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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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IV. Ecosmomics: An Independent, UniVersal, Source Code-Script of Generative Complex Network Systems

B. Our Own HumanVerse Genome Studies

Mitchell, Melanie. Complexity: A Guided Tour. Oxford: Oxford University Press, 2009. Reviewed more in A Cosmic Code, we note for still another view of genomes distinguished not by discrete molecules, but dynamical, communicative networks – which then, by inference, ought to be rightly seen as “genetic” in kind.

The complexity of living systems is largely due to networks of genes rather that the sum of independent effects of individual genes. (275) In the old genes-as-beads-on-a-string view, as in Mendel’s laws, genes are linear - each gene independently contributes to the entire phenotype. The new, generally accepted view, is that genes in a cell operate in nonlinear information-processing networks, in which some genes control the actions of other genes in response to changes in the cell’s state – that is, genes do not operate independently. (275-276)

Moghadam, S. Arbabi, et al. A Search for the Physical Basis of the Genetic Code. Biosystems. May, 2020. We cite because this entry by University of Alberta biophysicists including Jack Tuszynski discuss several ways that life’s genomic endowment can be rooted in and given a deeper substantial, innately fertile basis.

DNA contains the genetic code, which provides complete information about the synthesis of proteins in every living cell. Each gene encodes for a corresponding protein but most of the DNA sequence is non-coding. In addition to this non-coding part of the DNA, there is another redundancy, namely a multiplicity of DNA triplets (codons) corresponding to code for a given amino acid. In this paper we investigate possible physical reasons for the coding redundancy, by exploring free energy considerations and abundance probabilities as potential insights. (Abstract)

Moore, David. The Developing Genome: An Introduction to Behavioral Epigenetics. New York: Oxford University Press, 2015. With everything that constitutes the nature and activity of genomes undergoing a whole-scale expansive renovation, a Pitzer College psychologist provides a good overview of the project. This late, historic revision harking back to Lamarck and Cuvier now has genetic phenomena spreading far beyond nucleotides to parental, personal, social, and environmental influences.

Morange, Michel. Genome as a Multipurpose Structure Built by Evolution.. Persepctives in Biology and Medicine.. 57/1, 2015. In a special issue on The Changing Concept of the Gene, the French biologist and philosopher reviews the history of genetics as a “progressive discovery of the complexity of the genome” from biomolecular nucleotides to gene regulatory networks to an integral system lately taking on epigenetic functions.

Morowitz, Harold. Phenetics, A Born Again Science. Complexity. 8/1, 2003. Another report of a major paradigm shift in biology from random, particulate genes to a systems integration of a phenotypic genetics which can generate metabolic networks.

If biology is governed by a hierarchy of phenetic laws, then replaying the tape (of life) might lead to a rather similar outcome particularly at the unicellular level. Our task as biologists is then to search for these laws rather than focusing on the thousand billion elements of sequence that must characterize the biosphere. (13)

Moss, Lenny. What Genes Can’t Do. Cambridge: MIT Press, 2002. In a review of the 20th century field of genetics, a philosopher argues that the concept of particulate genes and a predetermined program has been superseded by their inclusion within complex, dynamic, epigenetic systems which are inherited in parallel with the genomic sequence. These aspects then form a complementarity of discrete and systemic influences.

Mukherjee, Siddhartha. The Gene: An Intimate History. New York: Scribner, 2016. The author is an Indian-born American physician, Pulitzer Prize winner, Columbia University professor of medicine and a CU/NYU Presbyterian Hospital cancer specialist. This 500 page tome represents a premier study of a long unknown, often intimated, bioinformatic nucleotide genome as an increasingly vital element of our existence. Chapters span The Missing Science of Heredity 1865 (Mendel) – 1935, The Dreams of Geneticists 1970 – 2001, to Post Genome 2015. Its copious content covers the main scientists, ethical issues with guidance from the Nobel laureate geneticist Paul Berg, now 90, epigenetics, eugenics, the human genome sequence, and onto CRISPR advances. On a Charlie Rose show (July 1), Dr. Mukherjee compared genomes to a vast encyclopedia. A major entry to welling historic realizations about how significant is this presence of a programmic genotype to our phenomenal nature.

Ndifon, Wilfred. A Complex Adaptive Systems Approach to the Kinetic Folding of RNA. BioSystems. 82/3, 2005. Prior to selection, RNA sequences act as self-organizing CAS as they fold into structural arrangements.

Specifically, a complex adaptive system (CAS) is characterized by the presence of a diverse ensemble of components that engage in local interactions and an autonomous process that selects a subset of those components for enhancement based on the results of the local interactions. (258)

Neumann-Held, Eva and Christoph Rehmann-Sutter, eds. Genes in Development: Re-reading the Molecular Paradigm. Durham, NC: Duke University Press, 2006. A stellar collection of papers which convey the range and depth of ferment and revolution in evolutionary theory. Stuart Newman, Gerd Muller, Brian Goodwin, Susan Oyama, Paul Griffiths, Evelyn Fox Keller, Sahorta Sarkar, those quoted below, and others describe a quite different genetic “code” than the mid to late 20th century molecular determinism. Much more is going on in terms of developmental systems, epigenetics, environmental contexts, processes along with parts, an informational vector, a malleable phenotype, constructivist interactionism, and so on. The work then begs a common agenda and nomenclature, properly attributed to a composite humankind. As a result, we gain not just another “synthesis” but a genesis cosmos with its own “self-organization, cohesiveness, emergence and selfhood” (Hoffmeyer).

Biosemiotics suggests that our universe has a built-in tendency (originating in the second law of thermodynamics) to produce organized systems possessing increasingly more semiotic freedom in the sense that the semiotic aspect of the system’s activity becomes more autonomous relative to its material basis. (Jesper Hoffmeyer, 139)

Process perspectives model phenomena by representing processes rather that players in structural or functional terms. Processualists identify units of evolution with processes rather than with objects or functions. (James Griesemer, 208)

Nicolau, Miguel and Marc Schoenauer. On the Evolution of Scale-free Topologies with a Gene Regulatory Network Model. BioSystems. In Press Online, 2009. University of Paris scientists contribute to the worldwide reconception of genomes in terms of complex systems. Much more than a collection of molecular objects, they are distinguished by equally real nested interrelations and topologies.

The results obtained show that, when the model uses a duplication and divergence initialisation, such as seen in nature, the resulting regulation networks not only are closer in topology to scale-free networks, but also require only a few evolutionary cycles to achieve a satisfactory error value.

Genetic regulatory networks (GRNs) are biological interaction networks among the genes in a chromosome and the proteins they produce: each gene encodes a specific type of protein, and some of those, termed Transcription Factors, regulate (either enhance or inhibit) the expression of other genes and hence the generation of the protein those genes encode.

Nijhout, H. Frederik. The Importance of Context in Genetics. American Scientist. September-October, 2003. An article on the new understanding of what genes are and how they are expressed. Rather than isolated, determinant molecules, strands of DNA interact as complex systems within cellular landscapes, often under environmental influences.

Noble, Denis. Genes and Causation. Philosophical Transactions of the Royal Society A. 366/3001, 2008. A contribution to the epoch rethinking of how we conceive informative, genetic domains from before the time of Gregor Mendel. As evoked by his 2006 The Music of Life, the salient shift moves from point-like, “digital” molecules to a “analogue” sense of genomic expression as if constantly edited and recast sentences and paragraphs. Once again, a complementarity of particle and wave, node and link in dynamic nets accrues, could one imagine father and mother.

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