Alternative splicing of pre-mRNA

Epitranscriptomics: a "new" field

Conclusion: Serious scientists have a 20 year history of their ability to link energy-dependent changes from electrons to ecosystems via the physiology of pheromone-controlled reproduction in the context of hydrogen-atom transfer in DNA base pairs in solution. This fact links hydrogen-atom transfer in DNA base pairs in solution to the fixation of RNA-mediated amino acid substitutions in hydrophobic supercoiled DNA, which protects all organized genomes from virus-driven entropy.
I reiterate: Hordenine lacks a meta-hydroxyl group compared to dopamine, rendering it unable to form hydrogen bonds to both residues Ser1935.42 and Ser1975.46 as dopamine does42 (Fig. 6).
—————————————————–
How brain develops before birth is tightly controlled by RNA modification

A new field called epitranscriptomics was born out of this knowledge.

See our section on molecular epigenetics from this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior
The obvious need to link energy-dependent changes from electrons to ecosystems in all living genera via base pairs and RNA-mediated amino acid substitutions was ignored.
But see: This gene editing technique could drastically reduce disease inheritance

My comment:

They used exogenous RNA interference and linked energy-dependent changes in base pairs to all biophysically constrained biodiversity via natural selection for energy-dependent codon optimality (endogenous RNA interference) and the physiology of pheromone-controlled reproduction, which biophysically constrains the virus-driven degradation of messenger RNA that links mutations to all pathology.

This was done at the level of base pair interactions, which link electrons to ecosystems. That fact refutes the pseudoscientific nonsense of neo-Darwinian theories and the nonsense of “Big Bang” cosmology. The gene-editing starts from the creation of energy and entropy is biophysically constrained.
See the other comments:
This is a report on Correction of β-thalassemia mutant by base editor in human embryos.
The food energy-dependent efficient base editing at single-base resolution has been reported in plant, yeast, human cells, mouse zygotes, and human tripronuclear zygotes. The facts were explained in the context of the pheromone-controlled physiology of reproduction, which links the microRNAome of plants to mammals in the context of RNA-mediated DNA repair.
There are more that ~1200 hemoglobin variants that attest to the food energy-dependent ecological adaptation of all human populations that are still found all over the world.
HbVar: A Database of Human Hemoglobin Variants and Thalassemias
There are more than 65,000 published works that link food energy-dependent microRNAs from hemoglobin variants to healthy longevity in humans.
See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
It  became obvious to Schrodinger (1944) that sunlight was the most likely anti-entropic source of all energy-dependent life and obvious to all other serious scientists that the virucidal energy of ultraviolet light was the key to energy-efficient hydrogen-atom transfer in DNA base pairs in solution that differentiates all cell types via amino acid substitutions in supercoiled hydrophobic DNA.
In 1991, Roger Penrose attested to the facts about food energy.

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?

See also: Microprocessor Recruitment to Elongating RNA Polymerase II Is Required for Differential Expression of MicroRNAs

…phosphorylation of RNA polymerase II recruits Microprocessor for co-transcriptional processing of non-UGU pri-miRNAs that would otherwise be poorly processed.

Reported as: Range of diseases may result when brain self-regulation goes awry, researchers say
Learn the difference between what “researchers say” and what serious scientist say about energy-dependent cell type differentiation. There is no such thing as self-regulation of the brain. Regulation is food energy-dependent and biophysically constrained by changes in the microRNA/messenger RNA balance.
See for validation: Identification of the Beer Component Hordenine as Food-Derived Dopamine D2 Receptor Agonist by Virtual Screening a 3D Compound Database (with my emphasis)

Although the G protein-biased D2R-agonist hordenine shares structural similarities to the balanced agonist dopamine, receptor–ligand interactions obtained after docking and energy minimisation in presence of a D2R homology model appear to be different. Hordenine lacks a meta-hydroxyl group compared to dopamine, rendering it unable to form hydrogen bonds to both residues Ser1935.42 and Ser1975.46 as dopamine does42 (Fig. 6).

