Re-inventing mutation-driven evolution (2)

By: James V. Kohl | Published on: December 20, 2016

… we suspected that splicing efficiency, as defined by the fraction of pre-mRNA converted into mature mRNA, must have contributed to temperature-dependent Cirbp mRNA accumulation

Splicing efficiency is energy-dependent in the context of temperature-dependent oscillations that link the sun’s anti-entropic virucidal energy to all biodiversity via Turing’s claims and my model.

In 1951, the brilliant British scientist Alan Turing published a paper proposing a theory in chemistry called morphogenesis, which explains how cells are grouped together within an organism.

According to Turing, oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.

Could Turing’s claim be linked to Peter Berean‘s claims about differences between “bio-functional information” and energy as information?

See also: Cellular Clocks and Metabolism

..each tissue and organ appears to have unique 24 hour cycles related to the specific functions of the organ and the unique metabolic functions. Also, cycles of available material and cellular activity appears to ubiquitous.

The cellular clock mechanisms are nutrient energy-dependent and linked RNA-mediated amino acid substitutions in supercoiled DNA to the differentiation of all tissues in all organs in all living genera via biophysically constrained protein-folding chemistry in the context of the physiology of reproduction.

See also: Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal

Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora.

There are no deep evolutionary traits because all traits are energy-dependent. All traits must link RNA-mediated autophagy from the innate immune system to supercoiled DNA in the context of the physiology of reproduction. That fact links everything known to serious scientists about nutritional epigenetics from autophagy to the biophysically constrained protein folding chemistry of all genera.

For example, nutrient energy-dependent supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. Phylogenetic trees may be established by patterns of viral latency.

Viral latency recapitulates the past effects of virus-driven energy theft on gene activation via what is known about energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution that link angstroms to ecosystems in all living genera. Nutrient energy-dependent gene activation links the mitochondria to effects that viruses had on hydrogen-atom transfer before the anti-entropic virucidal effects of ultraviolet light linked ecological variation to ecological adaptation of organized genomes in species from bacteria to archaea.

Placing bacteria and archaea into different domains of life was a mistake made by Carl Woese who did not link the nutrient energy-dependent physiology of reproduction from autophagy to supercoiled DNA because he failed to consider the role of virus-driven energy theft in all pathology. That pathology is exhibited in the number of viruses in archaea compared to the number of viruses in ecologically adapted bacteria  and in ecologically adapted humans.

See also: Stanford manufactures gene-engineered cells to cure the incurable

1) To fix this, Stanford researchers use a virus to deliver a correct version of the gene onto batches of skin cells, then coax them to form sheets of healthy skin.

2) Cells are nurtured in a broth of sugars, carbohydrates, fats, growth factors and hormones, warmed at body temperature: 98.6 degrees Fahrenheit.

The virus links the natural information processing of all cell types from the innate immune system to autophagy and the nurturing helps to ensure that the pluripotent state leads to energy-dependent biophysically constrained protein folding chemistry that typically links the pheromone-controlled physiology of reproduction to all biodiversity via RNA-mediated amino acid substitutions and supercoiled DNA, which protects all organized genome from virus-driven entropy.
See also: Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

In addition, over the past 15 years, a myriad of non-coding, but functional RNAs have been discovered, including microRNAs and long non-coding RNAs that can regulate transcription [42] but more commonly translation [43] of protein coding genes. Mutations affecting non-coding genes can thus lead to changes in the repertoire of proteins that determines cell behaviour in developmental programmes, resulting in phenotypic evolution. Long non-coding RNAs have been associated with development and evolution but they are less well studied than shorter microRNAs and small RNAs [44].

During the past 15 years nutrient energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated protein folding chemistry to all biophysically constrained biodiversity via autophagy and supercoiled DNA in the context of the physiology of reproduction. There are now more than 56,000 published works that link energy as information from changes in hydrogen-atom transfer in DNA base pairs in solution to all extant biodiversity via the physiology of reproduction.
See: microRNA (56,324 citations)
See also: Long noncoding RNAs in the p53 network

p53 regulates the expression of a repertoire of lncRNAs, and some of these lncRNAs are critical regulators of cell cycle arrest, DNA damage repair, chromosomal stability and apoptosis, altogether contributing to tumor-suppressor function of p53. LncRNAs are dysregulated in a variety of cancers and therefore can be utilized as biomarkers for disease progression and as therapeutic targets.98

Energy-dependent changes in the microRNA/messenger RNA balance are linked from every aspect of biophysically constrained protein folding chemistry to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans. The sun’s anti-entropic virucidal energy has been linked to DNA damage repair, chromosomal rearrangements and chromosomal stability. Rather than continue to ignore the facts about energy-dependent healthy longevity for comparison to virus-driven energy theft and all pathology, some people may still be interested in seeing this:
What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.


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