terrarium-eco-system

Science journalists or paid propagandists?

2016 Orchids give off human ‘body odor’ to attract mosquitoes
See also:

Were humans present in the orchid’s habitat long enough and often enough for this coevolution to take place? More likely, other animals emit the same body odors as humans. There should be a mention of this.

See also: SICB Annual Meeting 2017
The 2017 SICB conference report by Pennisi may be pending. Hopefully, a 2017 conference report from at least one ethical science journalist will mention this presentation and place it into the context of Pennisi’s 2015 and 2016 conference reports.
See: Differential Expression of Putative Pheromone-detecting Cells and Receptors in the Olfactory Epithelium of an African Cichlid Fish

Across taxa, chemical signals convey crucial information, such as fitness, social status, and reproductive state. It is well established that several fish species use chemosensory signaling during reproduction, with individuals possessing mechanisms to detect sexually-relevant olfactory signals at a reproductive advantage. In fishes, odorants are detected by one of three main olfactory receptor neuron (ORN) types located in the olfactory epithelium. Crypt cells, an ORN unique to fishes, is hypothesized to function in pheromone detection, and one family of recently described receptors known as vomeronasal-like type 1 receptors, or V1Rs, are hypothesized to bind these sexually-relevant compounds. Here, we tested whether social status and/or reproductive state might influence crypt cell and V1R expression in the olfactory epithelium of highly social African cichlid, Astatotilapia burtoni. Males exist as either dominant (reproductively active) or subordinate (reproductively suppressed), and females cycle between gravid (reproductively receptive) and mouthbrooding parental care states. Using the crypt cell marker s100, we found that gravid, ready to spawn females had more crypt cells in their olfactory epithelium compared to reproductively suppressed brooding females. Similarly, in situ hybridization for one of the six V1Rs in fishes, V1R4, revealed different levels of expression in animals of different reproductive and social status. Since reproduction can be considered the most important event in any animal’s life, gaining insight into the cellular and molecular mechanisms that mediate the detection of sexually relevant stimuli is important in understanding how reproduction is coordinated.

Here is how reproduction is coordinated in species form microbes to humans.

Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link sunlight to energy-dependent changes in chirality and autophagy via the receptor-mediated cellular and molecular mechanisms that mediate the detection of relevant stimuli. If you do not think that explains how top-down causation is linked to all energy-dependent biodiversity, it is probably because you want to pretend that you don’t know it does.
Karen Maruska stopped pretending she did not know how to explain the diversity of sticklebacks when she left Russel Fernald’s group, and set up her lab (circa 2012, which was the last time I had the pleasure of speaking with her and some of her friends).
Pennisi and other journals have helped to stop the refutations of neo-Darwinian nonsense by reporting bits and pieces of what serious scientists know about all energy-dependent cell type differentiation in all living genera.
Background: 2015 All in the (bigger) family
Excerpt from Pennisi (2015)

Last week, at a special symposium of the annual meeting of the Society for Integrative and Comparative Biology (SICB) here, Harrison and many others reported new parallels between these two very successful groups of animals and new insights about what it took for an ancient aquatic crustacean to give rise to insects, which have thrived on land. Insects and crustaceans “are the most divergent organisms on the Earth, and as biologists we’d really like to understand how that came to be,” says Jonathon Stillman, a marine environmental physiologist at San Francisco State University’s environmental research center in Tiburon.

“It’s not unanimous that crustaceans and insects have won the day, but it’s now the more strongly supported point of view,” says Greg Edgecombe, a systematist at the Natural History Museum in London.

The old view of insect evolution may explain why paleontologists have had so much trouble identifying the ancestral insect: They were looking for something that had insectlike and millipedelike traits, rather than a crustacean. “We’ve been looking from the wrong perspective,” says Thorsten Burmester, a comparative physiologist at the University of Hamburg in Germany.

My comment: published at 2:54 pm on 1/29/15

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

See: A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA
Excerpt from the journal article:

Identical amino acid substitutions in particular genes also underlie several examples of repeated evolution including insecticide resistance in insects (GABA), tetrodotoxin resistance in snakes (NaK-ATPase), C4 photosynthesis in plants (PEPC), and dark pigmentation in mice and birds (MC1R) (Stern 2013).

Differences in energy-dependent RNA-mediated amino acid substitution underlie every example of how ecological variation has been linked to ecological adaptation in all living genera since 1973, when Dobzhansky published: Nothing in Biology Makes Any Sense Except in the Light of Evolution

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds. 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. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Alternative splicing of pre-mRNA

Energy-dependent alternative splicings 1996 – 2016 (2)

See also: Energy-dependent alternative splicings 1996 – 2016

Re: Rs3827760 is Val370Ala and EDARV370A

No matter what it is called, Val370Ala may be the best example of how nutrient energy-dependent biophysically constrained pheromone-controlled viral latency protects all organisms from virus-driven energy theft and all pathology.
For example, see: Genome recoding by tRNA modifications

The succession of mRNA codons controls the synthesis of polypeptides through the complementarity between each of the 64 possible codon triplets and the tRNA anticodons that decode the 20 amino acids of the cellular proteome. Central to the mRNA decoding process is the backward compatibility of the codon : anticodon recognition that is mediated by tRNA.

See also: In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory

Highlights:

•    Epigenetic regulation represents a key mechanism of learning, memory and cognition.
•    Chromatin topology is emerging as a major regulator of neuronal gene expression.
•    Dynamic chromatin topology changes correlate with activity-dependent transcription.
•    DNA double-strand breaks facilitate induction of immediate early gene transcription.

All their highlights can be placed into the context of this article from 2005.
Feedback loops link odor and pheromone signaling with reproduction
The feedback loops determine whether of not a species survives via links from energy-dependent autophagy to learning, memory, RNA-mediated amino acid substitutions and supercoiled DNA.
BDNF Val66Met and COMT Val158Met are also examples that link energy-dependent changes in base pairs from single nucleotide polymorphisms to life history transitions in morphological and behavioral phenotypes.

See also: Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision

Our findings revealed a differential impact of BMP signaling on appendage fate specification that has ancient roots and occurs repeatedly throughout vertebrate evolution.

This was reported by Bob Yirka as: Researchers identify signals during embryonic development that control the fate of skin cells to be sweaty or hairy

The fate of all cell types is energy-dependent and RNA-mediated via natural selection for codon optimality. See for example:
rs3827760, also known as 1540T/C, 370A or Val370Ala, is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2. This SNP links the mouse model of cell type differentiation to humans. That fact has been known for at least 3 years.
See:

  1. Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
  2. A genetic basis of variation in eccrine sweat gland and hair follicle density
  3. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation

Other energy-dependent base pair changes link natural selection for codon optimaility from SNPs to RNA-mediated amino acid substitutions and differences in intelligence and/or unexplained death risk.
A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence
An insertion/deletion polymorphism within 3’UTR of RYR2 modulates sudden unexplained death risk in Chinese populations
Few people can place the findings on energy-dependent codon optimaility into the proper context of natural information processing. How many do you know who might claim that natural selection links mutations to evolution?

