Energy-dependent alternative splicings 1996 – 2016

By: James V. Kohl | Published on: December 26, 2016

(click to enlarge)

Highlights:

1) Alternative splicings of messenger RNA link the sun’s anti-entropic virucidal energy as information to DNA repair.

2) DNA repair links fixation of amino acid substitutions in supercoiled DNA to healthy longevity.

3) Supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.

4) Genomic entropy is less likely to occur in the context of the physiology of reproduction and transgenerational epigenetic inheritance of ecologically adapted morphological and behavioral phenotypes.

5) Preventing virus-driven energy theft from causing skin cancer with a vitamin B3 supplement exemplifies how the nutrient-dependent pheromone-controlled physiology of reproduction is linked from the transgenerational epigenetic inheritance of ecologically adapted individuals to healthy longevity in all living genera.

See first:

1) Dietary lutein and pheromone-controlled brain development

2) 2016 obfuscated facts about energy as information

3) Energy-dependent oscillating gene networks organize life

Alternative splicing and the evolution of phenotypic novelty (2016)

Alternative splicing is a process whereby multiple functionally distinct transcripts are encoded from a single gene by the selective removal or retention of exons and/or introns from the maturing RNA [1–4]. The process is highly regulated, involving trans-acting splicing factors and cis-acting regulatory motifs (see [5] for review) and so is susceptible to hereditary and somatic mutations [6].

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

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).

Watch as an entire issue of Phil. Trans. R. Soc. B attempts to put alternative RNA splicings back into the context of ridiculous theories about evolution across millions of years. The attempt to do that comes 20 years after we detailed the facts that link energy-dependent RNA-mediated events from the de novo creation of G protein-coupled receptors in yeast to all biodiversity via the pheromone-controlled physiology of reproduction in species from microbes to humans.
See for comparison: A possible role of DNA methylation in functional divergence of a fast evolving duplicate gene encoding odorant binding protein 11 in the honeybee

Two years ago, I sent this link about the refutation of macroevolution to Ryszard Maleszka because of our shared interest in the honeybee model organism.

Subject: Birds, bees, and dogs

In truth, for all the undoubted charms of dogs, their breeding is nothing other than degeneration.

I alerted him to the forthcoming SFN poster presentation “Gene co-expression network analysis in a free-living, behaviorally polymorphic species”

The presentation was published on 10/16/15 as: Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

The genome of the white-throated sparrow (Zonotrichia albicollis) contains an inversion polymorphism on chromosome 2 that is linked to predictable variation in a suite of phenotypic traits including plumage color, aggression and parental behavior. Differences in gene expression between the two color morphs, which represent the two common inversion genotypes (ZAL2/ZAL2 and ZAL2/ZAL2(m) ), may therefore advance our understanding of the molecular underpinnings of these phenotypes. To identify genes that are differentially expressed between the two morphs and correlated with behavior, we quantified gene expression and terrirorial aggression, including song, in a population of free-living white-throated sparrows. We analyzed gene expression in two brain regions, the medial amygdala (MeA) and hypothalamus. Both regions are part of a ‘social behavior network’, which is rich in steroid hormone receptors and previously linked with territorial behavior. Using weighted gene co-expression network analyses, we identified modules of genes that were correlated with both morph and singing behavior. The majority of these genes were located within the inversion, showing the profound effect of the inversion on the expression of genes captured by the rearrangement. These modules were enriched with genes related to retinoic acid signaling and basic cellular functioning. In the MeA, the most prominent pathways were those related to steroid hormone receptor activity. Within these pathways, the only gene encoding such a receptor was ESR1 (estrogen receptor 1), a gene previously shown to predict song rate in this species. The set of candidate genes we identified may mediate the effects of a chromosomal inversion on territorial behavior.

Ryszard Maleszka’s response was extremely harsh.

The link that you provide is to a website that promotes the nonsense of creationism… please do not send me such crap

Responses like his make it impossible to determine why someone who studies the honeybee model organism of nutrient energy-dependent pheromone-controlled cell type differentiation thinks that creationism is crap. Doney Maney’s group has linked the nutrient energy-dependent pheromone-controlled cell type differentiation from honeybees (invertebrates) to vertebrates (birds). In the context of links from the birds to the bees, creationists start from the creation of energy and rarely make unsupported claims about mutations and evolution.

