energy-dependent Archives

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

The eternal significance of microRNAs (2)

April 12, 2018

by James Kohl with No Comment Adaptations base editing Cytosis Diseases & Disorders Ecology RNA Directed

Summary: What is known for sure, however, is that biological processes called “nature” are not simplistic. Neither is the entity called “the environment.” The two separate worlds overlap and intertwine so only a single interactive one exists. Yes, it may be simpler to look at each singly, but one does so at intellectual peril.
The Immune Landscape of Cancer (2018)

Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes.

More than 725 collaborators linked the anti-entropic virucidal energy of sunlight from the energy-dependent creation of microRNAs and biophysically constrained viral latency to cell type differentiation via autophagy.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

What is known for sure, however, is that biological processes called “nature” are not simplistic. Neither is the entity called “the environment.” The two separate worlds overlap and intertwine so only a single interactive one exists. Yes, it may be simpler to look at each singly, but one does so at intellectual peril.

Richard P. Feynman placed the intellectual peril into the context of food energy and human idiocy.
See:

See also: The Translation Machinery Is Immune from miRNA Perturbations: A Cell-Based Probabilistic Approach

Mature microRNAs (miRNAs) are non-coding RNA that regulate most human genes through base-pairing with their targets.

Base-pairing is energy-dependent and biophysically constrained. See: Structural diversity of supercoiled DNA and the parody: All About that Base (Meghan Trainor Parody) 12/10/14
Others now appear to be following on the heels of the late Eshel Ben-Jacob’s works, which showed that the “stochastic nature of miRNA action” is light energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans.
See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination
MicroRNA-based regulation is obviously the key to biophysically constrained viral latency in the context of everything known about the eternal significance of microRNAs.
See also: microRNA
The quantized energy-dependent differential expression of microRNAs has been linked to healthy longevity or from virus-driven energy theft to all pathology in more than 71,000 indexed published works.
Serious scientists now know that John McCain’s glioblastoma can probably be effectively treated with the microRNA-mediated immunotherapy that led to the remission of Jimmy Carter’s brain cancer.
See: John McCain’s brain cancer prognosis is ‘not very good,’ medical expert says
The reporters touch on the likely link from melanoma to brain cancer via microRNAs, and then dismiss it.
See for comparison: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
Would you like to target the regulation of your cell death genes?
See: The Remarkable Cancer Treatment That Helped Jimmy Carter Combat Brain Tumor

…his doctors have said he no longer needs cancer treatment thanks in part to a groundbreaking new kind of medication that trains the immune system to fight cancer tumors.

Anyone who is interested in learning how to prevent all diseases of the body and the brain (e.g., suicide prevention) may want to select the following link. Broad Anti-tumor Activity of a Small Molecule that Selectively Targets the Warburg Effect and Lipogenesis.
The Warburg Effect links virus-driven energy theft to all pathology in the context of sympatric speciation, which is food energy-dependent and controlled by feedback loops that link the food energy to the pheromone-controlled physiology of reproduction.
Unfortunately, the Warburg effect is commonly used to explain mutation-driven evolution outside the context of the food energy that is required for sympatric speciation. Biologically uninformed theorists continue to display what Feynman referred to as human idiocy — as if no one on Earth can stop them.
But see: Cytosis. You could learn that the cure for all pathology is food energy-dependent and microRNA-mediated in the context of biophysically constrained viral latency.
See also: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
Anyone who makes claims about “viral evolution” should be forced to explain why they have not learned how fixation of RNA-mediated amino acid substitutions have been linked to healthy longevity.

Editor’s summary: Five antigenic sites in the virus surface hemagglutinin protein, which together comprise 131 amino acid positions, are thought to determine the full scope of antigenic drift of influenza A virus. Koel et al. (p. 976) show that major antigenic change can be caused by single amino acid substitutions.

Brain gene expression profiling studies of suicide and depression using oligonucleotide microarrays have often failed to distinguish these two phenotypes. Moreover, next generation sequencing approaches are more accurate in quantifying gene expression and can detect alternative splicing.

Who doesn’t want others to know that our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation included a section on “molecular epigenetics” and alternative splicing? See: From Fertilization to Adult Sexual Behavior

Sympatric Speciation vs Pseudoscientific Nonsense (1)

April 7, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity

Summary: The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
For a historical perspective, see:
1996 From Fertilization to Adult Sexual Behavior

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

For obfuscation of our claims about cause and effect, which have since been linked to all biodiveristy, see: Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection (2016)
Simply put, no new mechanisms were revealed. The well-known mechanisms of energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation were simply placed into the context of more unintelligible rhetoric.
See for comparison: 2013 Alternative splicings and amino acid substitutions (redux)
Tracking niche variation over millennial timescales in sympatric killer whale lineages

Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

For more information on the current perspective, which is the same as the historical perspective, see:
2018 Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

…speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.

