IV. Ecosmomics: Independent Complex Network Systems, Computational Programs, Genetic Ecode Scripts

C. Our Own HumanVerse (Epi) Genomic Heredity

Van Nimwegen, Erik. Scaling Laws in the Functional Content of Genomes. Trends in Genetics. 19/9, 2003. More thoughts on the perception of common natural principles at work.

In this article I show that, for many high-level functional categories, the number of genes in each category scales as a power-law of the total number of genes in the genome. The occurrence of such scaling laws….suggests that the exponents of the observed scaling laws correspond to universal constants of the evolutionary process. (479)

Van Speybroeck, Linda, et al. Epi-Geneticization: Where Biological and Philosophical Thinking Meet. Fagot-Largeault, Anne, et al, eds. The Influence of Genetics on Contemporary Thinking. Berlin: Springer, 2007. In a volume that explores how changing views of genomes work their way into social discourse, Ghent University philosophers survey the epic revolution from 20th century discrete deoxyribonucleic acid molecules, (of course necessary first had to find and name all the pieces). Much more is now seen to be going on which involves a whole array of interconnective network, hierarchical, modular, and informational processes and patterns. By these lights, genomic systems are suffused by and exemplify the same self-organizational properties found throughout nature. But a further conceptual step is then invited, we add. A clear implication would be that these universal, independent propensities that serve organic development and behaviors ought to be appreciated as truly “genetic” in kind. In such regard, they take on a guise and role as a cosmic parental code, with both an original parental independence while being instantiated everywhere in developmental evolution, universe and human in a 21st century temporal, unfolding gestation.

Via the notion of context, a means is found to transcend a reductionist view on genes as sole organizers of both biological organisms and biological knowledge. Within an epigenetic framework, genes no longer stand for inviolable molecular atoms ‘causing’ the organism, but rather for temporarily relatively stable units which take form within a biological system, i.e. a dynamic self-organizing system in which the partaking factors interpret one another, and through this interpretation construct each others functional meaning. (125-126)

Van Speybroeck, Linda, et al, eds. From Epigenesis to Epigenetics: The Genome in Context. Annals of the New York Academy of Sciences. Volume 981, 2002. Conference proceedings which discuss a 21st century revolution in genetics as it moves beyond discrete genes to ‘epigenetic’ effects ranging from self-organization to topological and environmental constraints. A paradigm shift is evident from a ‘gene-centric’ emphasis to genomic systems which can reflect the influence of complexly organized dynamic networks.

Vetsigian, Kalin, et al. Collective Evolution and the Genetic Code. Proceedings of the National Academy of Sciences. 103/10696, 2006. Co-authors are Carl Woese and Nigel Goldenfeld. An elaboration of the proposal that life first evolved in a horizontal, communal milieu with cooperative sharing and transfer of gene material. Freeman Dyson has lauded this effort, and he goes on to say that after the vertical, Darwinian phase, via biotechnology we have again entered a radical new mode of horizontal gene creation.

A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. (10696) Evolution of the genetic code, translation, and cellular organization itself follows a dynamic whose mode is, if anything, Lamarckian. (10701)

Villarreal, Luis and Guenther Witzany. The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology. Genomic Insights. 6/1, 2013. A UC Irvine biologist and an Austrian natural philosopher offer another way to appreciate the real presence of reciprocal community propensities even for this biomolecular realm. Please search each name for more work.

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. In this review, we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioral motifs of cooperative RNA consortia. In addition to molecular biological perspectives, this may lead to a better understanding of genetic code evolution and dynamics. (Abstract)

However, because reductionist approaches do not well explain emergent consortia or group behav¬iors, systems biology tried a more holistic approach to explain properties that emerge out of complex systems. Like systems theory, which investigates the capacity of formal systems, systems biology defines a system as a quantity of elements and a quantity of relations between these elements. Both assume that the relations between the elements of a system and its possibilities of behavior can be represented formally (mathematically) without respect to any kind of realization (circumstances, history). This means that the dynamic relations, as well as the quantities of elements that constitute these relations, are subject to formalizable (computational) procedures such as algorithms. (7)

Watson, James, et al. DNA: The Story of the Genetic Revolution. New York: Knopf, 2017. With geneticist coauthors Andrew Berry and Kevin Davis, the 500 page illustrated volume by the now nonagenarian codiscoverer of the nucleotide double helix is a most authoritative survey. This programmic, narrative aspect of our personal and social lives, in sickness and health, body, brain and behavior, along with ancestry studies, seems to be now rising to a preeminent definition and reference.

