III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

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

Ruiz-Mirazo, Kepa, et al. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chemical Reviews. 114/1, 2014. Reviewed more Systems Chemistry, Spanish scientists extensively presage a revolutionary genesis cosmos.

Sahtouris, Elisabet. A Tentative Model for a Living Universe. www.ratical.org/LifeWeb. The paper is available at the LifeWeb website: click on Biophilosophy by Elisabet Sathouris. A holistic biologist critiques the mechanical model of a barren, universe where life is a fleeting tangent in light of an imminent paradigm shift to a creative, organic reality. This is visible not by material reduction but through an “integral science” which includes the entire human experience of self, world and cosmos. As a result, autopoietic systems is are seen to spontaneously generate a holoarchy of living, sentient, dynamically interactive beings. And in passing, here is an example of a woman’s sense of a much more nurturing cosmology.

Instead of projecting a universe of mechanism without inventor, assembling blindly through particular, atomic and molecular collisions a few of which came magically to life and further evolved by accidental mutations, I propose that there is reason to see the whole universe as alive, self-organizing endless fractal levels of living complexity as reflexive systems learning to play with possibilities in the intelligent co-creation of complex evolving systems. (2)

Salthe, Stan. Natural Philosophy and Developmental Systems. Systems Research. 18/403, 2001. A veteran biologist and philosopher perceives and recommends the return of an integral knowledge of a cosmic and earthly gestation.

Natural philosophy is being revived by way of grounding it in thermodynamics and information theory. This discourse systematizes information from all the sciences so that every field of knowledge of nature supports every other as parts of a concept of general evolution. (403)

Sanchez, Ignacio, et al.. Solvent Constraints for Biopolymer Folding and Evolution in Extraterrestrial Environments.. arXiv:2310.00067. We choose and place this entry by University of Buenos Aries astrochemists in our main organic ecosmos section because it well conveys an innately fertile essence on it’s own developmental course. Into this October, however might such a phenomenal biologic milieu and personal planet bearing result ever be able to dawn on us in.

We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects a related to the chemical composition of biopolymers and depend on the solvent in which they occur. We show that molecular information and energy landscape theories allow us to explore the limits that solvents impose on biopolymers. We consider water, alcohols, hydrocarbons, halogenated, aromatic media which may take part in alternative biochemistries. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets. (Excerpt)

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)

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