Reported as: Baleen Whale Genomes Point to Evolution With Gene Flow

Large baleen whales in the Balaenopteridae family (commonly known as rorqual whales) have undergone sympatric speciation — speciation without clear geographic barriers between them — despite ongoing hybridization…

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

Viruses are the dynamo of change that we see in the modern genome. . . .

Cytosis_Booklet_Science.pdf (63 KB) (Log in or Register [for free] to download.) The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
Cytosis is described as: A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
The collaborative efforts of 20 serious scientists who validated the details in the game include the mention of Stephen J. Bush. See: Bush, SJ et al., (2017) Alternative splicing and the evolution of phenotypic novelty

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
See for comparison: Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication
Reported as: RNA Replication Paper Retracted
Szostak and others got busted for their pseudoscientific nonsense about non-enzymatic emergence by someone who understands quantized energy as information-dependent RNA-mediated top-down causation. People over age 10+ who play the cell biology game “Cytosis” may now force all biologically uninformed theorists to retract their claims, which typically have been placed into the context of mutation-driven evolution.

Part 3: Light-controlled cell biology (revisited)

March 23, 2018

by James Kohl with No Comment Adaptations Autophagy biophotonics Diseases & Disorders Ecology Light Energy Physics RNA Directed RNA interference RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Your cells are constantly being shed and replaced—so is your body ever completely refreshed? Does anything remain of the body that existed on Jan. 1, 2017? 2007? The day you were born? (video)

Out of Order: Undaunted

…as I prepared for this issue’s Special Report on Microbiomics (starting on page 19), I am stunned by what I am only starting to understand. That our individual existence as humans may only be 10 percent of what we see in the mirror—and that perhaps only 1 percent of our personal ecological genome is a human genome…

When you understand the concept of biophysically constrained energy-dependent ecology (Frohlich, 1968), you may begin to understand the difference between ecological adaptation and evolution. Each cell type represents biophysically constrained viral latency, not mutation-driven evolution.

Outside the context of energy-dependent RNA-mediated DNA repair (aka autophagy), no cell types exist. Bacteria become archaea and archaea become L-forms and the L-forms become non-cells. The energy for cell type differentiation comes from sunlight or from food. It is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Theorists used the term “de novo” in the context of de novo transcription and other aspects of energy-dependent cell type differentiation that they cannot explain with their ridiculous theories. For instance, David Sinclair has touted pseudoscientific nonsense until now.

He knows that the cell biology game, “Cytosis” for ages 10+ has exposed him to ridicule, and obviously won’t go away without a fight to maintain some scientific credibility.

State of art:
TDP-43 and FUS, two RNA-binding proteins (RBPs), have been recently the subject of increased attention due to their role in Amyotrophic Lateral Sclerosis (ALS) and FrontoTemporal Lobar Degeneration (FTLD). In non-pathological conditions, these proteins are mostly found in the nucleus where they participate to mRNA biogenesis and regulation of alternative splicing. However, TDP-43 and FUS are also present in the cytoplasm and they are able to shuttle from one compartment to another. TDP-43 and FUS notably participate in cytoplasmic functions such as mRNA transport and localized translation, which are of critical importance for neuron physiology. In neurons of ALS and FTLD patients, TDP-43 and FUS form insoluble cytoplasmic aggregates with fibrillar structure that can further spread the disease to other areas of the brain.

If this is the state of the art, was the information used to treat the late Stephen Hawking, or was he left to suffer unnecessarily until he died?

Polymaths and paradigm shifts: from Asimov to Bear (4)

March 14, 2018

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology RNA Directed

Saying Goodbye to the RNA World Theory

RNA has a limited ability for catalysis compared to peptides, and would have struggled to maintain its catalytic activity under the changing temperature conditions of early Earth. Carter and Wills also argued that if an RNA world existed, it would have been unlikely for it to incorporate peptides later on.

See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

The energy-dependent creation of ATP synthase has since been linked to this claim from McEwen et al., (1964):

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

By starting with the energy-dependent de novo creation of enzymes, others have linked Schrödinger’s claims from “What is Life” (1944) to all biophysically constrained biodiversity.
Say Hello again to Schrödinger at 75 – The Future of Biology
Let Timothy J. Cunningham, who disappeared from the CDC last month, reintroduce you. See his publications on:
1)”Racial Disparities in Age-Specific Mortality”
2) “Sex-specific relationships between adverse childhood experiences”
3) “Associations between antioxidants and all-cause mortality”
and
4) “Health and Safety Issues for Travelers”
Serious scientists know that all racial/ethnic disparities are food energy-dependent, RNA-mediated, and pheromone-controlled in the context of enymes, metabolism, and amino acid substitutions. Fixation of the RNA-mediated amino acid substitutions differentiates all cell types in all living genera — including sex differences in cell types.
See for examples our section on molecular epigenetics from this 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior

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…

See for comparison, this nonsense: Caenorhabditis elegans glia modulate neuronal activity and behavior

Introduction: a brief on evolution of neuroglia

“Nothing in biology makes sense except in the light of evolution”. — Theodosius Dobzhansky (1900–1975)

Evolution of the nervous system proceeded through an increase in number and complexity of the nervous elements and through their specialization into electrically excitable neurons connected through defined synaptic contacts and electrically non-excitable neuroglia forming networks through intercellular gap junctions. Intercellular chemical neurotransmission is, however, characteristic for both forms of the neural cells that express appropriate receptors and are capable of secreting neurotransmitters. The evolution of the nervous system was not a straight journey from less complex and accomplished networks to the more refined ones; at the turning point between invertebrates and vertebrates, a fundamental metamorphosis occurred that changed the overall structure of the central nervous system (CNS).

The difference in the energy of two photons has since been linked from the proton motive force to the creation of enzymes and metabolism of food. The pheromone-controlled physiology of reproduction in species from bacteria to humans has linked DNA methylation from the creation and fixation of RNA-mediated amino acid substitutions to viral latency and all biodiversity. Timothy J. Cunningham placed that fact into the context of his history of published works.
For comparison, see: On the Difference between Physics and Biology: Logical Branching and Biomolecules (2018) and The Large Scale Structure of Space-Time(1975) George FR Ellis was a coauthor of both published works.
He, and others like him, failed to link Physics and Chemistry from molecular epigenetics to what is known about energy-dependent RNA-mediated biophysically constrained cell type differentiation to all biodiversity on Earth. Framing what is known to all serious scientists about cell type differentiation in the context of what Ellis might think is a logical representation of biomolecules attests to his lack of logic across the time-space continuum of his life.
See for comparison: Olfaction Warps Visual Time Perception (2017).
See also Odor-induced mood state modulates language comprehension by affecting processing strategies (2016)
The 2016 citation to The impact of natural odors on affective states in humans can now be linked to the accurate representations of top-down biophysical constraints on food energy-dependent pheromone-controlled feedback loops. The feedback loops are required to biophysically constrain viral latency.
See: What is life when it is not protected from virus driven entropy (video)

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 for comparison: Gay, Straight, and the Reason Why: The Science of Sexual Orientation (2011)

Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (pp. 210- 211)

See also: Gay, Straight, and the Reason Why: The Science of Sexual Orientation, 2nd edition (2016)
From the second edition of LeVay’s book:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect… (p. 115)

LeVay cites Kohl et al., (2001) Human pheromones: integrating neuroendocrinology and ethology.
He has never mentioned the fact that the effects of virus-driven entropy on cell type differentiation were linked human sexual orientation in The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) and in the book chapter he cited in the first edition of Gay, Straight, and the Reason Why: The Science of Sexual Orientation.
See for comparison: Always follow your nose: the functional significance of social chemosignals in human reproduction and survival (2015) This article is part of a Special Issue “Chemosignals and Reproduction”
John Cacioppo, a Founder of Social Neuroscience, Dies

The University of Chicago psychology professor made fundamental contributions to understanding the neural mechanisms of social experiences.

My comment to The Scientist:

I hope John Cacioppo is remembered for this refutation of neo-Darwinian pseudoscientific nonsense:

Although peptide chemistry has been with us since amino acids first formed, the social role of oxytocin did not exist prior to the evolutionary sculpting of the vertebrate brain.

He may have been one of the first social scientists to recognize the fatal flaw that others continue to include in their works. All other serious scientists, like him, start with the energy-dependent creation of enzymes and amino acids. Only pseudoscientists still start with the evolution of the vertebrate brain.

I remember when he and his wife turned towards me and smiled — after I asked the speaker from Argentina about the role of oxytocin in a rodent model. No studies were being done for the obvious reason that few people knew where oxytocin came from.

I invited the speaker to lunch and we laughed a lot about the works that tried to link oxytocin to differences in behavior without linking the differences to altered RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse

RIP John Cacioppo

See also: Multilevel integrative analyses of human behavior: social neuroscience and the complementing nature of social and biological approaches (2000)
Nothing published during that 12-year period and nothing published before or since then suggests the the neuroarchitecture of intelligent creatures somehow evolved.
For comparison, see: Human pheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic niches that affect behavior (2012) Presented at the Society for Social Neuroscience Annual Meeting 2012
See also: Neuroglia in C. elegans (2018)

The nematode C. elegans is one of the most important model organisms for understanding neurobiology. Its completely mapped neural connectome of 302 neurons and fully characterized and stereotyped development have made it a prototype for understanding nervous system structure, development, and function. Fifty-six out of C. elegans‘ total of 959 somatic cells are classified as neuroglia. Although research on worm glia has lagged behind studies focused on neurons, there has been a steep upswing in interest during the past decade. Information arising from the recent burst of research on worm glia supports the idea that C. elegans will continue to be an important animal model for understanding glial cell biology. Since the developmental lineage of all cells was mapped, each glial cell in C. elegans is known by a specific name and has research associated with it. We list and describe the glia of the hermaphrodite form of C. elegans and summarize research findings relating to each glial cell. We hope this lecture provides an informative overview of worm glia to accompany the excellent and freely available online resources available to the worm research community.