Most creationists seem to already know that Schrodinger (1944) put his claims into the context of how cow manure contains enough energy to make things grow in the context of the addition of a minimal amount of anti-entropic energy from sunlight. Dobzhansky (1973) put that fact into the context of energy-dependent amino acids substitutions that differentiate all cell types in all individuals of all species, not just the birds and the bees. Amino acid substitutions in cytochrome C, which is a small, water soluble heme protein associated with the inner membrane of the mitochondrion, differentiate the cell types of yeasts, molds, insects, and mammals.

Excerpts:

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids.
….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.

In this example, a artificially-induced nutrient-dependent pheromone-controlled ecological adaptation links what invertebrates eat from energy-dependent autophagy to supercoiled DNA via their physiology of reproduction.
The study on graphene-fed silkworms reminded me of the first published work that linked the pheromones of a moth species to its biophysically constrained behavior via its ability to find food and reproduce.
Pheromones: a new term for a class of biologically active substances
Anna Di Cosmo’s probably is familiar with all the other studies that have replicated those findings in all other living genera. In fact, I think that most serious scientists realize all living genera must eat. Anna’s group has published her group’s findings on cell type differentiation in marine invertebrates and the molecular mechanisms clearly extend to terrestrial invertebrates.
See: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

The facts about natural selection and energy-dependent RNA-mediated amino acid substitutions seem to have escaped the attention of neo-Darwinian theorists since the time that Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for linking the 1933 Prize Schrodinger and Dirac shared in Physics to all energy-dependent biologically-based cause and effect.

Again, we see how ridiculous it is for Ryszard Maleszka, Peter Berean or anyone else to claim I have not proved that energy is information. All biologically active substances exemplify links from energy-dependent metabolic networks to genetic networks.

Genetic networks are biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. People demonstrate their ignorance best when it is a complete misrepresentation of everything known to all serious scientists about biophysically constrained energy-dependent RNA-mediated protein folding chemistry.

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? (Roger Penrose 8 August 1991)

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution. (Jay R. Feierman 25 July 2013

For comparison, Peter Berean invented a weasel word: “bio-functional information.” That’s like defining the energy-dependent changes in morphology as “mutations” without linking them from the biologically-based physiology of reproduction to behavior in the years since Schrodinger (1944) linked physics to biology with his claims about the anti-entropic energy of the sun. Even worse is the claims made by other theorists and atheists who ignored Darwin’s “conditions of life.” The theorists and atheists seem to be dumber that the dirt that Schrodinger placed into this context:

“Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)”

See how the sun’s anti-entropic energy was linked to all biodiversity via what is currently known to all serious scientists about physics, chemistry, and the conserved molecular mechanisms of cell type differentiation that link ecological variation to ecological adaptations from the birds to the bees via hydrogen-atom transfer in DNA base pairs in solution that link angstroms to ecosystems in all living genera via alternative RNA splicings and the physiology of reproduction.
See also this definition of intrinsic:

belonging to a thing by its very nature:

Intrinsic Photosensitivity Enhances Motility of T Lymphocytes (published 20 Dec 2016)

Organisms have evolved a multitude of photoreceptors tuned to different light frequencies and coupled to diverse cellular responses. Plants, algae, bacteria and protozoa express red, blue/green and UV-light receptors that mediate photosynthesis, phototropism and phototaxis¹.

The claim that organisms evolved photoreceptors and intrinsic photosensitivity is absurd. The energy-dependent biophysically constrained chemistry of RNA-mediated protein folding links the anti-entropic virucidal energy of sunlight to the de novo creation of all G protein-coupled receptors. That is how chemotaxis and phototaxis are linked to the physiology of nutrient energy-dependent pheromone-controlled reproduction in species from archaea to humans.

Anyone who reports that organisms evolved energy-dependent intrinsic molecular mechanisms that link sunlight to the de novo creation of all biodiversity via cell type differentiation in all living genera is a pseudoscientist.