Reported as: The food ingredient hordenine in beer activates the reward centre in the brain
See also:  Cell volume change through water efflux impacts cell stiffness and stem cell fate
Serious scientists have a 20 year history of their ability to link energy-dependent changes from electrons to ecosystems via the physiology of pheromone-controlled reproduction in the context of hydrogen-atom transfer in DNA base pairs in solution. This fact links hydrogen-atom transfer in DNA base pairs in solution to the fixation of RNA-mediated amino acid substitutions in hydrophobic supercoiled DNA, which protects all organized genomes from virus-driven entropy.
I reiterate: Hordenine lacks a meta-hydroxyl group compared to dopamine, rendering it unable to form hydrogen bonds to both residues Ser1935.42 and Ser1975.46 as dopamine does42 (Fig. 6).
 

Alternative splicing of pre-mRNA

1996-2016: Ignoring alternative splicings of pre-mRNA

Range of diseases may result when brain self-regulation goes awry, researchers say
There is no such thing as self-regulation of the brain. Regulation is food energy-dependent and biophysically constrained by changes in the microRNA/messenger RNA balance. The entire range of diseases is linked from the virus-driven degradation of messenger RNA to the mutations that some theorists claim may sometimes be beneficial.The theorists the make those ridiculous claims are biologically uninformed science idiots.

See for comparison: Microprocessor Recruitment to Elongating RNA Polymerase II Is Required for Differential Expression of MicroRNAs. (2017)

…phosphorylation of RNA polymerase II recruits Microprocessor for co-transcriptional processing of non-UGU pri-miRNAs that would otherwise be poorly processed. In contrast, UGU-positive pri-miRNAs are robustly processed by Microprocessor independent of RNA polymerase association.

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

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

How can the fact from 1964 that ATP-dependent RNA synthesis is energy-dependent continue to be ignored? RNA synthesis is clearly linked to energy-dependent healthy longevity, which strongly suggests that the virus-driven degradation of messenger RNA has been the only obvious link to understanding the difference between normal and disease biology for more than 50 years.

Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?

Excerpt (with my emphasis)

It is possible to detect changes in neuronal activity via the use of TC methods. TC captures a snapshot of the tissue at a moment in time, which affords the inference of neuronal activity at that time. An increase in neuronal activity can be identified either by staining for immediate early genes (IEGs), such as c-fos [24]…These methods offer insight into brain-wide information processing. An additional option that might provide a faster readout is RNA FISH. Given that mRNA transcription occurs prior to protein translation, RNA FISH could detect upregulation of IEG mRNA immediately after a behavioral experiment.

Conclusion (with my emphasis):

Emerging from the field of neuroscience, TC and optogenetics now constitute a powerful approach to the study of general biological questions and diseases by enabling the control and measurement of functional changes in living tissue [85], followed by cellular and molecular phenotyping at the whole-organ level.

The late, Robert L. Moss and colleagues linked the food energy-dependent metabolism to pheromones and the energy-dependent activation of c-fos in genes that secrete gonadotropin releasing hormone (GnRH), which is the central regulator of all vertebrate physiology and behavior.
See: Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males (1992)
See also: Influence of male rats on the luteinizing hormone-releasing hormone neuronal system in female rats: role of the vomeronasal organ (1993)
By 1991, the link from the hypothalamic secretion of GnRH to human behavior already was almost perfectly clear.
See: Gonadotropin releasing hormone and human sexual behavior in Neuropeptides and Psychiatric Disorders (1991)

The universality of the GnRH-induced behavioral response in the nonhuman species (from lizard to monkey) and the endocrine-pituitary actions of GnRH in pituitary secretion of LH and FSH, couples with the possible relationship between human sexual behavior deficits and gonadotropin dysfunction, provided good justification to proceed with further investigation into the behavioral effects of GnRH on human sexual behavior. (p. 61)

During the next two and a half decades, pseudoscientists (e.g., social scientists) and most theorists (i.e., biologically uninformed science idiots) ignored the facts that linked the epigenetic effects of mammalian pheromones from c-fos activation from GnRH secretion to the secretion of other hormones that affect behavior in all vertebrates and invertebrates. Despite repeated advice to learn to differentiate between “effects” and “affects,” the pseudoscientists and theorists remained horribly confused.
For comparison, see the attempt to clarify cause and effect in: Correction for McEwen, Brain on stress: How the social environment gets under the skin (January, 2013)

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

See also: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors (2012)

2‘Effect(s)’ and ‘affect(s)’. In context, sensory input effects hormones that affect behavior. An effect of sensory input on hormones can result in behavioral affects/affects on behavior.