The worm research community seems to be largely unaware of this fact: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
The have failed to link food odors from the pheromone-controlled physiology of reproduction to ecological adaptatation manifested in morphological and in behavioral diversity.

Polymaths and paradigm shifts: from Asimov to Bear (3)

March 14, 2018

by James Kohl with No Comment Adaptations Alternative Splicings biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA–Mediated Epigenetic Heredity

Polymaths and paradigm shifts: from Asimov to Bear (2)

“Teilhardism And The New Religion: A Thorough Analysis of the Teachings of Pierre Teilhard de Chardin”, p.18, TAN Books

The evolutionist thesis has become more stringently unthinkable than ever before. — Dr. Wolfgang Smith (2015).

A Chat with Information Scientist Pedro Marijuán (2017)

I’ve based my informational scheme of the cell on this thinking of “distinction on the adjacent” — where molecular recognition is the essential phenomenon over which biological complexity has been developed.

Biological complexity develops in the context of the olfactory code. Molecular recognition of food odors and pheromones biophysically constrains viral latency.

See: Fundamental principles of the olfactory code Volume 164, February 2018, Pages 94-101 open access

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response.

Alternative splicing of microRNAs (aka pre-mRNAs) are required for a behavior response.

The splicing code Volume 164, February 2018, Pages 39-48

…the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

Algorithms define nothing. The availability of quantized energy as information must be linked to biophysically constrained viral latency and all biologically based cause and effect.

What is code biology? Volume 164, February 2018, Pages 1-10

The great discontinuities of the history of life, in other words, can be explained as the result of the appearance of new codes.

New codes do not automagically occur. The new codes are energy-dependent and RNA-mediated in the context of the fixation of amino acid substitutions that differentiate the cell types of all living genera.

On universal coding events in protein biogenesis Volume 164, February 2018, Pages 16-25

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases…

The energy-dependent creation of the tRNA synthetases links hydrogen-atom transfer in DNA base pairs in solution to all energy-dependent biodiversity.

How prokaryotes ‘encode’ their environment: Systemic tools for organizing the information flow Volume 164, February 2018, Pages 26-38

An important issue related to code biology concerns the cell’s informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows.

Quantized energy is the information that flows through every cell type in all prokaryotes.

Causation, constructors and codes Volume 164, February 2018, Pages 121-127

A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

The diverse range of processes starts with the creation of energy-dependent enzyme action. The anti-entropic virucidal energy of sunlight was first linked to the creation of all biodiversity on Earth in 1944: What is Life?

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)

If you think you can link anything except sunlight to all biodiversity on Earth, see: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
If you know that serious scientists do not link viruses to the evolution of anything except pathology, see:
Schrödinger at 75 – The Future of Biology – September 2018
The future of biology will not be left in the hands of biologically uninformed theorists.

Virus-mediated archaeal hecatomb in the deep seafloor

Carl Zimmer refutes theistic evolution (2)

March 11, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Diseases & Disorders Ecology RNA Directed RNA–Mediated Epigenetic Heredity

Carl Zimmer refutes theistic evolution (1)
Carl Zimmer recognizes the need for a new definition of what heredity is. But he refuses to tell others what he knows about the role that viruses play in the transgenerational epigenetic inheritance of all pathology.
Examples of inherited pathology typically include his misrepresentations among others who fail to link ecological variation to ecological adaptation in the context of energy-dependent biophysically constrained viral latency.
See: Ancient Viruses Are Buried in Your DNA by Carl Zimmer
His conclusion:

In other words, early embryos may have come to depend on the tricks viruses use to manipulate them. “We’re exploiting a property that has evolved for the virus’s benefit,” Dr. Katzourakis said.

No experimental evidence of biologically-based cause and effect suggests anything except virus-driven pathology has evolved.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

We estimated that viral infections were responsible for the abatement of 1.0 to 2.2% day−1 (on average 1.6% day−1) of the bacterial abundance and 2.3 to 4.3% day−1 (on average 3.2% day−1) of the archaeal abundance in deep-sea sediments (Fig. 6).