For example, most science journalists are like pseudoscientists. Intrinsic Photosensitivity was reported as: Sunlight offers surprise benefit—it energizes infection fighting T cells

“We found that sunlight makes hydrogen peroxide in T cells, which makes the cells move. And we know that an immune response also uses hydrogen peroxide to make T cells move to the damage,” Ahern says. “This all fits together.”

It fits together because experimental evidence of biologically-based cause and effect links chemotaxis from the energy-dependent de novo creation of olfactory receptor genes to phototaxis, which enables energy-dependent foraging for nutrients. Simply put, they link everything known to serious scientists about the energy-dependent links from angstroms to ecosystems in all living genera, but they report that the conserved molecular mechanisms are evolved intrinsic molecular mechanisms.

When viruses invade or cells turn malignant, the immune system mobilizes a small cohort of naïve or immature CD8 T cells, a crucial subdivision of the immune system charged with killing virus-infected and cancerous cells.

The “mobilization” of T cells is energy-dependent and the mobilization links “intrinsic photosensitivity” to supercoiled DNA via the innate immune system.

…researchers have discovered that a metabolic oscillator acts as the conductor of cell division.

That fact links Einstein’s claims about energy and Turing’s claims about oscillations to everything known about energy-dependent autophagy and supercoiled DNA, which protects all organized genomes from virus-driven energy theft.

Compare that claim to what was reported in the context of the Top 10 science stories of 2016: Gravitational waves, Zika, Proxima b and more
Gravitational waves
Zika virus
Proxima b
Three-parent baby
Arctic sea ice loss
Ancient human migration
Minimal genome
Alzheimer’s treatment
Antarctic ozone hole
Artificial intelligence
Each of these reports is an example of publication bias. None link energy to cell type differentiation and none link virus-driven energy theft to all pathology.
See for comparison:
Does ‘publication bias’ affect the ‘canonization’ of facts in science?

…as molecular biologists worked to unravel the details of the eukaryotic RNA interference (RNAi) pathway in the early 2000s, they wanted to understand how the RNAi pathway was initiated. Based on work with Drosophila cell lines and embryo extracts, one group of researchers made the claim that the RNAi pathway is initiated by the Dicer enzyme which slices double-stranded RNA into short fragments of 20–22 amino acids in length (Bernstein et al., 2001). Like many scientific facts, this claim was too broad to be validated directly in a single experiment. Rather, it comprised a number of subsidiary assertions: an enzyme called Dicer exists in eukaryotic cells; it is essential to initiate the RNAi pathway; it binds dsRNA and slices it into pieces; it is distinct from the enzyme or enzyme complex that destroys targeted messenger RNA; it is ubiquitous across eukaryotes that exhibit RNAi pathway. Researchers from numerous labs tested these subsidiary hypotheses or aspects thereof to derive numerous lines of convergent evidence in support of the original claim. While the initial breakthrough came from work in Drosophila melanogaster cell lines ((Bernstein et al., (2001), subsequent research involved in establishing this fact drew upon in vitro and in vivo studies, genomic analyses, and even mathematical modeling efforts, and spanned species including the fission yeast Schizosaccharomyces pombe, the protozoan Giardia intestinalis, the nemotode Caenorhabditis elegans, the flowering plant Arabidopsis thaliana, mice, and humans (Jaskiewicz and Filipowicz, 2008). Ultimately, sufficient supporting evidence accumulated to establish as fact the original claim about Dicer’s function.

Dicer’s function is energy-dependent. They ignored the fact that the de novo creation of G protein-coupled receptors is required to link energy-dependent changes from angstroms to ecosystems via the RNAi pathway, which links autophagy to supercoiled DNA and protection from virus-driven energy theft and genomic entropy in all living genera.
See for comparison: WEBINAR: Studying Kinetics of Chromatin Assembly with SWATH-MS

The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. The nucleosomes together with the non-histone proteins define a stable chromatin structure. Despite its stability, this structure is disassembled and reassembled during DNA replication, repair, recombination or transcription. During all those processes, defined chromatin regions become accessible to be bound by the required factors, resulting in extensive nucleosome turnover at given genomic loci. The dual nature of chromatin requires a continuous interplay between stable and dynamic structures, which has to be coordinated at the molecular level to maintain the epigenetic information stored in the chromatin structure.