Compare the people who think in terms of mutation-driven evolution to those who know the energy-dependent differences between archaea and bacteria. The greater energy-dependent stability of organized genomes in bacteria can be liked to the stability of eukaryotes. The instability of archaea genomes can be linked from virus-driven energy theft to the degradation of messenger RNA and negative supercoiling of DNA.
All cell type stability link the sun’s anti-entropic virucidal energy from the creation of all biodiversity to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy, which links mutations to all pathology.
See for instance, (2013) MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination

The authors

…address long-standing fundamental questions linked to compelling clinical needs—how to distinguish between the aberrant dynamics of epithelial–hybrid–mesenchymal transitions during tumorigenesis vs. the normal programs of embryonic development and tissue regeneration.

The “normal programs” are energy-dependent and biophysically constrained by the physiology of reproduction.The senior author should have received the 2016 Nobel Prize for linking energy-dependent autophagy to supercoiled DNA, but the Prize is not awarded posthumously, as I recall.

Politicized “science” often prevents the Prize in Physiology or Medicine from being awarded to anyone whose works challenge the ridiculous theories about mutation-driven evolution. Those who present experimental evidence of how cell type differentiation is biophysically constrained by energy-dependent changes in the microRNA/messenger RNA balance tend to be virtually ignored.

Even some of the creationists I have encountered want others to keep thinking in terms of evolution rather that energy as information. Peter Berean, for example, decided to invent the term “bio-functional information” when he realized that the sun’s anti-entropic virucidal energy was the only obvious link from microRNA flanking sequences to all healthy longevity and that virus-driven energy theft was the link to all pathology.If you want to learn how serious scientists are combating evolution to fight disease on two fronts, see any claim made by an old earth creationist, or any claim made by any atheist. The similarities led Peter Berean to substitute “bio-functional information” for de Vries 1902 definition of “mutation.”

See for comparison:

2003 Bacterial self–organization: co–enhancement of complexification and adaptability in a dynamic environment

2006 Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information

2009 Learning from Bacteria about Natural Information Processing

See also: CRISPR study reveals unexpected roles of non-coding RNAs

Royal Society’s Sir Venki Ramakrishnan Agrees to Post Public Evo Audio

…the public discussion from the recent “new trends” in evolution conference will be posted shortly online on the Royal Society event webpage.

Suzan Mazur helped force them to do what they claim they would do:

Recorded audio of the presentations are available below.

It’s been six weeks and the recorded audios from the audience are not available.

If the recorded comments become available, the public discussion may help to reveal that the fate of all cell types is energy-dependent and RNA mediated via natural selection for codon optimality and autophagy.

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

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Each week’s science news brings additional representations of facts that refute all neo-Darwinian pseudoscientific nonsense by linking Darwin’s “conditions of life” to all biodiversity. Most science news outlets still report and/or tout pseudoscientific nonsense because the reporters missed the fact that life is nutrient-dependent and the physiology of reproduction is controlled by pheromones is species from microbes to humans.
Can you imagine how embarrassed you would be if you had not learned that all organisms must eat or they cannot reproduce, which means they could never have become an organism of a species? What’s worst is that no experimental evidence of biologically-based cause and effect support claims that one species evolved into another. For comparison, this recent report shows changes in organized genomes that link the nutrient-dependent pheromone-controlled physiology of reproduction in moths to bacteria and from bactreria to humans via conserved molecular mechanisms of RNA-mediated protein folding chemisrty.

Engineers create programmable silk-based materials with embedded, pre-designed functions

… the researchers created a surgical pin that changes color as it nears its mechanical limits and is about to fail, functional screws that can be heated on demand in response to infrared light, and a biocompatible component that enables the sustained release of bioactive agents, such as enzymes.

The news article cites: Directed self-assembly of silk fibroin into bulk materials: with the subtitle: Programming function into mechanical forms from the nano- to macroscale,
I look forward to learning why they are claiming that energy-dependent assembly is “directed self-assembly.”

Alternative splicing of pre-mRNA

Energy-dependent alternative splicings 1996 – 2016

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  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

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”

Ryszard Maleszka’s response was extremely harsh.

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).

See also: Two fatty acyl reductases involved in moth pheromone biosynthesis

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.

See also: Researchers map genome-wide changes that drive T cell maturation and exhaustion

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.

See also: New Research May Change Accepted View of Cell Cycle Control

 …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
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)
 

terrarium-eco-system

Energy-dependent self-organization and self repair

Energy-dependent autophagy links food odors and pheromones from the innate immune system and RNA-mediated feedback loops to the physiology of reproduction in all living genera via chromosomal inheritance. Transgenerational epigenetic inheritance is nutrient-energy-dependent and pheromone-controlled.
That fact has been established in the extant literature since 1933, when Thomas Hunt Morgan won the Nobel Prize in Medicine, and Erwin Schrodinger shared the 1933 Prize in Physics with Paul A.M. Dirac.
See for example: From Fertilization to Adult Sexual Behavior December 1996

Research has established the broad mammalian developmental plan that genes on the sex chromosomes influence gonad development which determines gonadal hormone production (or its absence) leading to modification of the genitalia and simultaneously biasing the nervous system to organize adult sexual behavior. This might be considered the “gonad to hormones to behavior” model. It is clear, however, that although this model generally works well it is incomplete. The model does not account for behavioral influences attributed to the environment or to genetic but nongonadal or hormonal factors. In this essay we probe those areas of sexual development that are neither differentiated by hormones nor activated by them. The concept of the environment used for our discussion is very broad; it incorporates considerations of both the molar and the molecular levels. The general sense of the word “environment” as something exterior to the person is retained, even if that something influences intraperson processes. In addition, we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.” Although many, and perhaps most, important sex differences arise from gonadal and hormonal development, also important are sex differences which are neither gonadal nor hormonal. All these factors affect the internal workings of the individual and intervene in structuring how the social environment might or might not modify sexual behavior. This discourse calls attention to features that are central to the so-called nature-nurture discussion.