The amount of virus-driven degradation of messenger RNA in archaea is clearly biophysically constrained via the energy-dependent physiology of the pheromone-controlled reproduction in bacteria. Neo-Darwinian theorists and so-called science journalists misrepresent the facts about how the virus-driven theft of quantized energy as information is biophysically constrained.
They trick people into believing that viruses and organisms evolve by failing to to mention that viral replication is not possible outside the context of energy theft from the host. Zimmer, for example, has consistently led others to believe in anything except how viral latency is biophysically constrained by what organisms eat and how metabolism is linked to reproduction.
Others like Zimmer are directly to blame for the level of ignorance reported in the context of this project.
The Global Virome Project

Our ability to mitigate disease emergence is undermined by our poor understanding of the diversity and ecology of viral threats, and of the drivers of their emergence.

The diversity and ecology of viral threats has always been linked to stress-induced changes in endogenous substrates. Light activation of endogenous substrates has been linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency and healthy longevity in species from bacteria to humans.
Nutrient-stress and social stress have been linked from the degradation of messenger RNA in bacteria to the creation of archaea and L-forms, in which the membrane required for biophysically constrained viral latency is missing.
Zimmer and many other biologically uninformed journalists ignore this threat: Beware ‘Disease X’: the mystery killer keeping scientists awake at night
The threat would not exist if de Vries 1902 definition of mutation had not been accepted by people with not enough common sense to know that food energy must be linked to heredity via biophysical constrained viral latency.
See: Polymaths and paradigm shifts: from Asimov to Bear (in prep)

BiondVax Universal Flu Vaccine Patent

January 31, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Cytosis Diseases & Disorders Ecology Model Organisms Nutrigenomics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Summary: …the dream to create an effective universal flu vaccine to ultimately eradicate the flu is placed into the context of claims about changes to the virus. The changes are energy-dependent ecological adaptations. No one claims that the virus mutates or that it evolves. Only biologically uninformed theorists make such ridiculous claims.
BiondVax Universal Flu Vaccine Patent Granted in India

The patent describes influenza vaccines comprised of multiple copies of several epitopes, such as M-001 which contains nine common and conserved influenza virus epitopes.

The use of the word epitope obfuscates cause and effect in the context of natural information processing, which is energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans. If they used the term conserved amino acid substitutions more people might understand the fact the fixation of amino acid substitutions biophysically constrains viral latency. Who knows what epitopes are or what they do or how they do it?
See for comparison: Learning from Bacteria about Natural Information Processing (Israel) and Generation of influenza A viruses as live but replication-incompetent virus vaccines, (China) which was reported as: Engineered virus has artificial amino acid allowing it to serve as a vaccine
Researchers in other countries, but not in the United States of America, have made scientific progress that helps to make sense of claims about energy-dependent natural information processing and RNA-mediated amino acid substitutions that biophysicaily constrain viral latency and typically prevent all pathology.
In this video, the dream to create an effective universal flu vaccine to ultimately eradicate the flu is placed into the context of claims about changes to the virus. The changes are energy-dependent ecological adaptations. No one claims that the virus mutates or that it evolves. Only biologically uninformed theorists make such ridiculous claims.

See for comparison: How to Build a Better Flu Shot (with my emphasis)
1) … the influenza virus has many rapidly mutating strains. And because the strains mutate so quickly…
2) …the mushroom head of hemagglutinin mutates rapidly, so antibodies against one type of head won’t work against a mutant version.
3) To infect the cell, the stalk of the hemagglutinin mushroom becomes completely rearranged from its normal state. “It’s a machine,” Krammer explains. “It doesn’t tolerate mutations well. If you introduce mutations, you destroy the machine, so the virus doesn’t like to change it.”
4) Other teams are testing headless stalks made by anchoring the stalk to a ferritin protein nanoparticle or by creating genetic mutations at the top, as potential vaccines too.
5) In a study published January 19 in Science, University of California, Los Angeles, virologist Ren Sun and colleagues identified eight genetic mutations that make the flu virus sensitive to a host cell’s interferons.
6) “The team was able to mutate this virus for interferon sensitivity without changing the immune response, which is a challenge.”
7) Fauci says one essential piece of information scientists need to build a universal flu vaccine is to understand how serial exposure to the virus and vaccination affects the immune system.
8) “This is what we call immunological imprinting. It’s controversial, but we need to know what the influence is to create a broadly effective flu vaccine,” Fauci says.
9) Understanding the effect of pre-existing immunity on virus evolution is also important, given that vaccination itself could influence how flu strains evolve, Fauci and colleagues note in a paper published last summer in Immunity
10) The paper describes a path toward making a universal flu vaccine. “I see this work falling into three buckets,” Fauci says. “There’s the bucket on antibody development, the bucket on boosting the immune response to flu, and finally the bucket on prior exposure and how that affects the immune system,” he says.
Fauci wants others to believe that viruses mutate and evolve but that immunological imprinting is controversial. He has many others to help people in the United States accept the claims about mutations and evolution and put the claims of serious scientists who understand the facts about immunological imprinting into the context of controversy.
My comment to The Scientist:

In this report from the NIH: Flu infection study increases understanding of natural immunity the focus on the change in the influenza virus was properly placed into context of energy-dependent changes in the virus, which are called ecological adaptations when they occur in human populations.

