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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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IV. Ecosmomics: A Survey of Animate Complex Network Systems

B. Our Own HumanVerse Genome Studies

Tsuchiya, Masa, et al. Emergent Self-Organized Criticality in Gene Expression Dynamics. PLoS One. June, 2015. In a contribution that can exemplify the current global frontiers of discovery, systems biologists from Japan and Latvia show by theory and experiment that even genomes can be found to exhibit this complex phenomena as everywhere else. The subtitle is Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line. BY these insights a novel 21st century conception of genetic form and activity is achieved, which is then seen as similar to neural network computations. By a turn toward a physical substrate, a further explanation is offered by way of statistical physics and thermodynamics. To reflect on this technical paper, by the mid 2010s the composite, also dynamically self-organizing, worldwide science seems to be reaching an emergent phase of finding a universal repetition of the same common system from universe to human.

Thus, it is natural to abandon a ‘single molecule’ level of explanation when considering self-organization into discrete ‘phenotypic states’ as stable attractor states in the gene-expression landscape. The emergence of a favored ‘globally convergent’ solution that attracts the system dynamics overcomes the problem of stochastic fluctuations related to a gene-by-gene regulation paradigm. (2)

To interpret biological regulation within the framework of physics, we must eliminate the need for Maxwell’s demons, i.e., intelligent agents that actively drive the system toward a desired goal. An attractor-based global dynamics under thermodynamically open conditions for all living matter enables regulation without the need for such intelligent agents. Then, seeing a cell dynamically controlling genome-wide expression, (we ask) What is the ‘driving force’ that attracts the entire system toward a few preferred global states, thus making the genome act as a single integrated system? Statistical mechanics postulates that energetically preferred configurations of a system arise through the satisfaction of relationships among its constituent parts subjected to external constraints. These correlations shape the state space of the cell as an ‘epigenetic landscape’. (2-3)

In the preceding paragraphs we observed genomes acting ‘as a whole’: the same transition point accounts for all the critical domains albeit with a different ‘amount of displacement’. If chromatin structural transitions are the material counterparts of such coherent dynamics, we can expect a corresponding typical arrangement of genes for critical states along the chromosomes. Three distinct states (super-, near- and sub-critical) in mRNA expression were revealed based on the theoretical framework of modern theoretical physics from a non-equilibrium self-organizing standpoint. (20)

Notably, this tells us that an ensemble behavior of barcode genes through on-off phase transitions on chromosomes has a similar dynamic ensemble behavior to a cascade of the on-off nerve firing bursts in neuronal networks. This indicates a non-trivial similarity between the coherent network of genomic DNA transitions and neural networks; coherent networks based on on/off switching of barcodes genes in SOC may imply the existence of rewritable self-organized memory in the genome acting as genome computing. (23)

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)

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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