IV. Ecosmomics: A Survey of Genomic Complex Network System Sources
B. Our Own HumanVerse Genome Studies
Gu, Xun. An Evolutionary Model for the Origin of Modularity in a Complex Gene Network. Journal of Experimental Zoology. 312B/2, 2009. An Iowa State University geneticist further explicates how genome systems are distinguished by universal dynamical geometries.
Scale-free cellular networks are organized into a complex topology by massive interactions (links) between nodes, which can be typically characterized by a power-law degree. In contrast, almost all cellular networks show the feature of modularity. The popular BA model (Barabasi and Albert) demonstrated the origin of scale-free property by the attachment preference, but not for the origin of modularity. We propose a BBA model (Biological BA) by introducing the random link-loss mechanism under the original BA model, showing that scale-free and modularity can emerge as a derived property of the BBA model. (Abstract)
Harmon, Amy. That Wild Streak? Maybe It Runs in the Family. New York Times. June 15, 2006. A report on the latest appreciations of a genetic, familial basis for risky behavior, obesity, homosexuality, and so on.
Hebert, Paul, et al. Introduction: From Writing to Reading the Encyclopedia of Life. Philosophical Transactions of the Royal Society B. 371/20150321, 2016. University of Guelph, Canada, and Royal Botanic Garden, Edinburgh biologists open a theme issue entitled From DNA Barcodes to Biomes. A DNA barcode, in its simplest definition, is one or few relatively short gene sequences taken from a standardized portion of the genome and used to identify species. This device which can easily curate and record the vast fauna and flora biodiversity was conceived by Hebert a decade ago and now has become a global project. Typical entries are Telling Plant Species Apart with DNA, Biodiversity Analysis in the Digital Era, Bioinventories with DNA Barcodes, and DNA Barcoding and Taxonomy. For more info see International Barcode of Life: Evolution of a Global Research Community by Sarah Adamowicz in Genome (58/5, 2015), which issue also has Abstracts from the 6th International Barcode of Life Conference. Further articles are DNA Barcodes for Ecology, Evolution, and Conservation by John Kress, et al in Trends in Ecology and Evolution (30/1, 2015), and From Barcodes to Genomes: Extending the Concept of DNA Barcoding by Eric Coissac, et al in Molecular Ecology (25/1423, 2016). This tagging method employs fast sequencing techniques, and is coming into use to catalog creatures, along with agricultural pests, invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and so on.
The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed. (Kress Abstract)
Heng, H. Q. Henry. The Genome-Centric Concept: Resynthesis of Evolutionary Theory. BioEssays. 31/5, 2009. An historic shift is much along, as this section and elsewhere reports, from an initial 20th century focus on nucleotides to a wholesale rethinking in terms of dynamical systems which suffuse and activate genomes. In this paper, a Wayne State University School of Medicine geneticist provides one of the most succinct contrasts and outlines so far. Such epigenetic, modular interrelations are then found to similarly carry and convey proscriptive information. These results are seen to imply a novel evolutionary synthesis in process beyond selection alone. One may also surmise that such universal nonlinear networks could themselves be seen as quite “genetic” in kind.
Self-organization refers to a process in which a higher-level pattern emerges spontaneously from the assembly of lower level components of the system. Diverse biological phenomena have been described as self-organizing (from the spontaneous folding of biomacromolecules to morphogenesis to the formation of ecosystems). Establishing the logical relationship between natural selection and self-organization presents a challenge for evolutionary theory. The genome-centric concept nicely incorporates these two concepts. Since self-organization is a diverse term spanning the fields of physics to social science, it is necessary to divide content of nature into distinct levels in order to understand multiple levels of interactive relationships between self-organization and selection. (521)
Hopkin, Karen. The Evolving Definition of a Gene. BioScience. December, 2009. A science writer reports on its constant revision as particulate DNA biomolecules become increasingly involved in epigenetic transcription processes.