See also this refutation of every aspect of neo-Darwinian evolutionary theory:

Nutrient-dependent/pheromone-controlled adaptive evolution: a model (June 2013)

Conclusion:

…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’.

Alternative splicings of pre-mRNA are the obvious link from natural selection for energy-dependent codon optimality and the physiology of pheromone controlled reproduction in species from microbes to humans. That fact was established in the context of this 1996 Hormones and Behavior review:
From Fertilization to Adult Sexual Behavior (1996)
See our section on molecular epigenetics (with my emphasis)

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.

Human sex differences were subsequently linked from the general principles of alternative splicing to sex differences in sexual orientation and sex differences in diseases. See 2006: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences
See also: 2009 Alternative splicing and disease

1. General principles of alternative splicing

1.1. Alternative pre-mRNA splicing regulates the function of the majority of protein-coding genes

The pre-mRNAs are now typically called microRNAs by serious scientists. It does not matter what pseudoscientists call them.  Food energy-dependent changes in the microRNA/messenger RNA balance have been linked from the information we provided about RNA-mediated cell type differentiation in our review to pheromone-controlled biophysically constrained viral latency in all living genera.
The virus-driven theft of quantized energy as information links stress from constraint-breaking mutations to all pathology. For comparison to what was known about pre-mRNA in 1996, a PubMed search for “microRNA” turns up more than 65,000 citations. The links from pre-mRNAs / microRNAs to healthy longevity or to virus-driven pathology are known to all serious scientists. Pseudoscientists are still touting their nonsense about de novo copy number variants and they keep trying to link mutations from genomic instabilities to evolution.
An Organismal CNV Mutator Phenotype Restricted to Early Human Development

De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities

Reported as: Copy Number Variation may be More Common Than we Thought 3/3/17 by LabRoots so-called science journalist Carmen Leitch.

Mutations don’t only involve differences in one or two bees or nucleotides, the individual letters that create the genome, some involve the replication of whole genes or portions of genes. Those mutations are called copy number variants, animated in the following video.

Does any intelligent serious scientist use the term bees and nucleotides interchangeably? Energy-dependent changes in base pairs must be linked to copy number variants and the number of variants is biophysically constrained by the physiology of pheromone-controlled reproduction in all living genera.
Simply put, food energy-dependent changes in base pairs link microRNAs to alternative splicings and from copy number variants to healthy longevity in all living genera.
See: Energy as information and constrained endogenous RNA interference At the time of my 2/15/17 recording for the Labroots virtual conference on Precision Medicine, the term microRNA had been used in 58,000 indexed works. The increase in use to more than 65,000, reflects how quickly serious scientists are making progress (at a rate of ~1000 new publications each month) Unfortunately, the link from energy-dependent microRNAs to alternative splicing has still been relatively ignored.
See also: microRNA alternative splicing 
See for additional historical perspective:  The connection between splicing and cancer (2006)
Summary

Alternative splicing is a crucial mechanism for generating protein diversity. Different splice variants of a given protein can display different and even antagonistic biological functions. Therefore, appropriate control of their synthesis is required to assure the complex orchestration of cellular processes within multicellular organisms. Mutations in cis-acting splicing elements or changes in the activity of constitutive or alternative splicing could have a profound regulatory proteins that compromise the accuracy of either impact on human pathogenesis, in particular in tumor development and progression. Mutations in splicing elements, for example, have been found in genes such as LKB1, KIT, CDH17, KLF6 and BRCA1, and changes in trans-acting regulators can affect the expression of genes such as Ron, RAC1 and CD44.