My Synopsis: Nutrient energy-dependent pheromone-controlled changes in RNA-mediated events link experimental evidence of biologically-based cause and effect from nature and nurture to differences in morphological and behavioral phenotypes.
Structural Brain Network Reorganization and Social Cognition Related to Adverse Perinatal Condition from Infancy to Early Adolescence December 2016

Brain development consists of a genetically controlled but environmentally modulated complex process starting early in fetal life, which makes it very sensitive to adverse intrauterine environment and/or to a premature exposure to extrauterine medium. Alterations in fetal brain development can result in long-term structural brain reorganization as well as in social cognition impairments in childhood and adolescence (Leitner et al., 2000; Wiles et al., 2006; Baschat, 2011; Guellec et al., 2011). Namely, intrauterine growth restriction (IUGR), a condition affecting 5–10% of all pregnancies involving a decrease in the amount of nutrients and oxygen arriving to the fetus, has consequences on the developing brain associated to short- and long-term impairments in both brain function and structure (Rees et al., 2008; Levine et al., 2015).

Discussion (excerpt):

Brain connectivity evolves during development, starting prenatally and continuing into adolescence (Hagmann et al., 2010; Yap et al., 2011; Dennis and Thompson, 2013; Ball et al., 2014; Dubois et al., 2014).

Conclusion:

These structural differences are related to a higher risk of social cognitive disorders in IUGR, being especially relevant the association with executive dysfunction and hyperactivity/inattention behavior.

My Synopsis: Nutrient energy-dependent pheromone-controlled changes in RNA-mediated events link experimental evidence of biologically-based cause and effect from nature and nurture to differences in morphological and behavioral phenotypes.
The reason there is no difference between my synopsis of our 1996 review and my synopsis of the article from 2016 is clear. In our review, the changes from fertilization to adults are nutrient-dependent and pheromone-controlled via the physiology of reproduction and transgenerational epigenetic inheritance of species-specific changes during the development of all morphological and behavioral phenotypes in species from microbes to humans.
The difference in the 2016 report is the claim that species-specific differences “evolve.” No experimental evidence of biologically based cause and effect suggests that any differences in cell types in any individual of any species “evolve.” Ecological variation must be linked from conserved molecular mechanisms of energy-dependent cell type differentiation to ecological adaptation. That cannot be done via theories of evolution.
See for instance: Mutation-Driven Evolution Jun 14, 2013
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Jun 14, 2013

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

See: DNA Damage
See also: Combining CNV and SNV Detection in a Single Test: An Alternative to Whole-Genome Sequencing (December 13, 2016)

This webinar will discuss a genomic strategy that detects single nucleotide variants and copy number variants in a single assay. This approach serves as a cost-effective alternative to whole-genome sequencing and shows promise for the field of cytogenetics.

This webinar will discuss a genomic strategy that detects single nucleotide variants and copy number variants in a single assay. This approach serves as a cost-effective alternative to whole-genome sequencing and shows promise for the field of cytogenetics.

See also: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system. Various psychoemotional states of the human nervous system can, in turn, disrupt the integrity of the chromosomal apparatus of target cells, for instance lymphocytes [41, 42]. Therefore, studies on the oppositely directional modulation of the mutagenic consequences of stress in rodents with the use of specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.

The fact that “chemosignals” have an antimutagenic effect links pheromones to anti-entropic epigenetic effects on cell type differentiation via the conserved molecular mechanisms that link food odors to all energy-dependent healthy longevity.

See: Feedback loops link odor and pheromone signaling with reproduction

See also: Combating Evolution to Fight Disease

…an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.

See also, my comments and the comment by Robert Frye on: Combating Evolution to Fight Disease

“An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short

This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X

The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.

See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000

A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.

RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events.

Submitted on Sat, 09/13/2014 – 08:58

James V. Kohl

Re: “Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations.”Now see: A mechanistic link between gene regulation and genome architecture in mammalian developmenthttp://www.sciencedirect.com/science/article/pii/S0959437X14000495 for the refutation of neo-Darwinian pseudoscientific nonsense.Experimental evidence of biologically-based cause and effect does not support ideas about mutations, natural selection, and the evolution of biodiversity.Experimental evidence of biologically-based cause and effect supports the fact that ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms.

Submitted on Tue, 07/15/2014 – 22:13

Robert Frye

I am concerned at the lack of understanding of basic evolutionary processes in the Perspective of Rosenberg and Queitsch. They assert that a cornerstone assumption of evolution is that mutations are ‘the sole drivers of evolution’. That is nonsense as the driver of evolution is not mutations or variation but selection, be it natural, artificial, kin or sexual selection. Mutation is but one of the factors that contribute to variation. In addition, we have known for a long time that mutations are not solely random, constant or gradual. I seem to remember from high school biology (1960’s) that the environment can effect mutation rates through heat, chemicals and radiation. Does the editorial process of Science not include Perspectives?

Submitted on Mon, 03/17/2014 – 14:28

James V. Kohl

Re:”…the driver of evolution is not mutations or variation but selection, be it natural, artificial, kin or sexual selection. Mutation is but one of the factors that contribute to variation.”I thought Robert Frye knew better than that, because he attended a 1993 symposium I organized and my 2007 Reiss Plenary session of The Mind’s Eyes: Modeling the Development of Diverse Sexual Preferences.Perhaps this is a different Robert Frye or one who thinks that sexual orientation arises via mutations and natural selection in human males but via nutrient-dependent pheromone-controlled cell type differentiation in yeasts as we reported in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertiliz… “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…”Robert: What about Anne’s rams. Are they among the selected mutants that you think may have evolved their exclusive homosexual orientation?

Submitted on Sun, 09/07/2014 – 20:51

James V. Kohl

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

Submitted on Fri, 03/07/2014 – 12:07

See for comparison: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
DNA damage repair is energy-dependent. The speed of light on contact with water must link quantized energy to DNA damage because an anti-entropic energy source is required For example, the virucidal anti-tropic effects of ultraviolet light on RNA-mediated protein folding chemistry link the innate immune system to supercoiled DNA via autophagy and the physiology of reproduction.
Supercoiled DNA protects organized genomes from virus-driven energy theft. RNA-mediated amino acid substitutions link the nutrient-dependent pheromone-controlled physiology of reproduction from supercoiled DNA to healthy longevity. Virus-driven energy theft links mutations to all pathology.
The field of cytogenetics links energy-dependent changes in the microRNA/messenger RNA balance from single nucleotide variations (SNVs) to copy number variations (CNVs) in all cell types. Virus-driven energy theft will continue to be linked to healthy longevity and all biodiversity via single nucleotide polymorphisms (SNPs) and natural translational selection for codon optimality. Virus-driven energy theft will continue to be linked from energy-dependent viral latency to all pathology.

Alternative splicing of pre-mRNA

Autophagy is the antiphage defense strategy

The “Antiphage Defense Strategy” in Vibrio anguillarum is called autophagy by many serious scientists. It links nutrient energy-dependent pheromone-controlled quorum sensing to viral latency, healthy longevity, symbiosis, reproduction, and biodiversity from microbial species to humans.

