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IV. Ecosmomics: A Survey of Genomic Complex Network System Sources

B. Our Own HumanVerse Genome Studies

Richards, Stephen. It’s More than Stamp Collecting: How Genome Sequencing can Unify Biological Research. Trends in Genetics. 31/7, 2015. In accord with how 2010s genome reading capabilities are wholly revising paleontology studies, a Baylor College of Medicine, Human Genome Sequencing Center, geneticist proposes to advance the life sciences by a similar emphasis and synthesis. Just as paleogenomics is achieving, scientists are beginning to employ these novel potentials across the Metazoan flora and fauna kingdoms. Going forward, we ought to recognize and employ this revolutionary approach via comparative orthologies and ontologies from arthropods to anthropopods (my word). With proper foresight, the establishment of a sufficiently complete spatial and temporal genome reference library should be of great value for ecological sustainability.

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to ‘big science’ survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. (Abstract)

Ridley, Matt. Genome. New York: HarperCollins, 1999. A lively chronicle of the twenty-three chromosomes of the human genetic makeup as viewed through the book of life metaphor.

In the beginning was the word. The word proselytized the sea with its message, copying itself unceasingly and forever. The word discovered how to rearrange chemicals so as to capture little eddies in the stream of entropy and make them live. The word transformed the land surface of the planet from a dusty hell to a verdant paradise. The word eventually blossomed and became sufficiently ingenious to build a porridgy contraption called a human brain that could discover and be aware of the word itself. (12)

Ridley, Matt. Nature via Nurture. New York: HarperCollins, 2003. The British science writer explains the current revolution in our understanding of genes and their relation to behavioral experience. The old view of particulate molecules that determine traits, unaffected by external influence, is being replaced by a conception of genetic systems as dynamic networks constantly responding to an organism’s environment in a two way dialogue. For human beings, a mutual drive between larger brains and complex culture and is encoded in and expressed by ones corresponding genetic information.

Ridley, Matt. The DNA behind Human Nature: Gene Expression and the Role of Experience. Daedalus. Fall, 2004. A succinct update based on the latest genetics research of how the molecular code is composed and operates. In this regard, the British science writer draws upon a literary analogy to reach a significant conclusion. We now know that the same 30,000 or so genes are found throughout the animal kingdom, from humans to worms, with a quite minute difference between us and chimpanzees. But if genotypes are appreciated as letters and words in sentences and paragraphs, it is their content, i.e. how these genes are expressed, that specifies the phenotype organism.

Rzhetsky, Andrey and Shawn Gomez. Birth of Scale-Free Molecular Networks and the Number of Distinct DNA and Protein Domains per Genome. Bioinformatics. 17/10, 2001. The same invariance evident throughout the natural realm is equally present in dynamic genetic systems.

Salthe, Stan. The Natural Philosophy of Ecology. www.nbi.dk/~natphil/salthe/natphilecol.2001. An essay on the need to rediscover an original unity in nature in order to find an “intelligible picture of the world.” So conceived, evolution is most of all the “irreversible accumulation of historical information.”

Sandoval-Motta, Santiago, et al. The Human Microbiome and the Missing Heritability Problem. Frontiers in Genetics. Online June 13, 2017. Universidad Nacional Autónoma de México researchers contribute to this on-going concern since 2008 when it was realized that the copious Human Genome Project data results could not yet fully explain organisms. We cited an extended Abstract in regard. A Google of the MH thtle phrase will get more hits, this paper is another instance of expansive inputs much beyond nucleotides alone.

The “missing heritability” problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this “missing heritability” have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account.

This hypothesis is based on several observations: (A) The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B) Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C) Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D) Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies. (Abstract)

Sansom, Roger. The Connectionist Framework for Gene Regulation. Biology & Philosophy. 23/4, 2008. The Texas A&M University philosopher finds a useful affinity to exist between this neuroscience approach, aka parallel distributed processing and neural networks, and molecular genomic systems. His own website cites an MIT Press forthcoming book: Ingenious Genes: How Gene Regulation Networks Evolve to Control Ontogeny. One more citation of nature’s consistent employ, under various terms and emphasis, of the same complex dynamics at each and every phase and instance.

Seringhaus, Michael and Mark Gerstein. Genomics Confounds Gene Classification. American Scientist. November-December, 2008. As noted herein, the intensive genome sequencing of human, primate, and other species have resulted in a total revision of what constitutes a gene. In this report, Yale University geneticists first review the last 70 years to illustrate a steady morphing from discrete molecules to a growing notice of systemic, repetitive networks, along with many epigenetic influences. In this bioinformatics age, how “genes” and their functions are defined, named, and classified is of much importance. But a leap of the author’s work is to perceive its deep affinity with the formative phase and current operative format of the World Wide Web. Common parallels occur by way of ontologies which gather distributed annotations and intelligence. One involves proteins, the other web pages. Might it then be imagined through an emergence from word to flesh to word that the globally collaborative Internet could be in some way genetic in kind?

Shapiro, James. Bacteria are Small but not Stupid: Cognition, Natural genetic Engineering and Socio-bacteriology. Studies in History and Philosophy of Biological and Biomedical Sciences. 38/4, 2007. Another article in the Towards a Philosophy of Microbiology section wherein the University of Chicago geneticist finds the newly appreciated relational network, communicative, and collaborative qualities of genomes and microbes to infer, in these simpler stages, a true cognitive sentience can indeed be seen at work. As Shapiro has often cited, and others increasingly, an historic change is now underway from centuries of a mechanistic scheme to an intrinsic developmental vitality that actively survives, evolves, and emerges on its own.

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. (807)

The realization that most DNA changes in bacteria (and eukaryotes too) occur by the action of natural genetic engineering systems removes the source of variation in the genome from the category of stochastic events or unpredictable accidents, and places it in the context of cellular biochemistry. (814) Bacteria certainly can use their cognitive capacities to activate DNA change when it can be useful in overcoming selective challenges. (814) Thus, the DNA segments that move through the genome, the places they move, and the sequences they rearrange can have both flexibility and predictability. (814)

The only way I know how to make sense out of the last fifty years of molecular biology is to abandon the mechanistic and atomistic ideas of the pre-DNA era and embrace a more organic, cognitive and computational view of cells and genomes. (816)

Shapiro, James. Genome Organization and Reorganization in Evolution. Van Speybroeck, Linda, et al, eds. From Epigenesis to Epigenetics: The Genome in Context. Annals of the New York Academy of Sciences, 2002. The University of Chicago microbiologist contrasts the ‘20th century of the gene’ and its reductionist method with a ‘21st century of the genome’ based on complex systems. As a result, evolutionary processes are revised from only random mutations and incremental selection to ‘non-random, genome wide rearrangements leading to novel genome system architectures.’

Shapiro, James. Genome System Architecture and Natural Genetic Engineering. Landweber, Laura and Eric Winfree, eds. Evolution as Computation. Berlin: Springer, 2002. In a contribution to the total rethinking of the nature of gene and genome, the old Mendelian version is supplanted by malleable information processing systems capable of nonrandom change guided by dynamic cellular networks. Once again an evolutionary trajectory with a sense of direction is implied.

Collectively, these discoveries set the stage for thinking of genomes as hierarchically integrated systems capable of biologically controlled change rather than as collections of autonomous genetic units subject to individual evolution by random variation. (3)

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