Pattern recognition: biogeochemical structure and function

By: James V. Kohl | Published on: May 25, 2015

Microbes Effect on the Brain


Recent research shows dramatic effects of microbe products from the gut on mental function—depression, stress, autism, and degenerative illness. In humans, many studies show microbes affect anxiety, mood, depression and social behavior. Direct effects are through secreted products, stimulation of the enteric nervous system and travel of microbes into the brain, while indirect factors are microbes’ influence on immune function affecting behavior. Microbes produce molecules that transform into hormones and neurotransmitters or they produce neurotransmitters themselves. Microbes effect on the brain includes fetal development and neurotransmitter function.

My comment: Thanks again for trying to lead others who are interested in learning about pattern recognition by providing them with facts. As you can see in the 5 articles linked below, you still are several years ahead of theorists who attribute increasing organismal complexity and biodiversity to mutations and evolution.
Like your articles, these articles individually and collectively attest to the importance of the anti-entropic energy of the sun to DNA repair and the physiology of reproduction, which links the creation of earth to the creation of amino acids and to the base pair substitutions and amino acid substitutions that differentiate all cell types.
Many others seem to have failed to notice that there is a pattern of creation. Nothing appears to be random. Viruses in the gut microbiome would link viral microRNAs from entropic elasticity to genomic entropy without the anti-entropic epigenetic effects of the sun and nutrient-dependent RNA-mediated amino acid substitutions that differentiate all cell types in all genera.
If anyone who has followed your accurate representations of biologically-based cause and effect placed them into the content of a book, it would be a best-selling way to connect your blog posts to everything known to serious scientists about biodiversity.
Patterns and ecological drivers of ocean viral communities
Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links
Structure and function of the global ocean microbiome
Eukaryotic plankton diversity in the sunlit ocean
Determinants of community structure in the global plankton interactome

Excerpts, conclusions,  and comments:

Patterns and ecological drivers of ocean viral communities


Such experimental and analytical progress, coupled to sampling opportunities from the Tara Oceans expedition, are advancing viral ecology toward the quantitative science needed to model the nanoscale (viruses) and microscale (microbes) entities driving Earth’s ecosystems.

My comment: This series of articles advances what is known about viral ecology and allows what is known to be placed into the context of science fiction that has become fact. See for example: The Darwin Code by Greg Bear.
Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

Here, we performed unbiased proteomic analyses of the dynamically changing protein landscape at damaged chromatin undergoing DNA replication. This yielded mechanistic insights into the pathways that ensure genomic stability during perturbed DNA replication.

My comment: Evolutionary theorists seem to have largely ignored the fact that genomic stability must be maintained throughout the life history transitions of organisms that mature and reproduce. For example, the bacterial flagellum reportedly re-evolved in 4 days. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.  That required orchestrated activity among many organisms with lineages that continued due to their nutrient-dependent pheromone-controlled physiology of reproduction.

Structure and function of the global ocean microbiome


Finding that temperature drives microbial community variation and revealing the high functional redundancy in ocean microbial communities at global scale have wide-ranging implications for potential climate change–related effects. The Tara Oceans data set supports progress not only toward a holistic understanding of the ocean ecosystem but also of microbial communities in general, by facilitating comparative analyses between ecosystems.

My comment: I wonder who did not know until now that thermodynamic cycles of protein biosynthesis and degradation link temperature-dependent instability to organism-level thermoregulation and the stability of organized genomes via the biophysically constrained chemistry of protein folding. See also: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)

Eukaryotic plankton diversity in the sunlit ocean


…biotic interactions, rather than competition for resources and space (62), are the primary forces driving organismal diversification in marine plankton systems.

My comment: The primary forces linked to biodiversity were not described in the context of Darwin’s ‘conditions of life.’ However, Dobzhansky (1973) linked them to primate species diversity. In Nothing in Biology Makes Any Sense Except in the Light of Evolution, he claimed:

Molecular studies have made possible an approach to exact measurements of degrees of biochemical similarities and differences among organisms. Some kinds of enzymes and other proteins are quasiuniversal, or at any rate widespread, in the living world. They are functionally similar in different living beings, in that they catalyze similar chemical reactions. But when such proteins are isolated and their structures determined chemically, they are often found to contain more or less different sequences of amino acids in different organisms. For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

Determinants of community structure in the global plankton interactome


The global ocean interactome can be used to predict the dynamics and structure of ocean ecosystems. The interactome reported here spans all three organismal domains and viruses. The analyses presented emphasize the role of top-down biotic interactions in the epipelagic zone. This data will inform future research to understand how symbionts, pathogens, predators, and parasites interact with their target organisms and will ultimately help elucidate the structure of the global food webs that drive nutrient and energy flow in the ocean.

My comment: The structure of all functional ecosystems is nutrient-dependent. The function of successful ecosystems requires a direct link from nutrient-dependent structures to the physiology of reproduction. In all genera, the direct link is RNA-mediated amino acid substitutions that differentiate cell types via their fixation in organized genomes of species that mature and reproduce. Nothing except nutrient uptake ensures successful reproduction. It links RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all genera via what is currently known about the physics, chemistry, and conserved molecular mechanisms that link atoms to ecosystems. See for examples in species from microbes to humans: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
See also, the invited review of nutritional epigenetics that replaces evolutionary theories about mutations with facts that link ecological variation to metabolic networks and genetic networks that enable successful reproduction and ecological adaptations in all species.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See also: Genome Digest

Unique miRNAs appear to link the nutrient-dependent pheromone-controlled life history transitions of bees to RNA-mediated metabolic networks and genetic networks in all genera via base pair substitutions and amino acid substitutions that differentiate cell types.
See for example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
 See also:

Posted by Jason Silva on Wednesday, May 20, 2015

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[…] See also: Microbes Effect on the Brain in my blog post from May 25, 2015: Pattern recognition: biogeochemical structure and function […]

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