The fact that all serious scientists have known about the link from energy-dependent base pair changes and alternative splicings of pre-mRNAs/microRNAs to all biophysically constrained pheromone-controlled biodiversity via the physiology of reproduction has been ignored by pseudoscientists. The pseudoscientists make claims about protein diversity, but they rarely make claims that include the fact that all protein diversity is biophysically constrained by the availability of food energy and the pheromone-controlled physiology of reproduction in species from microbes to humans.

See for comparison:  2017 The Functional Impact of Alternative Splicing in Cancer

We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer, and some of them could potentially be considered alternative splicing drivers (AS drivers).
Reported as: Can alternative splicing lead to cancer?
See also:  Alternative splicing, an important mechanism for cancer
Complete structure of mitochondrial respiratory supercomplex decoded by John Hewitt with this comment to his FB page:

SARCASM ALERT: Do you think this may be important to our understanding of how energy-dependent changes are linked from atoms to ecosystems and biophysically constrained by the epigenetic effects of food odors and pheromones on RNA-mediated cell type differentiation that protects all organized genomes from the virus-driven degradation of messenger RNA, which has been linked from mutations to all pathology?

Here’s why I asked: Investigating biomolecular recognition at the cell surface using atomic force microscopy (2014)

The fission yeast pheromone receptor is a kind of G protein-coupled receptor (GPCR), a typical membrane receptor protein oncell surface. These receptors are activated by pheromone binding and then enable cellular signal transduction (Kohl et al., 2001).

See also: Hanbury Brown and Twiss interferometry of single phonons from an optomechanical resonator

Reliably generating non-classical states of their motion is of interest both for addressing fundamental questions about macroscopic quantum phenomena as well as for developing quantum technologies in the domains of sensing and transduction.

Sensing and signal transduction link quantum mechanics to classical physics in the context of quantized energy as information that must be linked from the physiology of pheromone-controlled reproduction to all biodiversity and to quantum souls.
Reported as: A way to measure and control phonons
…individual phonons moving in a crystal follow the laws of quantum mechanics as opposed to classical physics.
See also Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors
 

 

Alternative splicing of pre-mRNA

Caught in an epigenetic trap: flag waving consequences

Egypt concert-goers arrested for raising rainbow flag
This is an example of “flag waving” consequences from another part of the world.

They are accused of “public indecency” and “inciting immorality among young people”, the sources said following Monday’s arrests.

Why? These protesters were probably caught in an epigenetic trap. See: Search Results for “epigenetic trap”
The colors of the rainbow link the anti-entropic virucidal energy of sunlight to epigenetically trapped water in supercoiled DNA and all biophysically constrained biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
The “rainbow” flag may be merely another example of human idiocy. Those who raise it typically know nothing about how water and the colors of the rainbow are linked from the energy-dependent RNA-mediated sexual differentiation of cell types in species from yeasts to humans. Yet, they tend to rally round their flag, not the flag of any country.
For example, “gay” liberals in the United States of America have rights that cost the lives of our veterans. They can raise their “rainbow” flag without being arrested.
Who do they thank for that privilege, and when did they begin to thank them?
If they don’t thank a veteran, do they ever thank serious scientists?
See also:
Sensing atoms caught in ripples of light
Amount of water in stem cells can determine its fate as fat or bone
Isolating water’s impact on vibrations within DNA

An epigenetic trap stabilizes singular olfactory receptor expression

Structural diversity of supercoiled DNA
Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
 

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Evolution outside the context of "the light of evolution"

Summary: The claim that two mutations led to the weekend resurrection of the bacterial flagellum cannot be supported with the claim that only one amino acid substitution differentiates the cell type of two different primate species (gorillas and humans) from two similar species (chimpanzees and humans). The fact that mutations are not amino acid substitutions can be supported in the context of food energy-dependent pheromone-controlled cell type differentiation in species from microbes to humans.
Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system (2015) with my emphasis. As a service to the community this article is available to view for free.

