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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

Sandefur, Conner, et al. Network Representations and Methods for the Analysis of Chemical and Biochemical Pathways. Molecular BioSystems. 9/2189, 2013. In this paper, Sandefur, University of North Carolina, Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, with Maya Mincheva, Northern Illinois University mathematical sciences, and Santiago Schnell, University of Michigan Medical School, Computational Medicine and Bioinformatics, seek to define the generic interconnective dynamics of such organic phenomena, and their invigorating presence in similar fashion for all manner of biomaterial systems. That is to say, a double domain, as if implicate and explicate, an independent universality, and its manifest instantiation. May one then ever imagine a natural genotype and phenotype?

Systems biologists increasingly use network representations to investigate biochemical pathways and their dynamic behaviours. In this critical review, we discuss four commonly used network representations of chemical and biochemical pathways. We illustrate how some of these representations reduce network complexity but result in the ambiguous representation of biochemical pathways. We also examine the current theoretical approaches available to investigate the dynamic behaviour of chemical and biochemical networks. Finally, we describe how the critical chemical and biochemical pathways responsible for emergent dynamic behavior can be indentified using network mining and functional mapping approaches. (Abstract)

Networks are comprised of nodes connected by edges. In graph theory, weighted edges are often used in place of edges. The systems biology definition of a network is broader and includes a variety of graphs. The nodes in a network generally represent biochemical components. Some examples include: genes and proteins in a transcription network; substrates, enzymes, and products in a metabolic network; and amino acids in a network representation of a folding protein. Interactions between components are represented by edges connecting the nodes. Examples include: activation of gene expression by a protein; product formation via a substrate and an enzyme; and electrostatic interactions between nodes in an amino acid network. Chemical or biochemical networks are static representations of the dynamic interactions of different species that occur in time and space. (2190)

Scharf, Caleb. Extrasolar Planets and Astrobiology. Sausality, CA: University Science Books, 2009. Reviewed more in Exoearths, still another take as we move closer and closer to a collaborative admission, a revolutionary Copernican realization, of a biologically fertile cosmic embryogenesis.

Schwartzman, David and Charles Lineweaver. Temperature, Biogenesis, and Biospheric Self-Organization. Kleidon, Alex and Ralph Lorenz, eds. Non-Equilibrium Thermodynamics and the Production of Entropy. Berlin: Springer, 2005. A cosmos that by its nature will inevitably evolve complex, cognitive living systems is said to be the accepted astrobiological paradigm. The presence of the right temperature regime on the surface of conducive planets is an imperative condition.

Big bang cosmology has given us an abiotic, deterministic model for the evolution of the Universe in which, as the Universe expanded and cooled from arbitrarily high temperature, an increasingly complex series of structures emerged including life and biospheres at least on terrestrial planets around Sun-like stars. (208)

Seckbach, Joseph, ed. Life As We Know It. Berlin: Springer, 2006. Volume 10 in the Cellular Origin, Life in Extreme Habitats and Astrobiology series. An extraordinary array of insights on the incarnate insistence of living entities and systems. Please check the publisher’s web posting for its expansive table of contents. Some samples: "Life as an Unfolding Biocosmos" by Joseph Svoboda, and "The Destiny of Life in the Universe" by Julian Chela-Flores.

Shapiro, Robert. Planetary Dreams. New York: Wiley, 1999. A contrast is set up between the negative materialist and positive organic positions as to whether an inherently self-organizing universe should be filled with intelligent beings. Bets are placed on the many intrinsic reasons for prolific life.

Siregar, Pridi, et al. A General Framework Dedicated to Computational Morphogenesis: Part II Knowledge Representation and Architecture. BioSystems. Online November, 2018. PS and Nathalie Julen, Integrative BioComputing, France, Peter Hugnagl, Charité – Universitätsmedizin Berlin and George Mutter, Harvard Medical School post a series of papers herein, the above being the longer essay, along with A General Framework Dedicated to Computational Morphogenesis: Part I Constitutive Equations. (Online July) and Computational Morphogenesis: Embryogenesis, Cancer Research and Digital Pathology (169-170/40). We cite because an insightful attempt is made, based on efforts back to the 1990s, to formulate a structural systems biology in accord with a physical foundations. By virtue of this view, nested, fractal arrays of active entities in community appear as life’s embryonic and morphological genesis evolves and emerges.

