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IV. Ecosmomics: A Survey of Animate Complex Network Systems

B. Our Own HumanVerse Genome Studies

Shea, Nicholas. Inherited Representations are Read in Development. British Journal for the Philosophy of Science. Online June, 2012. In a series of articles over recent years, the Oxford University philosopher of biology has proposed that our understandings of genomic activity, broadly conceived, could benefit by viewing this as semantic representations. In regard, an affinity to cognitive memories is drawn upon as they “represent” or contain one’s corpus of lived and learned experience. (Quote 1) A companion paper might be “Developmental Systems Theory Formulated as a Claim about Inherited Representations” in Philosophy of Science (76/1, 2011) where epigenetic and environmental influences are factored in via the DST school. (Quote 2)

Recent theoretical work has identified a tightly constrained sense in which genes carry representational content. Representational properties of the genome are founded in the transmission of DNA over phylogenetic time and its role in natural selection. However, genetic representation is not just relevant to questions of selection and evolution. This article goes beyond existing treatments and argues for the heterodox view that information generated by a process of selection over phylogenetic time can be read in ontogenetic time, in the course of individual development. Recent results in evolutionary biology, drawn both from modelling work, and from experimental and observational data, support a role for genetic representation in explaining individual ontogeny: both genetic representations and environmental information are read by the mechanisms of development, in an individual, so as to lead to adaptive phenotypes. Furthermore, in some cases there appears to have been selection between individuals that rely to different degrees on the two sources of information. Thus, the theory of representation in inheritance systems like the genome is much more than just a coherent reconstruction of information talk in biology. Genetic representation is a property with considerable explanatory utility. (Abstract 1)

Developmental systems theory (DST) is often dismissed on the basis that the causal indispensability of nongenetic factors in evolution and development has long been appreciated. A reformulation makes a more substantive claim: that the special role played by genes is also played by some (but not all) nongenetic resources. That special role can be captured by Shea’s ‘inherited representation’. Formulating DST as the claim that there are nongenetic inherited representations turns it into a striking, empirically testable hypothesis. DST’s characteristic rejection of a gene versus environment dichotomy is preserved but without dissolving into an interactionist casual soup, as some have alleged. (Abstract 2)

Sherman, Rachel and Steven Salzberg. Pan-Genomics in the Human Genome Era. Nature Reviews Genetics. 21/243, 2020. Johns Hopkins University computational biologists describe an expansion of the multinational project to sequence all creaturely genomes so as to achieve an entire integrative pan-species genome database. Such an accomplishment just now possible can help preserve biodiversity and converse environments.

Since the early genome era, the scientific community has relied on a single “reference” genome for each species. As sequencing costs dropped, thousands of new genomes have been sequenced which led us to realize that a single reference genome is inadequate. By sampling a diverse set of individuals, one can begin to assemble a pan-genome: a collection of all the DNA sequences that occur in a species. Here we review efforts to create pan-genomes for an array of species from bacteria to humans, and consider computational methods that have been proposed to capture, interpret and compare pan-genome data. (Abstract excerpt)

Shou, Chong, et al. Measuring the Evolutionary Rewiring of Biological Networks. PLoS Computational Biology. January, 2011. As the Abstract details, a team of Yale University, University of Toronto, and Stanford University bioinformatic specialists including Mark Gerstein contribute another take on nature’s inherent penchant for genomes to employ dynamical organizations. In regard, could one say that by drawing on such mathematical propensities, a genome might know what it is doing?

We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or “rewire”, at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. (Abstract)

Skar, John. Introduction. Philosophical Transactions of the Royal Society of London A. 361/6, 2003. To a dedicated issue on “Self-organization: The Quest for the Origin and Evolution of Structure” with papers by a constellation of authors such as Lee Smolin and Ian Stewart.

These discoveries, along with others in genetics, will drive scientists to consider mutations as no longer necessarily random events but actively generated by the cell’s epigenetic network, and for evolution to be an integral part of the self-organization of living organisms. (1052)

Smith, Laura, et al. Unraveling the Epigenetic Code of Cancer for Therapy. Trends in Genetics. 23/9, 2007. As other citations herein note, a major revolution is underway in our understanding of the nature and activity of genetic processes. Not yet mainstream or fully worked through, it involves a salient shift from the 20th century emphasis on molecular DNA and RNA to this ancillary domain of how ‘genes’ transcribe and translate into the vast variety of proteins and cells. Cancer treatment is a frontier area because it has lately been realized that such cellular decay (also aging deficits) are due more to errors in transmission, rather than point to point genes. And all this seems to beg an analogy with written language where how words are grammatically used in sentences and paragraphs is just as important, probably more so.

It is now evident that an additional layer of information required for proper gene expression is encoded in the genomic sequence and exceeds the information of the four bases: adenine, thymine, guanine and cytosine. This is achieved in the form of epigenetic modifications, which in their entirety represent the ‘epigenome’ (from the Greek prefix epi-, meaning ‘on’ or ‘over’). Epigenetic modifications are heritable and can be transmitted to daughter cells during cell divisions. Most importantly, they leave the option for reprogramming in the context of development and differentiation. (449)

Snyder, Michael and Mark Gerstein. Defining Genes in the Genomics Era. Science. 300/258, 2003. Now that genomes, the entire genetic coding system for a certain organism, are becoming sequenced and transcribed, a new concept of what a gene is results. Rather than particulate in kind, they are more like “a complete chromosomal segment responsible for making a functional product.” (258)

Stoltzfus, Arlin. Mutation Biased Adaptation in a Protein NK Model. Molecular Biology and Evolution. 23/10, 2006. A University of Maryland biologist argues that genetic change is not an accidental variant that passively awaits selection. Rather, new gene configurations act as an “immanent directional orienting factor” upon evolutionary pathways. See also Stoltzfus’ Mutationism and the Dual Causation of Evolutionary Change in Evolution and Development (8/3, 2006) and Google his name.