For an evolutionary approach to energy-dependent autophagy that fails to address any aspect of how virus-driven energy theft causes all pathology see: (12/7/16) Part I: Living together: The symbiosis of host-microbial interactions (12/7/16)
See also: 12/7/16

….McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri (V. fischeri), a type of luminescent bacteria that enables the squid to hunt at night. McFall-Ngai and collaborators have identified the molecular mechanism by which nascent Hawaiian bobtail squid select V. fischeri from the thousands of other bacteria in their habitat. V. fischeri induces developmental changes in the squid that drive daily rhythms of gene expression, which are necessary to control bacterial growth, a crucial cycle in this symbiotic partnership.


Bobtail squid select bacteria that become luminescent. The squid do not not select archaea. That fact exemplifies how natural selection for energy-dependent codon optimality links top-down causation from the sun’s anti-entropic biological energy to ecological adaptation.
Whether or not you accept this fact, energy-dependent natural selection continues in the context of symbiosis among the most ecologically adapted species.
“The four stages of acceptance: ― J.B.S. Haldane
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.”

Natural selection cannot link mutations to evolution in the context of symbiosis because the interactions among species are far too complex.

…the pattern of microbial exchange is “likely circular in nature.” That means that captive dragons contribute microbes to their environment, and they reacquire these same microbes from their environment, repeating this exchange in an ongoing cycle without other external sources of microbial diversity.

Pattern recognition is essential to the understanding of how the microbiome of bobtail squid is linked to symbiosis via the microbiome in all other living genera via the anti-entropic virucidal energy of sunlight.

Search Results for “McFall-Ngai”

Beneficial microbes kill beneficial mutations
1/15/15 Excerpt: McFall-Ngai, Bonnie Bassler, Anna Di Cosmo and others, continue to show that Darwin’s ‘conditions of life’ are nutrient-dependent and pheromone-controlled by linking:
1) metabolic networks,
2) genetic networks,
3) reproduction in microbes,
and
4) reproduction in their model organisms.

Environment epigenetically shapes the immune system
1/15/15 Excerpt: 1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Quantum physics, quantum biology, and quantum consciousness
2/15/15 Excerpt: One would think that the representations of McFall-Ngai that appear to link light-induced amino acid substitutions from the stability of DNA in luminescent microbes to the stability of DNA in squid would invite more attention to details than attempts to pirate ideas about epigenetic links from Turin’s links and my links from quantum physics to Gunther Witzany’s Life is physics and chemistry and communication.

8/25/15 Excerpt: See also my invited review of nutritional epigenetics. I submitted it by request for a special issue of “Nutrients” and posted the submission to Figshare.com on April 11, 2014, after the submission was returned without review.

See also:  Quorum Sensing Determines the Choice of Antiphage Defense Strategy in Vibrio anguillarum

6/25/16 Excerpt: Quorum sensing links the physiology of energy-dependent reproduction and virus-driven energy theft from the microRNAome of and light organ of bobtail squid to the bull sperm microbiome, which links microRNAs in breast milk to human brain development. The bacteria that populate the light organ have already been linked by Bonnie Bassler’s group and Margaret McFall-Ngai’s group to everything known about the physiology of energy-dependent reproduction in all living genera.

Alternative splicing of pre-mRNA

The futility of The Battlefield FB group

Apparently, Paul Hartley blocked me from further discussion of his OP about dinosaurs and gladiators before I could ask if he thought “The Battlefield” is a “false flag” group. Does anyone else think that?
 

If so, do you think it can survive publication of experimental evidence that links responsive supramolecular systems to stepwise changes in the assembly of metal complexes via induction of a light-driven rotary motor scaffold akin to the bacterial flagellum of P. fluorescens?

See: Dynamic control of chirality and self-assembly of double-stranded helicates with light

Others are claiming that partial unwrapping of the supercoiled DNA complex precedes the photoisomerization steps, which link energy-dependent autophagy to inversion of the chirality in helicates. That explains how energy-dependent RNA-mediated isomerization establishes the difference between metastable and stable helicates, which links amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy. For example, supercoiled DNA protects the organized genomes of dinosaurs and gladiators from stress-linked pathology until stress-linked changes in pH overcome the ability of the innate immune systems to protect the organized genomes via the light-induced changes in hydrogen-atom transfer in DNA base pairs in solution.
See for comparison: Team combines quantum physics and photosynthesis to make discovery that could lead to highly efficient solar cells

They claim plants evolved to control responses to the sun’s biological energy. As proof of concept their “…design incorporates a heat engine photocell that absorbs photons from the sun and converts the photon energy into electricity.”

Via the comparison of two simple quantum mechanical photocell systems, they found that “…by simply incorporating two photon-absorbing channels, rather than only one, the regulation of energy flow emerges naturally within the photocell.”

They linked the natural emergence of the energy flow in their design to the natural energy of photosynthesis in plants in an attempt to explain how green became the predominant color of plants on Earth. Others found molecular structures that prevent death via the accumulation of excess energy in plants.

The design of the molecular structure of their quantum heat engine photocell is similar to “…the structure of photosynthetic molecules that incorporate pairs of chlorophyll.” But wait. They claimed that the plants evolved molecular mechanisms after the natural emergence of energy flow was linked to photosynthesis and molecular structures that prevent death caused by the accumulation of excess energy.When I see such a convoluted representation of energy-dependent biologically-based cause and effect that does not include any mention of virus-driven energy theft or the physiology of reproduction, I am inclined to call researchers like this “biologically uninformed science idiots.”Many people hate it when I do that. What would you call them? But some of them are plagiarists, too.

See: Modern Science refutes the Evolutionary theory

Tomi Aalto’s blog is a continuation of his plagiarism. His posts can be compared to more than 800 of mine on my domain.

The difference is that Suzan Mazur acknowledged RNA-mediated.com as an information source in her book: Royal Society: The Public Evolution Summit

From page 3: “Some of the social momentum over the last year, in particular, has come via coverage of the evolution discourse in a flurry of books and from these diverse venues…”

James Kohl — RNA-mediated.com

In “Darwin’s Children” (2003) Greg Bear also acknowledged me and the International Paleopsychology Project, where I first encountered him and Eshel Ben-Jacob, who died last year. See this tribute to Eshel’s works.

He mastered the concept of energy-dependent autophagy and linked everything known about Schrodinger’s anti-entropic virucidal energy of sunlight to the nutrient-dependent physiology of pheromone-controlled reproduction in species from microbes to humans.
Theorists still hate it when that happens, and they continue to tell others who are biologically uninformed that not enough is known to link virus-driven energy theft to all pathology.

What does Tomi Aalto, or any other plagiarist hope to accomplish by taking bits and pieces of my works, or the works of others, without the ability to link the energy-dependent de novo creation of G protein-coupled receptors from energy as information to all biodiversity and also link virus-driven energy theft to all pathology? That inability to link top-down causation to any model of biologically-based cause and effect led to this criticism of my 2013 review.