After 96 hours of incubation of AR2 and Pf0-2x at room temperature on SMM, two breakout mutations were visible, conferring first slow (AR2S and Pf0-2xS) and then fast (AR2F and Pf0-2xF) spreading over the agar surface (Fig. 1A). The AR2F strain produces flagella, but we could not detect flagella in electron microscopy samples for AR2S (Fig. 1B). Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

The claim that two mutations led to the weekend resurrection of the bacterial flagellum cannot be supported with the claim that only one amino acid substitution differentiates the cell type of two different primate species (gorillas and humans) from two similar species (chimpanzees and humans). The fact that mutations are not amino acid substitutions can be supported in the context of food energy-dependent pheromone-controlled cell type differentiation in species from microbes to humans.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model for comparison to: Mutation-Driven Evolution
The cell biology game “Cytosis” will help to end the neo-Darwinian pseudoscientific nonsense touted in the context of mutation-driven evolution.
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!
The virus-driven degradation of messenger RNA causes the mutations that all serious scientists have linked to all pathology. Protection from the virus-driven degradation of messenger RNA is food energy-dependent and pheromone-controlled. In Dobzhansky’s example, the alpha chains of hemoglobin differ “… in a single amino acid (out of 141) in the gorilla.” Pseudoscientists must now try to place that fact back into the context of their ridiculous theories without linking a single amino acid substitution in the organized genomes of all other species to all biodiversity on Earth, which is what some Young Earth Creationists (YEC) have done.
Watch as the pseudoscientists try and fail to account for more than 1200 nutrient-dependent pheromone-controlled hemoglobin variants in human populations.
The pseudoscientists must ignore the facts about the hemoglobin variants: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations (2014) with my emphasis

Hemoglobinopathies are the commonest single-gene genetic disorders in humans, resulting from pathogenic genome variants in the human α-like and β-like globin gene clusters (reviewed in 1). Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

See for comparison: In the Light of Evolution

In this cross journal series, BMC Biology, BMC Evolutionary Biology and Biology Direct  bring together a collection of articles exploring how evolutionary principles applied across the spectrum of biology can shed light on a diverse range of topics from molecules to ecosystems, and with a particular emphasis on human genetics, interactions with the environment, and health and disease. Selected research articles will be included in addition to invited reviews and comment.

We will consider Research manuscripts of exceptional interest on the following topics (with my emphasis)
•    Evolution of morphological change
•    Understanding and treating disease in the light of evolution
•    Origins of evolutionary complexity
•    Human evolutionary biology in a post-genomic era
•    Anthropogenic effects on evolution
•    Evolutionary insights into genome variation, and vice versa
•    Host-parasite interactions
•    Evolutionary lessons from large-scale genomics
•    Insights from ancient DNA on human origins
•    Molecular mechanisms of evolution
•    Applied microbial evolution 
•    Evolutionary ecology
•    Genomics and the evolution of development

The only consideration of the nutrient energy-dependent pheromone-controlled physiology of reproduction that links RNA-directed DNA methylation from atoms to ecosystems via fixation of amino acid substitutions in organized genomes may be the articles about  Host-parasite interactions.  The interactions involve energy-dependent ecological adaptations or extinction. Virus-driven energy theft causes the extinctions via the theft oif quantized energy as information. Theft comes after the creation of virucidal light, which is the ultraviolet light that comes from sunlight. That fact, which indicates “agency” in the context of “creation” is not likely to be considered in the context of Insights from ancient DNA on human origins.
Clearly, Dobzhansky (1973) knew that all neo-Darwinian theorists were biologically uninformed science idiots and that they always would be. The fact that he placed the virucidal energy of ultraviolet light into his expressed “Creationist” views with a title that refuted all the pseudoscientific nonsense attests to his sense of humor, and the inability of theorists to “get the joke.”