Despite the biological relevance of these processes, little is known about the order of chromatin assembly steps, the molecular mechanisms that coordinate the required cellular machinery in time and the quality control of this assembly.

The order of chromatn assembly steps is energy-dependent.
See also: Disentangling genetic and epigenetic determinants of ultrafast adaptation
See also: New type of traveling wave pattern could contain biological coordinates
See also: Really big brains can evolve only if constraints on energy intake are lifted
See also: Autonomous Metabolic Oscillations Robustly Gate the Early and Late Cell Cycle

Claims about intrinsic photosensitivity were linked to autonomous metabolic oscillations outside the context of how the energy-dependent oscillations are biophysically constrained. See for comparison:

Detection of transient synchrony across oscillating receptors by the central electrosensory system of mormyrid fish

Controlled fluorescence in a beetle’s photonic structure and its sensitivity to environmentally induced changes

The obvious need to link energy-dependent ocsillations to controlled fluoresence in all cell types may force people like Larry Kisner Sr., and Mark Armitage to link fluorescence in dinosaur osteocytes to the weekend resurrection of the bacterial flagellum via my model of energy-dependent top-down causation.

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
If you know someone who is suffering from a neurodegenerative disease or any other form of pathology, please attribute their suffering to the lack of understanding that theorists display for anything known to serious scientists about all the links from energy-dependent RNA-mediated healthy longevity that prevent all the pathology.
For example, see: Study confirms ‘sniff test’ may be useful in diagnosing early Alzheimer’s disease
The link from the sense of smell to neurodegenerative diseases has been detailed in the literature published by serious scientists for more than three decades.
See: Olfactory dysfunction in Alzheimer’s disease and Parkinson’s disease
The link from the anti-entropic virucidal energy of the sun to cancer prevention has been detailed since Schrodinger (1944)
See also: Digital imaging biomarkers feed machine learning for melanoma screening
Reported as: Researchers develop automated melanoma detector for skin cancer screening

Malignant or benign?: An image of a skin lesion is processed by a new technology to extract quantitative data, such as irregularities in the shape of pigmented skin, which could help doctors determine if the growth is cancerous. Credit: Rockefeller University
See also:
Role of Nicotinamide in DNA Damage, Mutagenesis, and DNA Repair (2010)
MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination (2013)
Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis (2015)
The Identification of Specific Methylation Patterns across Different Cancers (2015)
Stability of the hybrid epithelial/mesenchymal phenotype (2016)
If like, Peter Berean, you think that serious scientists have not proved that energy is information in the context of links from what organisms eat to the physiology of reproduction in all living genera, please define the weasel words you must continue to use in your ridiculous stories like those that tell others about mutation-driven evolution, based on de Vries 1902 definition of mutation.
Mutation theory

Other mutationist theories were developed after de Vries’s work, including German-born American geneticist Richard Goldschmidt’s “hopeful monsters” theory and American paleontologists Stephen Jay Gould and Niles Eldredge’s punctuated equilibrium theory. Those ideas not only remained faithful to the saltationist basis for new species formation but also championed de Vries’s devotion to the pure Darwinian belief that all variation proves beneficial.

Energy-dependent variation is beneficial and it links the innate immune system from autophagy to supercoiled DNA via the fixation of RNA-mediated amino acid substitutions in the organized genomes of all genera. Fixation occurs in the context of the physiology of energy-dependent reproduction. Virus-driven energy theft links mutations from variation to negative supercoiling of DNA and all pathology in all living genera.
There is no such thing as a beneficial mutation because virus-driven energy theft links amino acid substitutions in viruses to all pathology. The stolen energy is used for viral replication, not cell type differentiation and that fact can be traced across species via what is known about the differences between archaea and bacteria, the differences between bacteria and eukaryotes, and the differences in morphology and brain development of infants infected with Zika virus.
Remember:
…for all the undoubted charms of dogs, their breeding is nothing other than degeneration.
For all the undoubted charms of other primates, you would not want to be the father or mother of a Zika virus-infected infant, especially if the infant looked more like a non-human primate than a human.
See also: Energy-dependent alternative splicings 1996 – 2016 (2)