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Would it not be more appropriate for others who are not atheistic antagonists to support my claims by citing and discussing my works, rather than make ongoing attempts to establish themselves as experts?

See for examples of what is expected of other serious scientists.

Role of olfaction in Octopus vulgaris reproduction

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).

Two fatty acyl reductases involved in moth pheromone biosynthesis also cites Kohl (2013) see #10

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.

Re: Tomi Aalto’s plagiarism and the plagiarism of others.


Larry Kisner Sr. suggested I contact Kevin Anderson in an attempt to publish what I have already published. He also refused — and Mark Armitage ignored my requests — to provide the slide that shows fluorescence in dinosaur osteocytes.

See my comment on the video by Mark Armitage. See also: Future Projects
 
The Influence of Carbon Dioxide Enhancement on Plant Growth
Thermoregulation in Honey Bees
Fossils of the Coconino Sandstone
Biochemistry and Taxonomy in Pine Trees
The Formation of Multiple Tree Rings in Bristlecone Pine Trees
 

Each of these projects focuses on aspects of my published and unpublished works that link the sun’s anti-entropic virucidal energy to RNA-mediated amino acid substitutions and biophysically constrained cell type differentiation in species from microbes to humans.

See for example: What is life when it is not protected from virus driven entropy  (video 6:37 minutes)

Abstract:

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.

See also: Metabolic Phenotyping Research

Excerpt: SARCASM ALERT

7. They will claim that the Extended Evolutionary Synthesis will have explanatory power when it automagically evolves into a model of top-down causation that links physics and chemistry to the conserved molecular mechanisms of biologically-based cause and effect, which serious scientists have detailed during the past century.

See for comparison:

Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells

Dual genomes: exposing the evolution industry

Pheromones and longevity in worms (and flies)

I posted this to one of my OPs on “The Battlefield,” which means I may be the next to go. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks
 

For comparison to what is known about the de novo creation of genes in mollusks, Anna Di Cosmo’s group cited my most recent review in Role of olfaction in Octopus vulgaris reproduction.

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). — p. 61

The facts link my model to biologically-based cause and effect from energy-dependent changes in angstroms to ecosystems in all living genera via the de novo creation of the genetic code. See also: Junk DNA’ Used To Sort Species

Now watch Lenski’s group claim that different species of viruses evolved in one month. Biologists watch speciation in a laboratory flask
Nutrient energy-dependent pheromone-controlled speciation can now be observed in the context of fluorescence, which links ecological variation to morphological and behavioral diversity to chromosomal rearrangements in C. elegans compared to P. pacificus, a predatory nematode with teeth. Researchers find chemical tag that locks chromosomes together during meiosis 

The ENEA study proposed that the image may have been created by an intense source of light, but no man-made light would produce the required strength.

Serious scientists have linked femotosecond blasts of UV light to RNA-mediated DNA repair and the repair has been linked via the natural fluorescence in DNA from dinosaur osteocytes to the weekend resurrection of the bacterial flagellum. One could look at the evidence in the discovery at Christ’s tomb from that perspective given the intensity of light energy as information that might be required to Resurrect Him.
For comparison, Lenski’s group has placed everything he knows into the context of evolved species of viruses during a month-long experiment that failed to include anything known about biophysically constrained energy-dependent RNA-mediated cell type differentiation in any living species. Again, see: Biologists watch speciation in a laboratory flask
The bottom line is always whether you choose to believe in theorists or in the evidence of biologically-based cause and effect — no matter when that evidence is discovered or where it is found.

See: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

Natural selection for energy-dependent codon optimality is the only obvious link to the de novo creation of olfactory receptor genes. And Svante Paabo is the senior author. Here he is again, supporting my model with others who understand the role of microRNAs. MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

Does everyone understand why Bill Ludlow blocked me after I commented on his OP from “The Battlefield?” about this:

Scientists Seek to Update Evolution

See also: Tertiary alphabet for the observable protein structural universe
From the journal article: “…the frequency of amino acids in different secondary-structural environments is closely related to thermodynamic propensities (20–24).”
From the news report: “Since protein structural states are really conformational ensembles, the language of statistical mechanics is most appropriate for describing their behavior.”
This is the language they use: “…we find that the emergent sequence variability is often in close agreement to the evolutionary variability…”
Instead of linking sunlight from thermodynamic cycles of energy-dependent protein biosynthesis and degradation to biophysically constrained cell type differentiation and all RNA-mediated biodiversity, they link emergence to evolution.
Welcome again to the world of biologically uninformed theorists. This time, “…we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs).”
The ability to take everything known to serious scientists and put it back into the context of unintelligible theories via use of terms like tertiary structural motifs far surpasses the ability of serious scientists to make sense of their pseudoscientific nonsense. Thus, the pseudoscientific nonsense will continue to kill us all.
See for comparison: The Pangenome: Are Single Reference Genomes Dead?

…when Tettelin, then at the Institute for Genomic Research (TIGR), and his colleagues compared eight isolates of Streptococcus agalactiae (or group B Streptococcus, GBS), they found not only the small, within-gene variations predicted by conventional genetics, but an average of 33 completely new genes with every new genome sequenced. “It was a shock,” says Tettelin. “We saw there were many regions—relatively large regions—of diversity.”

All that diversity is energy-dependent and linked from the pheromone-controlled physiology of reproduction to all  morphological and behavioral phenotypes in all living genera.

Thanks to Anna Di Cosmo for sharing this example of energy-dependent de novo transcriptome assembly.

Abstract conclusion:

The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.

No serious scientist I know examines morphogenesis outside the context of feedback loops that link odor and pheromones to the physiology of reproduction in species from microbes to humans via the de novo creation of G protein-coupled receptors (GPCRs). How many pseudoscientists do you know who skip past the de novo creation of GPCRs and proceed to link mutations from natural selection to evolution outside the context of everything known to serious scientists about biologically-based cause and effect (i.e., energy-dependent biodiversity)?The lack of discussion and/or support from other creationists for my presentations of accurate information like this may suggest to others that this is a “false flag” group. Note that after I blocked those who I know participate in other “false flag” groups, there has been no discussion of my OPs. If you tried to evaluate the content presented here, would you get the impression that this is a group in which the admins are Creationists? When did you realize the de novo creation of genes for olfactory receptors must precede the de novo creation of photoreceptors to link chemotaxis and phototaxis to energy-dependent cell type differentiation, which is our only protection from the viral apocalypse?

See: Pterosaurs Hijack Royal Society Evo Meeting

See also: Royal Society: The Public Evolution Summit

Page 11- 12 Re: … evolution of genome invading RNA networks that edit host genomes.

… Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication

He is the author of Life is physics and chemistry and communication.