The definitive insider's history of the genetic revolution--significantly updated to reflect the discoveries of the last decade. James D. Watson, the Nobel laureate whose pioneering work helped unlock the mystery of DNA's structure, charts the greatest scientific journey of our time, from the discovery of the double helix to today's controversies to what the future may hold. Updated to include new findings in gene editing, epigenetics, agricultural chemistry, as well as two entirely new chapters on personal genomics and cancer research. This is the most comprehensive and authoritative exploration of DNA's impact--practical, social, and ethical--on our society and our world.

Watters, Ethan. DNA is not Destiny. Discover. November, 2006. A popular entry to an expansive appreciation of the literate efficacy of our genetic complement.

A human liver cell contains the same DNA as a brain cell, yet somehow it knows how to code only those proteins needed for the functioning of the liver. Those instructions are found not in the letters of the DNA itself but on it, in an array of chemical markers and switches, known collectively as the epigenome, that lie along the length of the double helix. (33)

Weiss, Kenneth. The Phenogenetic Logic of Life. Nature Reviews Genetics. 6/1, 2005. In this imaginative, illustrated contribution, the Penn State University geneticist proposes a mostly unnoticed, in-between, domain whereof the genotype emerges into its phenotype. Such ramifying translation is seen to occur by way of modularities, repetitive patterning, sequestration of autonomy, fractal branching, information feedback, altogether a logic of relational principles. Watch for Ken and Anne Buchanan’s new book The Mermaid’s Tale: Four Billion Years of Cooperation in the Making of Living Things in 2009 from Harvard University Press.

However, a more complete evolutionary synthesis, often classified under the catch-phrase the ‘evolution of development’ (EvoDevo), has been emerging, facilitated by advances in molecular genetics that have revealed elements of a unifying phenogenetic logic of life — the phenomena that connect biological phenotypes with their underlying genetic bases. ‘Logic’ is the operative concept, because unlike the stereotype according to which genes are independent, bead-like functional units that are linearly arranged along a chromosome, phenogenetic phenomena are the higher-order, ‘emergent’ results of structure and interaction.

Weiss, Kenneth and Anne Buchanan. Genetics and the Logic of Evolution. Hoboken, NJ: Wiley, 2004. Penn State University biological anthropologists achieve an accessible, cogent review of current novel understandings of genetic systems. Instead of discrete DNA pieces, there is a growing notice of recurrent modular patterning in genomes, a repetitive sequestration, due to a small number of ubiquitous regulatory genes. I have recently heard Ken Weiss speak about the presence of such “invisible general principles” beyond a Darwinian compass, whose algorithmic iteration serves to spawn a “nested serial homology” from DNA to physiology, cells to organs. Together with John Whitfield’s new book on such mathematical recurrences from microbes to ecologies, a once and future natural genesis springing from and exemplifying a common source becomes evident.

Whitfield, John. Across the Curious Parallel of Language and Species Evolution. PLoS Biology. 6/7, 2008. The British science writer reports in this online journal on the dawning realization that the molecular DNA code is strongly isomorphic and isodynamic with linguistic structures. One might add that an implication of this has not yet registered that human knowledge is genetic in kind, and that both codes must spring from the same innate source. By its employ, much as if people are as “genes,” we might intentionally continue creation.

Languages are extraordinarily like genomes…there could be very general laws of lexical evolution to rival those of genetic evolution. (1370)

Wills, Peter. Informed Generation: Physical Origin and Biological Evolution of Genetic Codescript Interpreters. Journal of Theoretical Biology. 257/3, 2009. A significant synthesis noted more in Quickening Evolution.

Witzany, Guenther. Life is Physics and Chemistry and Communication. Annals of the New York Academy of Sciences. Online December, 2014. In a current series of articles, the Austrian philosopher is trying to gather a number of themes into a better appreciation of the nature of genomes, and the universe they arise from and must reflect. After a noting an ancient dichotomy between a holistic oneness or atomist multitudes, starting with a 20th century linguistic basis, increasing recognitions have taken on algorithmic, computational, natural grammar and language aspects. A materialist cast is inadequate, our task is to properly interpret this equally real, more important biosemiotic quality. The preferred approach, due to James Shapiro, John Mattick, many others, is to view an integral genome wherein discrete nucleotides join in networks and communities, see also Witzany 2014 in Cooperative Societies.

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