

A crucial question for the origin of life is the following: when do chemical kinetics become evolutionary dynamics? In this Account, we review properties of “prelife” and discuss the transition from prelife to life. We describe prelife as a chemical system where activated monomers can copolymerize into macromolecules such as RNA. These macromolecules carry information, and their physical and chemical properties depend to a certain extent on their particular sequence of monomers. We consider prelife as a logical precursor of life, where macromolecules are formed by copolymerization, but they cannot replicate. Prelife can undergo “prevolutionary dynamics”, including processes such as mutation, selection, and cooperation. Prelife selection, however, is blunt: small differences in rate constants lead to small differences in abundance. Life emerges with the ability of replication. In the resulting evolutionary dynamics, selection is sharp: small differences in rate constants can lead to large differences in abundance. (Abstract excerpt)

Cooper, Geoffrey, et al. Modular Redox-Active Inorganic Chemical Cells: iCHELLs. Angewandte Chemie. Online September, 2011. Researchers from corresponding author Lee Cronin’s University of Glasgow laboratory show how polyoxometalates (POM) clusters of tungsten, phosphorous, oxygen, and other elements, if mixed in a saline solution, appear to spontaneously assemble themselves into spherical forms. As Cronin notes in his talk above, the work could stand as a latter day Stanley Miller experiment. The resulting unit is a hybrid inorganic chemical cell or iCHELL. By varying their metal oxide content, cell-like membranes appear, along with inklings of self-replication. The POM agglomerates then exhibit an enhanced functionality with redox, catalytic, photochemical, and magnetic properties. For a review of this frontier work, see “Life-like Cells are Made of Metal” in the New Scientist for September 14, 2011.

The grand aim is to construct complex chemical cells with life-like properties, because the development of non-biotic inorganic chemical cells could be one route to probe how life emerged from the “inorganic world” around 4.3 billion years ago.

Coveney, Peter, et al. Theory, Modelling and Simulation in Origin of Life Studies.. Chemical Society Reviews. 41/5430, 2012. Reviewed more in The Origin of Life, another essay that proceeds to join living systems with an innately self-organizing cosmos.

Cronin, Leroy. Hybrid-Chemo-Robotic Systems for Embodied Chemical Evaluation. Sayama, Hiroki, et al, eds. ALIFE14: Proceedings 14th International Conference on the Synthesis and Simulation of Living Systems. Cambridge: MIT Press, 2014. A keynote by the University of Glasgow chemist (search here and LC lab site) about an inherently organic, life generating, natural cosmos being revealed by the latest findings. The whole large volume is free online at the publisher’s site and is filled with similar contributions and confirmations.

How did chemistry turn into biology and what is the role of evolution in the emergence of life and the design of ALIFE? I will discuss how the fields of chemistry, robotics, computer science are coming together to explore this problem viewing the assembly of life as a chemical-computational problem embodied in a non-conventional ‘hetrotic’ computing architecture, and using this idea to search for, and design new, artificial life systems.

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