Biologos bastardized it all again (3)

“The bacteria feed on chemicals that are released when water seeps down through the rocks. The rocks contain iron ions that can react with sea water and produce hydrogen, which the bacteria can use as an energy source for producing their own organic matter,” says Lever.

See: From hydrogen atom transfer in DNA base pairs to ecosystems 3/2/16

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent & pH-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Critical limits for enhanced medical care already include what is known about the RNA-mediated physics and chemistry of biologically-based ecological, social, neurogenic and socio-cognitive niche construction. The epigenetic landscape is clearly linked to the physical landscape of supercoiled DNA and top-down causation is manifested in increasing organismal complexity in species from microbes to humans. In all vertebrates and invertebrates the reciprocal relationships of species-typical nutrient-dependent & pH-dependent morphological and behavioral diversity are enabled by microRNAs, adhesion proteins, and pheromone-controlled reproduction. Ecological variation and biophysically constrained natural selection of nutrients cause the RNA-mediated behaviors that enable ecological adaptations, which include development of the brain during life history transitions. Ideas from population genetics typically exclude ecological factors, which must be linked to cell type differentiation. Theories are integrated with an experimental evidence-based approach that establishes what is currently known in the context of this mammalian model.

Reported a few weeks later without the link from hydrogen-atom transfer in DNA base pairs of supercoiled DNA.

Genome scale patterns of supercoiling in a bacterial chromosome 3/30/16

During transcription, the moving RNA polymerase creates a region of positive supercoiling (overwinding) in front of itself and negative supercoiling (underwinding) behind^7,8. In Escherichia coli, these negative supercoils are relaxed by the action of Topoisomerase I and the positive supercoils are relaxed by ATP-dependent DNA gyrase, so that the balance between the activities of the two enzymes determines the overall level of supercoiling^7,8. This is referred to as unconstrained supercoiling. Supercoiling can also be constrained by nucleoid-associated proteins such as H-NS, HU and FIS. HU is present in ∼30,000 dimers per cell^9,10 and is the most conserved NAP across bacterial species.

They published on the magic of biophysically constrained protein folding chemistry, which was then taken to a favorite model organism of directed evolution, Escherichia coli.
Reported as: DNA Supercoiling Combats Environmental Challenges 4/4/16

Studies in human and yeast cells investigating the supercoiling of DNA have been completed, but the present study looks at the genome of a favorite model organism, Escherichia coli.

For comparison, in our section on molecular epigenetics from this 1996 review of RNA-mediated cell type differentiation, we linked food energy-dependent alternative splicings of pre-mRNA (aka microRNAs) to cell type differentiation in species from yeasts to mammals via the physiology of pheromone-controlled reproduction. The pheromone-controlled physiology of reproduction in yeasts is linked to the production of ethanol by yeasts. The ethanol is an anti-septic. It kills bacteria. When it kills too many so-called “good bacteria,” the link to virus-driven pathology becomes clearer. The viruses in the bacteria that have been biophysically constrained are killed or activated by stress, which causes all virus-driven pathology.
See: From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Twenty years later this report that Deep-Sea Viruses Destroy Archaea 10/12/16 linked everything known to serious scientists about biophysically constrained viral latency to all biodiversity. The number of viruses in archaea compared to the number of biophysically constrained viruses in ecologically adapted bacteria in the water is obviously the best method for determining the age of the Earth. Unfortunately, pseudoscientists do not use the evidence from the virus-driven hecatomb to link viruses to all pathology. They also do not use evidence of polycombic ecological adaptations as the link to biophysically constrained healthy longevity.

How a ‘shadow zone’ traps the world’s oldest ocean water 11/10/17

The trapped nutrients biophysically constrain viral latency via the light-activated fixation of carbon in all cell types of all living genera. That is how light-activated microRNA biogenesis in plants must be linked from biophysically constrained viral latency to ecological adaptations and healthy longevity in species from microbes to humans.