Hosseini, Sayed-Rzgar and Andreas Wagner. Genomic Organization Underlying Deletional Robustness in Bacterial Metabolic Systems. Proceedings of the National Academy of Sciences. 115/7075, 2018. University of Zurich, Institute of Evolutionary Biology and Environmental Studies biologists continue with perceptions, in so many words, of a missing generative source for life’s evolutionary development and organic viability. See also herein The Architecture of an Empirical Genotype-Phenotype Map by Jose Aguilar-Rodriguez, et al for another angle by this central European collaboration.
From the organismal and the anatomical levels down to the molecular level, all complex biological systems manifest astonishing organization and order that are counterintuitive and challenging to explain by evolutionary mechanisms. In this study, we focus specifically on one aspect of this biological organization: the arrangement of metabolic genes in bacterial genomes. We show that this organization ensures a substantially higher robustness to large-scale gene deletions than expected from random genomic ordering. We systematically investigate the possible evolutionary mechanisms behind the emergence of such robust organizations. Our analysis provides several lines of evidence indicating that bacteria may have gained a robust genome organization through pervasive gene loss events. (Significance)
Houle, David, et al. Phenomics: The Next Challenge. Nature Reviews Genetics. 12/12, 2010. Another ‘-omics’ word as genetic studies continues to burst beyond the 20th century DNA helix. In this case, with various web definitions, it generally considers systems transferences between genotypes and phenotypes. And with other epigenetic turns, within a major-multi-level expansion, an evolutionary tandem trajectory of program and organism may be quite revealed.
Ideker, Trey, et al. A New Approach to Decoding Life: Systems Biology. Annual Review of Genomics and Human Genetics. 2/343, 2001. After bioinformatic sequencing of the human genome, the next research phase is to appreciate the complementary network properties of gene expression. By this approach a multilevel informational hierarchy of complex processes from DNA and protein interactions to organisms and ecologies can be constructed.
Istrail, Sorin, et al. The Regulatory Genome and the Computer. Developmental Biology. 310/2, 2007. Coauthors include Smadar Ben-Tabou De-Leon and Eric Davidson whom discuss the pros and cons of this often implied analogy, but which is rarely considered in any sufficient depth.
In summary, a view of the evolutionary process leading to complex animals is that the essential properties of the genomic computer discussed in this essay were the condition for, and predate, complex animal forms: first came the properties of the genomic computer, including logic processing CRMs and regulatory network subcircuits, and then came programs for development built on these properties, and hence the animals. (195)
Information: Its Interpretation, Its Inheritance, and Its Sharing.
Philosophy of Science.
The Tel Aviv University geneticist contends that life’s evolution is most characterized by an emergent sequence of new ways to store and transmit information: genetic, epigenetic, behavioral and cultural-symbolic inheritance systems. A factor which facilitates specialization, division of labor and new levels of organization and individuality is the communal sharing of environmental information.
Jablonka, Eva and Eors Szathmary. The Evolution of Information Storage and Heredity. Trends in Ecology and Evolution. 10/5, 1995. Comments on the appearance of major evolutionary transitions due to novel inheritance systems from molecules to epigenetic and linguistic systems.
Jablonka, Eva and Marion Lamb. The Evolution of Information in the Major Transitions. Journal of Theoretical Biology. 239/236, 2006. The philosophical biologist teams of the above authors and of John Maynard Smith and Eors Szathmary, have in their respective books (please search site), expanded evolutionary theory into a recurrent sequence from genes to societies. The ‘major transitions’ of the latter pair is complemented by Jablonka and Lamb which emphasizes an ascendant message from DNA to symbols. A lapse in the Maynard Smith and Szathmary stages is then said to be an underplay of the emergence of a multicellular nervous system. Both approaches, which have gained currency, describe a developmental scale that facilitates the axial rise of an immaterial informative quality, as if acorn to oak to acorn, word to flesh to word.
We have argued that in two of the major transitions – the evolution of social groups and the evolution of linguistic communities – learning through and from others had a key role. Such social learning, like most forms of learning, requires a nervous system, so the evolution of the nervous system and the processing of neural information were preconditions for the transitions that depended on behavioral transmission. (244)