…organic diversity becomes, however, reasonable and understandable if the Creator has created the living world not by caprice but by evolution propelled by natural selection. It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

There is no support for the ridiculous claim that Creation is a “process” that began some 10 billion years ago. There is a model that places all human biodiversity into the context of food energy-dependent ecological adaptations that protect all organisms from the virus-driven degradation of messenger RNA in the context of their pheromone-controlled physiology of reproduction.
Watch as the facts about Creation are removed from consideration because the focus of these articles is on support for ridiculous theories. Remember this:

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

  1. Dosage-sensitive genes in evolution and disease

    For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typic…

  2. Q&A: Where did the Neanderthals go?

    Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2–3% Neanderthal DNA. However, it is still hotly debated why the Neandert…
  3. Biological function in the twilight zone of sequence conservation

    Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast ‘twilight zone’ in which sequence subject to transient or lower cons…
  4. Examining non-LTR retrotransposons in the context of the evolving primate brain

    Researchers have long sought to understand the genetic basis of the cognitive differences between primates, with particular focus on the human brain. Although all mutational types have worked in concert with e…
  5. Q&A: What is human language, when did it evolve and why should we care?

    Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign ‘language’ i…
  6. Peto’s Paradox: how has evolution solved the problem of cancer prevention?

    The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-hu…
  7. Non-model model organisms

    Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but moder…
  8. Can a biologist fix a smartphone?—Just hack it!

    Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encode…
  9. Open questions: Tackling Darwin’s “instincts”: the genetic basis of behavioral evolution

    All of us have marveled at the remarkable diversity of animal behaviors in nature.
A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Optogenetics replaces fMRI but not pseudoscientific nonsense

Summary: The ability to evaluate spaciotemporal influences on health compared to virus-driven pathology must include a link from quantized energy to the creation of ATP and the creation of RNA. Hunting people down who are aware of that fact is difficult because most of them have ignored the facts from this 1964 publication.
Ed Boyden and Optogenetics: The Future of Neuroscience (video) (transcript)

What I’m trying to do now is see whether we can help people pilot crazy projects that don’t quite fit in. I started talking to people about the craziest things they could think of that wouldn’t ever get a government grant or pass peer review—when other people have to tell you whether they think it’s a good idea or not. There’s something to be said for trying to hunt those ideas down.

The ability to evaluate spaciotemporal influences on health compared to virus-driven pathology must include a link from quantized energy to the creation of ATP and the creation of RNA. Hunting people down who are aware of that fact is difficult because most of them have ignored the facts from this 1964 publication.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

See: Cell diversity and network dynamics in photosensitive human brain organoids (2017)

…neuronal activity within organoids could be controlled using light stimulation of photosensitive cells, which may offer a way to probe the functionality of human neuronal circuits using physiological sensory stimuli.

See for comparison: Nonlinear cavity optomechanics with nanomechanical thermal fluctuations Reported as: Nanoscale motion sends light into overdrive

The higher harmonics of the produced light signals carry different kinds of information about the nanostring motion. For example, we demonstrated that they allow measuring the energy of the vibration with a high accuracy. This could potentially lead to direct observations of quantized energy in the string, as we would expect from the theory of quantum mechanics.

Direct observations of quantized energy and the virus-driven energy theft that is linked from mutations to all pathology can be considered in the context of  Olfaction Warps Visual Time Perception
My summary: Biophysically constrained neural energy links multisensory inputs from quantum consciousness to quantum souls at subsecond scales via the sense of smell in bacteria.The claim that space-time is warped by the distribution of mass and energy is linked to the perception of time outside the context of optogenetics because chemotaxis is the first link from pH-taxis to phototaxis via the de novo creation of G protein-coupled receptors.
Boyden may not know that he must find someone who knows how to link the measurements from Cryo-ET and Cryo-EM to the light-activated endogenous substrate in all cell types that links the physiology of pheromone-controlled reproduction to all biodiversity via the energy-dependent de novo creation of G protein-coupled receptors.
Dr Topol:

Only this year, “microbiome,” “epigenome,” and “CRISPR” got in. The New Yorker had a big profile on optogenetics. That’s mainstream, in the New Yorker.

Phytoremediation was also added. I wonder who else realizes that phytoremediation is the link from the microbiome to the epigenome via CRISPR (the innate immune system of bacteria, which protects them from the virus-driven degradation of their messenger RNA).

Alternative splicing of pre-mRNA

Sexual communication signals: New Insights!

