Energy-dependent epigenetic translation to mRNA stability (2)

However, unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

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The unfolded protein response (UPR) handles unfolded/misfolded proteins accumulated in the endoplasmic reticulum (ER). However, it is unclear how vertebrates correctly use the total of ten UPR transducers. We have found that ER stress occurs physiologically during early embryonic development in medaka fish…

ER stress links the virus-driven degradation of messenger RNA to all pathology in all living genera. Negative supercoiling in DNA links the degradation of messenger RNA from mutations via the accumulation of unfolded/misfolded proteins. For comparison, the nutrient energy-dependent pheromone-controlled physiology of reproduction in bacteria links the growth of trees in the forest to cell type differentiation in birds that have different diets.

Untangling the knots in cell stress

“We found that at first the production of short chain collagen causes a certain transducer to be activated for quality control.” Collagen is the most abundant protein in vertebrates, providing external support for cells.

In the next stage of development, cells received a signal from main actor proteins and started to produce longer-chain collagen. In response to this new ER stress, a new UPR transducer was activated to produce components to export the larger collagen out of the ER. Without this, larger collagen would be unable to leave the cells and do its job.

“This showed us that different UPR transducers are activated to cope with different ER stresses caused by different proteins,” says Ishikawa.

ER stresses are not caused by proteins. Unfolded/misfolded proteins accumulate outside the context of energy as information and biophysically constrained supercoiling of functional DNA. See: Structural diversity of supercoiled DNA
The supercoiled DNA of soil bacteria links the energy-dependent growth of trees to the diet of the birds and the bees.
See: Genome divergence and diversification within a geographic mosaic of coevolution

Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

Coevolution was reported as energy-dependent biophysically constrained ecological adaptation in: The seeds of speciation

The details of the crossbill-lodgepole mosaic have been studied extensively, but it’s not been clear whether South Hills crossbills are genetically isolated by coevolution with pine in that one tile of the mosaic. If they are, the birds’ [nutrient-dependent] adaptation to the tree’s defenses might be setting the South Hills crossbills on the road to the origin of a new species.

For comparison to claims about new species of birds being created by evolution across 6000 years, see also: Talking Trees—Secrets of Plant Communication

When one tree is sick, nearby trees may share nutrients through their roots to help it get well again. If a lodgepole pine sapling springs up in the shade of a thick forest, older trees somehow sense that it doesn’t get enough sunlight to make food for itself, so they may share their bounty. They even change their root structure to open space for saplings.

The complexity of systems biology among all energy-dependent ecosystems is difficult for serious scientists to place back into the context of coevolution and impossible to place back into the context of Mutation-Driven Evolution (p 196)

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

See also: Hypothalamic microRNAs flip the switch for fertility

Figure 1) MicroRNA-gene network controlling GnRH transcription: the timely switch in GnRH expression from repression to induction leads to puberty onset

MicroRNAs are the link to GnRH transcription from what we referred to as pre-mRNAs in our section on molecular epigenetics from this 1996 review: 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.

If microRNAs are not the link from energy-dependent epigenetic translation to mRNA stability, theorists will need to find experimental evidence of how the sun’s anti-entropic virucidal energy as information is linked from top-down causation to hormones and behavior, and present that evidence to serious scientists for consideration.