Skar, John and Peter Coveney, eds. Self-organization: The Quest for the Origin and Evolution of Structure. Philosophical Transactions of the Royal Society of London A. 361/6, 2003. A Nobel Symposium considers the growing realization of an innate dynamical drive toward emergent complexity from space-time to ecosystems. Altogether these findings imply a quite different animate, oriented universe which seems to develop akin to a living organism.

In summary then, self-organization seems to be characterized by the almost spontaneous creation of global or semi-global patterns developed from local interactions among independent and autonomous components or agents. (1054)

Smith, Eric. Before Darwin. The Scientist. 22/6, 2008. An article in this ‘Magazine of the Life Sciences’ wherein the Santa Fe Institute biologist observes that evolution may be off-putting for the general public because it is not rooted in a conductive physical or chemical substrate. Smith, often a collaborator with Harold Morowitz, contends that ecological principles of metabolic biosynthesis in fact are in place prior to Darwinian selection and would serve as an inherently fertile milieu for life’s origin. An extensive technical piece by Eric Smith on the “Thermodynamics of Natural Selection” is noted in the A Thermodynamics of Life section.

When we consider what would be required for metabolism to have self-organized without supervision, we realize there a rich, hierarchical, modular structure of the extant metabolism of the biosphere that looks far from accidental. The functions that particular chemicals fulfill, in the context of both the network and the constraints of the geochemical environment, suggest that the presence of these chemicals as a foundation for life may be required from first principles. (38)

Smith, Eric, et al. Core Metabolism as a Self-Organized System. Rasmussen, Steen, et al, eds. Protocells: Bridging Nonliving and Living Matter. Cambridge: MIT Press, 2009. Along with Harold Morowitz and Shelley Copley, an attempt to root animate activity in a physical ground with dynamically fertile propensities. In so doing, initial ‘ergodic’ processes are seen to explore a range of configurations, from which a preferred state or ‘contingency’ is selected, but guided by an essential self-creativity.

Life exists in a nonequilibrium flux of energy flowing both from the sun and from geochemical sources, through the biosphere, to heat that is radiated into space. Here, we develop the view that the basic chemical reaction networks that underlie life have emerged as a form of structure that is a direct result of the prebiotic version of this energy flow. The emergence of these structures during the origin of life is a particular instance of more general thermodynamic phenomena in which sources of unrelaxed free energy can spontaneously induce ordered dynamical states that create channels for their relaxation by means of energy flow through the channels. (433) The proposition that a self-organized protometabolism emerged deterministically as the first step toward life is also a proposition that the dynamics of life are continuous with the dynamics of geochemistry, particularly in the realm of metabolism. (435)

Smith, Ian, et al, eds. Astrochemistry and Astrobiology. Berlin: Springer, 2013. Reviewed more in Astrobiology, an epic scientific discovery is underway of an animate cosmic materiality that seems predisposed to spawn and form complex, proactive, biomolecules into protocellular vital systems.

Smolin, Lee. The Self-organization of Space and Time.. Philosophical Transactions of the Royal Society of London A. 361/1081, 2003. Further insights into a relational universe which evolves into sentient complexity because these properties favor its cosmic replication through populations of black holes. A 2003 talk by Lee Smolin on "Science and Democracy" where he lucidly presents the physical necessity of a self-organizing cosmos is now posted online at http://www.ted.com/index.php/talks/lee_smolin_on_science_and_democracy.html.

Smoot, George. Wrinkles in Time. New York: Morrow, 1993. The astrophysicist who led the COBE satellite team which detected primordial ripples as seeds for galaxy formation offers a diametricly opposite view from his mentor Steven Weinberg, showing how much ones predilection colors what is seen.

I must disagree with my old teacher. To me the universe seems quite the opposite of pointless. It seems that the more we learn, the more we see how it all fits together - how there is an underlying unity to the sea of matter and stars and galaxies that surround us. Likewise, as we study the universe as a whole, we realize that the “microcosm” and the “macrocosm” are, increasingly, the same subject. By unifying them, we are learning that nature is as it is not because it is the chance consequence of a random series of meaningless events; quite the opposite. More and more, the universe appears to be as it is because it must be this way; its evolution was written in its beginnings - in its cosmic DNA, if you will. There is a clear order to the evolution of the universe, moving from simplicity and symmetry to greater complexity and structure. (296)

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