Thus, it is of interest to consider the possibility that biases or nonrandomness in the rate of origin of new variants by mutation (and more generally, by mutation and altered development) are a general cause of nonrandomness in evolution, a possibility that cuts across traditional scientific disputes over selection versus drift, the Modern Synthesis versus the Neutral Theory, and morphological versus molecular evolution. (1853)

Stotz, Karola. Experimental Philosophy of Biology. Studies in History and Philosophy of Science. 40/2, 2009. A University of Sydney philosopher contributes to the 21st century project to reinvent and redefine genetic phenomena beyond older particulate “genes” so as to include the equally present layers of interactive, relational networks

In this vision the ‘gene’ is relieved of its unrealistic and mystical status as the sole embodiment of life. Instead, genes become prosaic ways to classify the template capacity of certain parts of the genome, a capacity that must be interpreted through a process of gene expression to yield any determinate result. Because of this limited and very context-dependent capacity, the gene is also stripped of its place as the sole unit of inheritance. (237) Inheritance is not embodied in mystical preformations of the phenotype but in the reproduction of the necessary factors of development that will self-organize to reproduce a similar developmental life cycle. Life is not situated in genes but in the particular organization of biomolecules that enables the system to maintain itself by reconstituting its own components from the template capacity in the genome, constructing the environmental factors necessary for this to occur, and ultimately reproducing copies of itself. (237)

Stotz, Karola. The Ingredients for a Postgenomic Synthesis of Nature and Nurture. Philosophical Psychology. 21/3, 2008. An introduction by the University of Sydney scholar to papers from a March 2007 Indiana University symposium on “Reconciling Nature and Nurture in Behavior and Cognition Research.” The shifting genetic paradigm from discrete “programs” to an “interactive” epigenetic context, which involves both the cellular organism and its external environment, is under review, and evokes a sense of molecular “letters and words” and their parsed usage in descriptive sentences and paragraphs. As a growing number of other fields realize, a dynamic dialogue of essential script and contingent evolutionary and developmental editing goes on. Other notable authors herein include Eva Jablonka, Paul Griffiths, Jason Scott Robert, and Edouard Machery.

In other words, the more complex an organism, the more complex the expression of its limited number of coding sequences….what is of particular importance during development is not the existence of some genes but their differential time- and tissue-dependent expression. In the last two decades development has become equated with differential gene expression, but what is hidden behind this equation is the complex network of molecules other than DNA (such as proteins and metabolites), cellular structures, three-dimensional cellular assemblages, and other higher-level structures that control or are otherwise involved not only in the differential expression of genes but in a wide range of other developmental processes decoupled from the direct influence of DNA sequences. (363)

Strohman, Richard. The Coming Kuhnian Revolution in Biology. Nature Biotechnology. 15/3, 1997. A notable statement of the shift underway from a determinism of particulate genes to an embryonic development due to informed dynamic systems similar to neural networks.

The theory is in trouble because it insists on locating the driving force solely in random mutations. An alternative theory of evolution that emphasizes the importance of nonrandom (epigenetic) changes during development could explain the problems now being encountered by evolutionary theory. (195) The cell is starting to look more like a complex adaptive system rather than a factory floor of robotic gene machines, and that is well and good….Many of us are guessing at some kind of complex adaptive system theory that can embrace discontinuous change at all levels of life’s organization. (197)

Sweatt, David. The Emerging Field of Neuroepigenetics. Neuron. 80/3, 2013. In a special Neuroscience Retrospective, a University of Alabama neurobiologist provides a past and future survey of this expansion of genetic phenomena beyond just point nucleotides. The admission that both genes and environment reciprocally interact and cross-contribute then requires a major rethinking such as “What Roles Do Epigenetic Mechanisms Play in Complex Human Diseases of the Nervous System?” and “Are Acquired Epigenetic Marks Transmitted Across Generations?” with regard to an “epigenome code.” See also in this issue The New Science of Mind and the Future of Knowledge by Nobel laureate Eric Kandel.

Over the past 25 years, the broad field of epigenetics and, over the past decade in particular, the emerging field of neuroepigenetics have begun to have tremendous impact in the areas of learned behavior, neurotoxicology, CNS development, cognition, addiction, and psychopathology. However, epigenetics is such a new field that in most of these areas the impact is more in the category of fascinating implications as opposed to established facts. In this brief commentary, I will attempt to address and delineate some of the open questions and areas of opportunity that discoveries in epigenetics are providing to the discipline of neuroscience. (Abstract)

Only infrequently do scientific discoveries force the recasting of a centuries-long philosophical debate. However, over the last 25 years, and indeed largely over the last decade, the emerging field of neuroepigenetics has necessitated the reformulation of the fundamental existential question of nature versus nurture. Based on recent discoveries in the broad field of epigenetics, it no longer makes sense to debate nature versus nurture. There is no longer a mechanistic dichotomy between nature and nurture (or genes and environmental experience, as is the more modern phrasing). Rather, it is now clear that there is a dynamic interplay between genes and experience, a clearly delineated and biochemically driven mechanistic interface between nature and nurture. That mechanistic interface is epigenetics. (624)

Trieu, Tuan, et al. Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes. Nature Scientific Reports. 9/4971, 2019. University of Missouri bioinformatic scientists Tuan Trieu (Vietman), Oluwatosin Oluwadare (Nigeria), and Jianlin Cheng (China) come together in mid America where they are developing better ways to visualize whole genome structures, as the paper illustrates. An improved image quality is achieved by a novel algorithm which can fully reveal these complex nucleotide packages

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