Viruses and the human-like microbiome

By: James V. Kohl | Published on: May 24, 2015

Ocean’s microbiome has incredible diversity – and human likeness


The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways.

The New Scientist article  reports on:

Structure and function of the global ocean microbiome

Journal article abstract conclusion:

…vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

My comment: The biophysically constrained similarities link viruses and viral microRNAs from the innate immune systems of bacteria to thermodynamic cycles of protein biosynthesis and degradation, which enable the entropic elasticity that is required to link atoms to ecosystems. Obviously, no physicochemical differences are likely to be found that prevent the links from atoms to ecosystems.  See, for example, my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
The link from atoms to ecosystems can be clarified by theoretical physicists who are willing to step away from their discussions of black holes and dark matter. Some of them may be now be more willing to discuss the anti-entropic epigenetic effects of the sun’s biological energy and how biophysically constrained membrane-contained photosynthesis is linked to nutrient-dependent microRNAs. The nutrient-dependent microRNAs enable the link from RNA-mediated DNA methylation to the RNA-mediated amino acid substitutions that repair DNA. The substitutions stabilize the organized genomes of all genera via fixation in the context of the physiology of reproduction.
Simply put, that is how the sun’s biological energy and the nutrient-dependent physiology of reproduction link what is known about the epigenetic effects of nutrients on metabolic networks and genetic networks to the epigenetic effects of pheromones on hormone-organized and hormone-activated behaviors in insects and mammals. See for review: From Fertilization to Adult Sexual Behavior and Nutrient-dependent/pheromone-controlled adaptive evolution: a model (Note: until now I used the term ‘adaptive evolution’ instead of ‘ecological adaptation’ to avoid reviewers who typically reject my submissions because they fail to support the evolution industry.)
Across species examples that link single base pairs to single amino acid substitutions and cell type differentiation in all cells of all individuals of all genera are included in my 2013 review article, which is an extension of our 1996 review and my 2012 review article Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
So far as I know, Anna Di Cosmo​ and the co-authors of Role of olfaction in Octopus vulgaris reproduction are the only researchers who have followed the extant literature on biologically-based cause and effect and cited my 2013 review. They also cited Elekonich and Robinson (2000): Organizational and activational effects of hormones on insect behavior.  That review linked our 1996 model of RNA-mediated cell type differentiation from yeasts to insects via the conserved molecular mechanisms.  Teresa Binstock provided details about the mechanisms in the section on molecular epigenetics. Other serious scientists who are willing to join those who are Combating Evolution to Fight Disease may be encouraged by the report in “Science Magazine” and in the “New Scientist.”
Those who are interested in an example of science fiction that has become scientifically established fact may be interested in reading The Darwin Code by Greg Bear. See also: Eukaryotic plankton diversity in the sunlit ocean

Decoding the ecological and evolutionary rules governing plankton diversity remains essential for understanding how the critical ocean biomes contribute to the functioning of the Earth system.

My comment: The ecological rules that link metabolic networks to genetic networks cannot be placed into the context of evolutionary rules, until evolutionary rules explain no evolution of microbes living in sediment at the ocean’s bottom for ~2 billion years, to re-evolution of the bacterial flagellum over-the-weekend.
See also: Partly human yeast show a common ancestor’s lasting legacy for comparison to accurate representations of biologically-based cause and effect that link the de novo creation of amino acids to membrane-contained biophysically constrained photosynthesis. Also see other articles published this week in “Science Magazine” that provide more information about the nutrient-dependent RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all genera via the physiology of the nutrient-dependent pheromone-controlled reproduction of some yeasts and all other species with sexually-differentiated cell types.
See also: Informing the biologically uninformed

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