Abstract:

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

The claims about quasispecies and hypercyclesthat dominate molecular biology and virology should have long ago long before now have been placed into the context of all reviews of neo-Darwinian pseudoscientific nonsense.

See for example: Major Evolutionary Blunders: Imagining That Life Is Only Chemistry

See also: “I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732).  — Lewis Thomas as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality

Alternative splicing of pre-mRNA

De novo gene creation: Ignoring the experimental evidence

Regularly Whiffing Essential Oils Can Retrain Lost Sense of Smell

It’s not entirely clear how olfactory training works on a neurological level.

Olfactory training links the experience-dependent de novo creation of G protein-coupled receptors to supercoiled DNA. Conserved molecular mechanisms link food odors and pheromones from the innate immune system to the physiology of reproduction. Simply put, autophagy protects all organized genomes from virus-driven entropy and all pathology via the de novo creation of odor receptor genes.
See for proof: Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

The 3D segmentation of high-resolution images provided by SXT reveals an unappreciated interconnectivity between distinct forms of chromatin. The continuous nature of like-chromatin, which is evident even in the nucleolus, supports the existence of non-stereotypic but extensive interactions between different chromosomes, which might have significant regulatory roles in transcription and other nuclear processes.

Natural selection for energy-dependent codon optimality is the obvious link to experience-dependent chromatin remodeling and the de novo creation of species-specific G protein-coupled receptors, which link chemotaxis and phototaxis from the innate immune system to the physiology of reproduction in all living genera. It is obvious to all serious scientists that energy-dependent receptor-mediated biophysically constrained cell type differentiation is the link from angstroms to ecosystems in all living genera. But, in the next sentence, these authors claim (with my emphasis):

Although sequence-specific association of co-regulated genomic loci is appealing, random interactions between loci with shared chromatin properties might be an equally effective way of modulating transcription levels.

No experimental evidence of biologically-based cause and effect supports that ridiculous claim about random interactions. No experimental evidence of biologically-based cause and effect has ever supported similar claims that link anything except the energy-dependent de novo creation of functional protein structures via the modulation of transcription.

Transcription is energy-dependent and biophysically constrained. It links the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and protects all organisms from all pathology via autophagy.

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo was reported as

Imaging Technique Reveals Movement of Genetic Material Within Nucleus

Chromatin functions to package DNA so that it can fit inside of a cell, and forms chromosomes. In the video above, take a trip through the nucleus of a cell; in the video below, DNA reorganization in the nucleus a mouse cell is illustrated.

…it had been thought that chromatin existed as a group of disconnected islands, but the latest report indicated that chromatin is compartmentalized into two areas of “crowding” that comprise a continuous network throughout the nucleus.

The continuous network of chromatin distributes energy as information in the context of hydrogen-atom transfer in DNA base pairs.  Energy-dependent changes in base pairs link quantized energy from angstroms to ecosystems in all living genera via changes in the microRNA/messenger RNA balance. The ability to image the changes has not been linked from chromatin remodeling to RNA-mediated amino acid substitutions and chromosomal rearrangements, because the detailed sequence of biologically-based cause and effect refutes all neo-Darwinian theories. Natural selection for codon optimality comes first, not natural selection for benefical mutations. There is no such thing as a beneficial mutation.

Reported also as: 3-D Imaging Technique Maps Migration of DNA-carrying Material at the Center of Cells
Excerpt:

Detailed 3-D visualizations show an unexpected connectivity in the genetic material in a cell’s nucleus, and provide a new understanding of a cell’s evolving architecture.

What architecture evolves? Does it evolve via mutation-driven evolution? How is that possible?

These unique 3-D reconstructions of mouse olfactory cells, which govern the sense of smell, were obtained using X-ray imaging tools at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). The results could help us understand how patterning and reorganization of DNA-containing material called chromatin in a cell’s nucleus relate to a cell’s specialized function as specific genes are activated or silenced.

The 3-D reconstructions govern the sense of smell via the de novo creation of G protein-coupled receptors in the mouse olfactory cells. The cells do not create or recreate themselves. Organization and reorganization of chromatin is energy-dependent.

“We’re trying to understand how the reorganization of chromatin affects gene expression,” Larabell said.

No you are not. You’re trying to avoid admitting that you got caught with your pants down after having missed all the experimental evidence of biologically-based cause and effect that refutes neo-Darwinian nonsense.

“No one’s been able to study this at the human level yet.” This research will hopefully lead to new insights about diseases and disorders that relate to gene expression. Already, the study’s results are being incorporated into models of cell development.

There is only one model of cell energy-dependent cell type differentiation during the development of all morphological and behavioral phenotypes in species from microbes to humans.
See for example: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

One of the precursors to Alzheimer’s disease, which attacks the brain’s nerve cells, is a loss of smell, so understanding this connection to olfactory nerve cells could perhaps serve as a diagnostic tool and perhaps unlock a deeper understanding of the degenerative disorder.

Who is claiming that this energy-dependent connection to the de novo creation of genes in olfactory nerve cells is not already understood by all serious scientists? Why are they lying about what is already known?

“This work highlights the power of multidisciplinary research,” said Mark Le Gros, associate director of the NCXT and a physicist who was responsible for the design and construction of the X-ray microscope. Le Gros, the lead author in this research, added, “This is an example of work that required a combination of molecular biologists and cell biologists with physicists and computer scientists.”

It highlights the ignorance of theorists. See for example: Search Results for “alzheimer”
For a historical perspective on the ignorance of theorists who are among the molecular biologists and cell biologists with physicists and computer scientists who published a paper that ignored all the accumulated experimental evidence of biologically-based cause and effect, see: Learning from Bacteria about Natural Information Processing

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

See also: From Fertilization to Adult Sexual Behavior
We included a section on molecular epigenetics, and nothing about the facts that we detailed has changed at any level of examination that links energy-dependent changes from angstroms to ecosystems in all living genera.

The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes, e.g., Boggs and Chinault (1994), Clemson and Lawrence (1996); Hansen, Canfield, and Gartler (1995). Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation (Manders, Stap, Strackee, van Driel, and Aten, 1996; Stein, Stein, Lian, van Wijnen, and Montecino, 1996).

See also The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity Published September 30, 2015
Their cited works link energy-dependent chromatin interactions from the determinants of nucleosome organization to G+C content and intrinsic nucleosome occupancy, which is linked to biophysically constrained cell type differentiation via chromosomal inheritance in primary human cells. The terms “promoter elements” and “self-renewal” are used to obfuscate the fact that energy-dependent RNA-mediated amino acid substitutions differentiate all cell types in all living genera in the context of autophagy and polycombic ecological adaptations. The nutrient energy-dependent fixation of the RNA-mediated amino acid substitutions in supercoiled DNA is not mentioned in the context of autophagy, which must be linked to physiology of reproduction. The game of hide the facts about virus-driven energy theft and all pathology continues to be played by experts who do not want anyone to know what they missed when they invented their theories and taught others to believe in them.
Reported Nov 22, 2016  as: Researchers uncover a survival mechanism in cancer cells

The results showed an inverse relation between H1.0 and the division of cancer cells: “As the H1.0 levels fall, the greater the potential of uncontrolled division of cells. In contrast, high levels of the protein prevent this process. We found that the disappearance of protein H1.0 is characteristic of cancer stem cells and it is necessary to maintain the ability of partition and the potential for growth creation.”