For example, one energy-dependent amino acid substitution causes increased virulence in the influenza virus, as clearly stated here: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Simply put, all serious scientists know that viruses do not mutate and evolve. Viruses steal the energy that biophysically constrains viral latency and some humans in some human populations fail to ecologically adapt as quickly as others.

Is Fauci, or anyone else who made claims in the article from The Scientist, a serious scientist? Unfortunately, the answer is no. Serious scientists do not believe that mutations can be linked to evolution. That gives them an edge if they are working in other countries, but not the United States of America.
See how serious scientists in some countries will maintain their edge, and continue to put theorists from the United States of America to shame — along with all the so-called science journalists who report the nonsense about mutations and evolution.
Controversy over evolution in Israel (2010)

There are many people who don’t believe the evolutionary account is correct,” he was quoted as saying. “There are those for whom evolution is a religion and are unwilling to hear about anything else. Part of my responsibility, in light of my position with the Education Ministry, is to examine textbooks and curricula.”

“…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.”

Those who learn about ecology are less likely to make claims about mutations or evolution.
Turkish schools to stop teaching evolution, official says (2017)

The secular opposition has long argued that the government of Recep Tayyip Erdoğan is pursuing a covert Islamist agenda contrary to the republic’s founding values.

Does anyone in the United States think that the Trump administration is pursuing a covert Christian agenda? If so, see:
Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

https://media.springernature.com/lw900/springer-static/image/art%3A10.1038%2Fs41467-017-02632-8/MediaObjects/41467_2017_2632_Fig6_HTML.jpg

The MicroRNAome Strikes Back: A Sokalian hoax (4)

January 25, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms RNA Directed RNA editing RNA methylation RNA-mediated epigenetic regulation of gene expression

In this Sokalian hoax series, all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera via the physiology of reproduction and autophagy, the innate phage defense mechanism.
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

I reiterate the most obvious facts by mentioning again:

Virus-mediated archaeal hecatomb in the deep seafloor

Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding, and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.

The John Templeton Foundation typically seems to be involved in funding research reported that obfuscates facts that link science to Biblical Genesis. The claims about understanding energy-dependent biomolecular recognition in biophysical systems, which must biophysically constrain viral latency, invite more criticism of the Templeton-funded biologically uninformed theorists.

Does the “Extended Synthesis” Replace or Not Replace Neo-Darwinism? — What Has Templeton Funded?

Many terms in science have a different meaning from the public usage, because they depend on particular definitions of the phenomena to which they apply.

See for comparison: Do Human Pheromones Exist? January 23, 2018

The people interviewed are not Nobel Laureates. For comparison, LInda Buck, co-author of Feedback loops link odor and pheromone signaling with reproduction is a 2004 Nobel Laureate.
I suspect that all serious scientists have since learned that pheromones biophysically constrain food energy-dependent viral latency in species from insects to mammals via the conserved molecular mechanisms of microRNA-mediated cause and effect. Serious scientists tend to be more likely than theorists or other pseudoscientists to recognize patterns.
For instance: Insect pheromone in elephants

SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.

That claim links what insects eat to the pheromone-controlled physiology of reproduction of s via the food energy-dependent creation of microRNAs in species from microbes to mammals.

See: Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, Signaling, and role of MicroRNA (with my emphasis)

Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.

insects, arachnids, and crustaceans are arthropods. No experimental evidence of biologically-based cause and effect suggest that complex mechanisms evolved in any species. For contrast, the link from microRNAs to juvenile hormone crosses species via the molecular mechanisms that link the food energy-dependent creation of microRNAs from what is known about gonadotropin releasing hormone (GnRH) pulsatility to luteinizing horrmone secretion via the food energy-dependent GnRH-directed physiology of pheromone-controlled feedback loops in all mammals.

That fact has been placed into the context of ecological variation and biophysically constrained ecological adaptations.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

…lack of genome information hinders the understanding of the adaptation…

See for comparison: Differential expression of microRNAs in luteinising hormone-treated mouse TM3 Leydig cells

Results showed that miRNAs might be involved in the regulation of LH to Leydig cells.

One way to understand the adaptations revealed in the context of mussel genomes involves ignoring all claims about how complex mechanisms “evolved to regulate” anything. The overwhelming systems complexity of biophysically constraints demand that all ecological adaptations be examined from the intelligent perspective of serious scientists.

The well-detailed understanding of how the light energy-dependent creation of microRNAs is linked to all nutrient-dependent pheromone-controlled ecological adaptations. But the facts were again placed back into the context of complex mechanisms that automagically evolved in Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

…pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4.

The established biodiversity is obviously pH-dependent and oxidative phosphorylation was linked to the stability of organized genomes in 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”. Other serious scientists moved forward in the context of the energy-dependent hydrophobicity of supercoiled DNA.
See: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Outside the context of the epigenetic effect of anti-entropic virucidal energy from sunlight on supercoiled DNA, or perhaps in the context of minimal exposure to ultraviolet light, the metagenomic diversity of bacteria in caves with sulfur water springs led Bautista et. al., (2018) to conclude:

…20,901 reads of bacterial 16S rRNA gene sequences spanning V1–V3 hypervariable regions corresponded to seven phyla: Proteobacteria, Firmicutes, Chloroflexi, Chlorobi, Bacteroidetes, Actinobacteria and Acidobacteria. Proteobacteria phylum dominance could be due to the increased presence of organic matter, not only of bat guano but also that caused by man and animals, directly or through infiltrations. For the UJAT5 sample, we generated 6,691 reads, which, due to the
physicochemical characteristics (Table 1) and relative frequency obtained (Figure 4), could confirm the presence of acidophilic Proteobacteria in VL caves. All the bacterial communities identified are characteristic of caves, while Acidobacteria, Proteobacteria, and Actinobacteria are typical of volcanic surface terrain.

Simply put, they seem to assume that the increased presence of organic matter is the food energy that supports the pheromone-controlled physiology of reproduction in the different species. But they do not link the creation of sunlight to differences in the food the organisms eat.
By skipping the link from the creation of sunlight — as did Nonomura (2018) in his Sokalian hoax, evolutionists have tried to convince others who are biologically uninformed that the eyes of blind cave fish exemplify evolution in the process of the fish becoming blind.
See: Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
See (pun intended) Blind Cavefish Can Produce Sighted Offspring (2008)

It’s a miracle! Blind cavefish, despite having adapted to their lightless environment for more than a million years, can produce sighted offspring in just a single generation, a new study reveals.

This means that even though the fish are blind, they basically have functional visual systems that have been deactivated by a few key mutations, said Jeffery, who was unaffiliated with the study.

See also: The fish evolved from surface-dwelling ancestors during the past million years. (2003)
Everything biologically uninformed theorists report must be linked toi evolution and back by mutations. They refuse to differentiate between mutations and food energy-dependent ecological adaptations because they cannot accept the fact that all biophysically constrained biodiversity is food energy-dependent and constrained by energy-dependent viral latency.
For comparison, what serious scientists see happening in the blind cave fish is the regression of food energy-dependent visual acuity in organisms that can find food without the energy-dependent creation of G protein-coupled photoreceptors. Only the energy-dependent creation of chemoreceptors is required to link pH-taxis to survival of the microbes and the blind cave fish via what is known about oxidative phosphorylation in other species that display receptor-mediated behaviors.
What science journalists see happen is causing them to back away from their pseudoscintific claims from the past. See for example:

Hydration as a design element in biomaterials Philip Ball January 24, 2018

John Hewitt January 24, 2018 N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

Enzyme-constrained interethnic biodiversity (3)

January 9, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Human Pheromones Model Organisms RNA Directed RNA-directed DNA methylation Variations

Excerpt: Understanding a “correlational mechanism” is like understanding mutation-driven evolution. You have a mutation. You have evolution. Thus, you understand the simple-minded magic of the correlation. No energy-dependent molecular mechanisms are required.
For comparison: Enzyme-constrained interethnic biodiversity is exemplified in Amish populations in the United States of America. Obviously, interethnic difference in genes matter.
See: Low cancer incidence rates in Ohio Amish (2009) Why Don’t The Amish Get Cancer? (2016)
See also: A null mutation in SERPINE1 protects against biological aging in humans (2017)
Reported as: An Internal Fountain of Youth: Why These Amish Live Longer And Healthier

Amish with this mutation also have significantly less diabetes and lower fasting insulin levels.

“The findings astonished us because of the consistency of the anti-aging benefits across multiple body systems,” said Dr. Douglas Vaughan, the lead author of the paper who has been studying PAI-1 for almost 30 years.