Virus-driven energy theft is clearly linked to the disappearance of H1.0 via everything known to serious scientists about autophagy. Energy-dependent RNA-directed DNA methylation stops the proliferation of undifferentiated cell types is all living genera and it links amino acid substitutions from biophysically constrained protein folding chemistry to supercoiled DNA and all biodiversity. Reports of negative supercoiling in bacteria link virus-driven energy theft from the creation of archaea to the transgenerational epigenetic inheritance of Zika virus-damaged DNA via the conserved molecular mechanisms of epigenetic top-down causation that links food odors from pheromones to the physiology of reproduction.
See also: How keeping active pays off in the olfactory system
open access with comments at Neuroscience: How keeping active pays off in the olfactory system

Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?
Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338. DOI: 10.3402/snp.v2i0.17338.

The article elucidates how the environment can broadly influence gene expression through an epigenetic effect chromatin – the way DNA is package and organized. This allows the environment to influence sensory function, to tune the olfactory sense to better suit the surrounding environment, because these environmentally regulated chromatin changes are coupled to cell longevity. This results in a change in the distribution of cells in the tissue that have made particular stochastic choices, where the stochastic choice is which olfactory receptor to express, without affecting the mechanism of stochastic gene expression.

I have since modeled nutrient-dependent pheromone-controlled adaptive evolution and uploaded the text and diagram, which are available here: http://dx.doi.org/10.6084/m9.f… I was advised I should have previously declared ownership of the domain Pheromones.com and my commercial involvement in marketing products based on animal models of common molecular mechanisms in species from microbes to man.

I have since published “Nutrient-dependent/pheromone-controlled adaptive evolution: a model” http://www.socioaffectiveneuro…

Model organisms exemplify the fact that the epigenetic effects of olfactory/pheromonal input result in nutrient-dependent amino acid substitutions and changes in phenotype associated with the pheromone-controlled physiology of nutrient-dependent reproduction. Included are example in microbes, nematodes, insects, other mammals, and a human population that adaptively evolved in what is now central China during the past ~30,000 years.

Alternative splicing of pre-mRNA

Energy-dependent purifying selection / autophagy (6)

See: Energy-dependent purifying selection / autophagy (5)

Simply put all aspects of biophysically constrained energy-dependent cell type differentiation must first be linked from the physiology of reproduction to ecological adaptations, or they must be linked from energy theft to the evolution of pathology.

See for contrast and comparsion: Finding your diagnosis in the brave new world of genetics-based medicine by John Hewitt

Excerpts:

  1. Typically all they have is a stack of diffuse paper reports and xeroxed publications from the primary medical literature with no clear explanation to tie everything together.
  2. This current state of affairs is not the direct fault of anybody in particular, but rather a side effect of an incomplete and evolving body of knowledge that necessarily contains significant ambiguity in its presentation.
  3. Having a ‘genomic sequencing’ reference (g.) would be a little more informative here for many reasons, namely, the presence of multiple transcription initiation sites (promoters), alternative splicing, the use of different poly-A addition signals, multiple translation initiation sites (ATG-codons), and the occurrence of length variations. Potentially, if exome sequencing draws on mRNAs after they are edited, (either in nucleus-specific or cytosol-specific editing), this would be an issue too, although RNA editing (post-transcriptional modification of bases, mostly A to G or A to I substitutions in humans) is quite rare.
  4. An important related question here is what tissue source got sequenced in the exome analysis—was it blood, skin, or epithelium? Because the same gene is typically spliced differently in different tissues it would also give different cDNAs in exome analysis of different tissues.
  5. Isoleucine is a hydrophobic amino acid and serine is a polar and uncharged amino acid. These are fairly different animals altogether and it is normally assumed that this kind substitution should have some significant effect on protein structure or function. The question is what effect?
  6. I will not delve much further into the other variants found in the genetic testing other than to note that the one for PGAP1 has a slightly different notation from the others, given as c.2525+4C>T. This annotation c.2525+4C>T appears to suggest that this variant is located +4 nucleotides apart from the last exonic nucleotide. This variant is predicted to be a “splice donor” which means that can alter the length of the resulting protein, a different transcript. PGAP1 has 22 exons and at least 11 splice variants. This variant has a mutation in the intron downstream of nucleotide position 2525. This creates a splice junction failure where the intron will not be spliced out and thus the variant will include protein sequence corresponding to the intron.

Thanks to John Hewitt for calling attention to this at a time when others are beginning to realize there is no such thing as “genetics-based” medicine. Personalized species-specific treatments across different human populations must link nutrient energy-dependent changes from angstroms to ecosystems.
All serious scientists will continue to attest to that fact. Even the best science journalists may not be able to cross disciplines and report on what is already known. For example, John Hewitt comes up short.
Excerpt (I paraphrase to reiterate):

I will not delve much further into the other variants found in the genetic testing other than to note that … [one variant] …. is predicted to be a “splice donor” which means that can alter the length of the resulting protein, a different transcript. PGAP1 has 22 exons and at least 11 splice variants. This variant has a mutation in the intron downstream of nucleotide position 2525. This creates a splice junction failure where the intron will not be spliced out and thus the variant will include protein sequence corresponding to the intron.

My comment: There is no need to delve any further into the differences in the splice variants. The differences link natural selection for energy-dependent codon optimality to the RNA-mediated fixation of amino acid substitutions in supercoiled DNA. Supercoiled DNA links chromosomal rearrangements to the physiology of reproduction, which prevents most of the transgenerational epigenetic inheritance of virus-driven energy theft. Virus-driven energy theft links negative supercoiling in DNA to all pathology in all living genera.
Until more people understand that fact, even the best science journalists are not likely to escape from the pseudoscientific nonsense touted by theorists who fail to link energy to healthy longevity and/or fail to link virus-driven energy theft to all pathology.
No one gets out of this alive who cannot understand that the splice variants are energy-dependent, which is why no one lives for ever. Eventually, the viruses steal too much energy and use it for their genomic stability.
Not only does that fact limit the life expectancy of all humans but the limits are predictably linked from nutrient stress and/or social stress to everything known about energy-dependent amino acid substitutions in the context of life history transitions, which link the energy-dependent differences in archaea to humans via differences in base pairs and amino acid substitutions.