See also: Diabetes and Alzheimer’s correlation mechanism understood!
Understanding a “correlational mechanism” is like understanding mutation-driven evolution. You have a mutation. You have evolution. Thus, you understand the simple-minded magic of the correlation. No energy-dependent molecular mechanisms are required.
For comparison, see: Aerobic Glycolysis in the Human Brain Is Associated with Development and Neotenous Gene Expression
The article links imaging to the required molecular mechanisms of behavioral development. Finally, all serious scientists can move forward as they should have been doing for more than a decade since Panksepp et al (2002) published Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind. His group won the same award that my group won for publication in 2001 of: Human pheromones: integrating neuroendocrinology and ethology.
Comparative approaches start with the creation of quantized energy and link it to aerobic glycolysis. Clearly, all serious scientists have been following the experimental evidence that led to publication of: Redefining neuroendocrinology: Epigenetics of brain-body communication over the life course (November 15, 2017) by Bruce McEwen and Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology (November 24, 2017), which was co-authored by Bruce McEwen.
Brain-body communication is food energy-dependent. The obvious link from the virus-driven degradation of messenger RNA to mutations and all pathology via gene losses has since led to the end of the hunt for drugs to treat some neurodegenerative diseases. See Enzyme-constrained interethnic biodiversity (6)
Unfortunately, even though Bruce McEwen set the stage for achieving world peace in the context of interethnic biodiversity, he did not win the 2017 Nobel Peace Prize as I predicted he would.
See: Predicting who wins the 2017 Nobel Prizes

Bruce McEwen has since helped others to link nutrient-stress and social stress from the virus-driven degradation of messenger RNA to amino acid substitutions in the context of the physiology of pheromone-controlled reproduction. For example, the substitution of one amino acid in the cell types of mammals protects them from the virus-driven energy theft that links amino acid substitutions in viruses to all pathology. McEwen’s works are the only known works of a serious scientist who has continued to refute the pseudoscientific nonsense touted by neo-Darwinian theorists since before 1964.

Indeed, most people who are not yet dead, probably do not know how people like Bruce McEwen have linked food energy-dependent “Interethnic Genetic Similarities and Differences” to world peace.
But see: Living in a Genetic World: How Learning About Interethnic Genetic Similarities and Differences Affects Peace and Conflict
Reported as: For groups in conflict, genes matter

“In conflict contexts, we often see attempts to emphasize genetic differences between groups. We saw that in Rwanda. We saw that in Bosnia,” Kimel said. “One thing we suggest in the paper is that groups like International Crisis Watch and Genocide Watch should go on heightened alert when they see this kind of rhetoric in conflict contexts.”

The paper also cites popular media reports on the genetic differences between groups with a history of conflict. Such articles are cause for concern, Kimel said, because they often fail to mention just how genetically similar humans are.

The similarities in all humans have been linked to interethnic differences in only two genes via publication of Brief report: Geographic variation in EGFR mutation frequency in lung adenocarcinoma may be explained by interethnic genetic variation. I reiterate: The full article can be downloaded from here:

Quantized energy-dependent viral trophism (2)

January 5, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Cytosis Diseases & Disorders Ecology Light Energy Model Organisms RNA Directed RNA-directed DNA methylation Subatomic

See first: Quantized energy-dependent viral trophism
Summary of Quantized energy-dependent viral trophism (2)
WTH*? The species evolved to F*- itself?
(H*eck) (*Fertilize)

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins Science 05 Jan 2018

…we compared chromosome-scale assemblies of the outcrossing nematode Caenorhabditis nigoni to its self-fertile sibling species…

The chromosome-scale assemblies extend across species to the fact that a difference in the diet of P. pacificus links its pheromone-controlled physiology of reproduction from C. elegans to the morphological and behavioral phenotypes of a predatory nematode with teeth via chromosomal rearrangements.
Reported as: Worm species lost 7,000 genes after evolving to fertilize itself

“The fact that all the selfing species lost the mss genes suggests that these genes, which are very useful for worms having male-female sex, are harmful for worms that are no longer having sex with each other,” Haag said. “What we are seeing is an evolutionary snapshot of how a species fine-tunes its reproduction.”

See for comparison to what is known by serious scientists: From Fertilization to Adult Sexual Behavior (1996) and System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes (2013) and Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes (2014).
For comparison to representations by pseudoscientists see Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system (2015)
The “Lost Sea Adventure” near Sweetwater, TN features fish that became blind within a few generations after they were placed into the water of the underground cave. The genes for phototaxis were no longer important to survival and the virus-driven degradation of messenger RNA destroyed everything except the subatomic particles that might be required for reassembly in the context of a return to an environment with sufficient quantized energy as information from sunlight.
The Scopes Museum in Dayton, TN is also an eye-opening way to inform yourself about the difference between “evolution” and ecological adaptations, which must be linked from the sun’s anti-entropic virucidal energy and the food organisms eat to their pheromone-controlled physiology of reproduction by facts, not by ridiculous theories with claims about species that automagically fine-tune energy-dependent pheromone-controlled reproduction.
For comparison: Scientific knowledge is drowning in a flood of research

A comic about the problems with the -omics

For comparison: Daniel L. Hurdiss and Ariane Briegel are like the brick-builders.
Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus (2017)
Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling (2014)