Alternative splicing of pre-mRNA

Epigenetics and autophagy vs mutations and evolution (7)

diseases-disorders

The Aquatic Ape / Waterside Ape divergence

See also: The Aquatic Ape: New evidence? (9/8/16)
Walt Patrick 

Now that I’m semi-retired…. My major focus is the development of village-scale energy sovereignty.
I believe that sustainable community stands on an interlocking foundation of effective and sustainable energy systems, and I’m working to develop ways that a community can meet its energy needs without having to rely on multi-national energy corporations.

My comment: Thanks to Walt for introducing me to Elaine Morgan’s work. He loaned me his copy of “The Aquatic Ape” in 1982. Thanks to Janissa Wilson for introducing me to Walt Patrick. Thirty-four years have passed, and I remember their friendship and their influence as if it was only yesterday.
See (from yesterday and earlier today):
The Waterside Ape — Sir David Attenborough considers whether new evidence will help a once widely ridiculed theory of human origins move towards to mainstream acceptance.
My comment: He takes a giant step forward in an obvious attempt to keep biologically uninformed theorists from being subjected to ridicule because they missed the paradigm shift.
He then takes small steps backwards to put the “The Aquatic Ape” back into the context of ridiculous theories, which he uses to link his divergence from claims in the “The Aquatic Ape.” He needs an evolutionary theory to evolve one theory into a new theory that becomes “The Waterside Ape.” Otherwise, he gets credit for nothing more than finally acknowledging what serious scientists have known for several decades.
The reports on the efforts of the serious scientists are exemplary. So is the attempt to put them all into the context of evolutionary theory at a time when energy-dependent changes have been linked from angstroms to ecosystems in all living genera in the context of energy as information.
See also:  A Chat with Information Scientist Pedro Marijuán
I’ve commented twice on this article, which is  on Suzan Mazur’s blog site, and both comments were promptly removed.
See for comparison: Kalevi Kull: Censorship & Royal Society Evo Event
My Jul 31, 2016 11:51am comment has not yet been removed:

James Kohl Founder at RNA-mediated.com

This response may not, at first, appear to be directed against the claims you have supported with your series of interviews. But watch closely as they squirm under the weight of experimental evidence that collectively refutes their ridiculous theories and philosophy.

The Origin of The Extended Evolutionary Synthesis: An Interview with Massimo Pigliucci

Moving forward:

Claims linked to the Extended Evolutionary Synthesis have since run out of “wiggle room”. Listen to: The Waterside Ape, which closes the case on how the nutrient-energy-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation via RNA methylation and RNA-mediated amino acid substitutions in supercoiled DNA, which differentiates all cell types in all living genera.

part 1
part 2
Ongoing attempts have failed to place everything known about biophysically constrained RNA-mediated protein folding chemistry and epigenetic effects on supercoiled DNA into the context of evolution. The attempts will continue to fail until researchers and theorists stop trying to make what is known fit into their theories about millions of years of evolution. No experimental evidence of biologically-based cause and effect links what is known about energy-dependent changes from angstroms to ecosystems in all living genera.
See also: Elaine Morgan is a tenacious proponent of the aquatic ape hypothesis: the idea that humans evolved from primate ancestors who dwelt in watery habitats. Hear her spirited defense of the idea — and her theory on why mainstream science doesn’t take it seriously.

See for comparison: Study Links RNA Alterations to Stomach Cancer  September 14, 2016

Written By: Xuan Pham Science Writer, PhD LabRoots

Description: I am a human geneticist, passionate about telling stories to make science more engaging and approachable.

For comparison: I am a medical laboratory scientist who has followed the literature on biologically-based cause and effect since 1982.

The historical perspective on the current literature clearly states this:

For several years it has been apparent that an ecological approach is imperative for all studies in population genetics, including those pertaining to man. It also offers a potentially useful point of view to the physical anthropologist, the ethnologist, and the archeologist, and it should provide an important integrative bridge between the various fields of anthropology. — Blood, Bulbs, and Bunodonts: On Evolutionary Ecology and the Diets of Ardipithecus, Australopithecus, and Early Homo

See also: Unravelling the genetic mystery behind mitochondrial disease

Excerpt:
Mitochondrial disease is an illness that robs its sufferers of energy, and damages muscles and major organs like the brain and heart. About one in 5000 babies – or one Australian baby born each week – are born with a severe form of the disease, which can often lead to an early death.

My comment: Virus-driven energy theft of quantised energy is the cause of all pathology. That fact is not a genetic mystery. It is fact known to all serious scientists who understand why Church et al., (2015) applied for this patent RNA-Guided Human Genome Engineering.

Viruses steal the energy that all cell types require for cell-type differentiation, which links ecological variation to ecological adaptation and healthy longevity in the absence of excess nutrient-stress and/or excess social stress. Stress-linked pathology is manifested when changes in hydrogen-atom transfer in DNA base pairs in solution facilitate codon usage in codon usage that enables their proliferation and prevent cell type differentiation.

The energy stolen by viruses is quantised energy:

See: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution

My comment: This is not a quantum theory of neural cell signalling throughout evolution. It exemplifies what is know to serious scientists about the obvious links from ecological variation to ecological adaptation, which is nutrient-energy-dependent and pheromone-controlled in species from microbes to humans.

See also: Two fatty acyl reductases involved in moth pheromone biosynthesis 7/18/16

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.

See also: Role of olfaction in Octopus vulgaris reproduction 1/1/15

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).

Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model is also cited in Two fatty acyl reductases involved in moth pheromone biosynthesis.

In my 2013 review, I concluded:

the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

The criticisms of my 2013 review may be of interest in the criticisms of Elaine Morgan’s works, since there is still no other model that links ecological variation to ecological adaptation.

In his Criticisms of the nutrient-dependent pheromone-controlled evolutionary model, Andrew Jones wrote:

James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

Andrew Jones did not offer any other model for comparison. He seemed to think that he could support his criticisms via his claim in his thesis:

Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.

The current state of college education in the United States of American and perhaps elsewhere is reflected in the thesis by Andrew Jones as a continuation of the pseudoscientific nonsense that is used to support hypothesis-free science with claims that a system of heredity and evolution through natural selection may exist outside the context of any model that links energy-dependent changes from angstroms to ecosystems in all living genera.

See this invited review of nutritional epigenetics, for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

Abstract:

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.

In 2004, Elaine Morgan suggested it might be another 10 years before her concept of ecological adaptation gained more acceptance. If not for students like Andrew Jones, acceptance of historical works that link angstroms to ecosystems in all living genera via experimental evidence of biologically-based cause and effect would already be accepted. Until the experimental evidence is accepted and the theories are declared by all serious scientists to be ridiculous, you and your loved ones will suffer and die from virus-driven pathology. Why aren’t you already as sick of that as I am after 40 years experience as a medical laboratory scientist?