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.Kalevi Kull

New insights in the evolution of sexual communication signals

Abstract excerpt:

Our research focuses on identifying a) the genes underlying sexual signals and responses in both sexes2-4, and b) ecological factors that may cause divergence in sexual communication. Factors that we found to affect sexual communication are closely related species with similar mating signals5, low nutritional quality, (toxic) secondary plant metabolites and pathogens6.

Elizabeth Pennisi reported on this 2017 conference presentation and claimed:

The results “demonstrate the importance of the social environment,” Halfwerk says. “One form does not attract males on its own, only in close proximity of the other form.” That result also parallels what’s been found in humans: that an attractive woman in a crowd of less attractive women also seems to attract more attention. But pinning down exactly why this happens should be much easier in moths than people, she notes. “That’s the nice thing about insects.”

See: Sexy females help ‘Plain Jane’ moths snag their mates

No experimental evidence of biologically-based sexual communication suggests that sex signals evolved. The fine-tuned systems of communication among individuals and species pose an evolutionary dilemma because they are food energy-dependent. Ecological variation must be linked from food energy to biophysically constrained ecological adaptations by the pheromone-controlled physiology of reproduction in all living genera. Also, everything known to serious scientists about energy-dependent top-down creation links the anti-entropic virucidal energy of sunlight from the creation of ATP to the creation of messenger RNA. That fact does not appear to be coincidental.

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

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

Detailed experimental evidence also links the virus-driven degradation of messenger RNA from mutations to all pathology. That fact leaves neo-Darwinian theorists and “Big Bang” cosmologists without any acceptable theory of anything or any theory of everything.

See for comparison: A New Physics Theory of Life and Jeremy England’s idea that “You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.” 

Theorists and philosophers cannot link energy as information or “big bang” cosmology to biodiversity without the creation of energy. Most of them ignore the fact that they do not know where the energy in a hydrogen atom came from.

Without the de novo creation of energy, they cannot link hydrogen-atom transfer in DNA base pairs in solution from microRNA flanking sequences to SNPs, and they cannot link food energy as information to fixation of RNA-mediated amino acid substitutions in organized genomes. For comparison, all serious scientists have linked what is known about the food energy-dependent fixation of amino acid substitutions to the structure and function of supercoiled DNA, and all serious scientists have linked energy-dependent RNA-mediated cause and effect to all biodiversity via the physiology of pheromone-controlled reproduction.

That fact helps to explain why Richard Feynman referred to some theoretical physicists as examples of human idiocy.

See: Food energy

That suggests Elizabeth Pennisi is a biologically uninformed. She reported: “That’s the nice thing about insects.” If she was not a biologically uninformed science idiot, she would have linked food energy to the physiology of reproduction in all invertebrates and vertebrates. That is how the pheromone-controlled physiology of reproduction is linked from ecological variation to all biodiversity via what is known to all serious scientists about ecological adaptation.
See: Feedback loops link odor and pheromone signaling with reproduction and Olfaction Warps Visual Time Perception

For comparison to the science reporting by Elizabeth Pennisi,  J.A. Parker is the only person besides me, who has reported on this 2017 conference presentation:

See also: All in the (bigger) family by Elizabeth Pennisi with my comment:

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 also: Sex differences in microRNA-mRNA networks: examination of novel epigenetic programming mechanisms in the sexually dimorphic neonatal hypothalamus

Integrating miRNAs and their broad actions on gene function into our conceptualization of the factors directing sexual differentiation of the brain could be a highly informative next step in efforts to understand the complexities behind these processes.

They linked sex differences in microRNAs to the sexual differentiation of all cell types in all living genera that sexually reproduce via microRNA-mRNA networks.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences

…miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here. Our investigation demonstrates the utility of miRNA sequences as classical phylogenetic markers, and shows this usage is robust to different algorithms of phylogenetic analysis and the analysis of fast-evolving lineages. Such a method provides novel characters for assessing phylogenetic relationships that will be of use in a range of contexts for resolving branches across the tree of life.

See also: 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).

Kohl (2013) is: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (June 14, 2013)

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

Elekonich and Robinson (2000) cited:  From Fertilization to Adult Sexual Behavior (1996)
At the time of our 1996 Hormones and Behavior review, microRNAs were called pre-mRNAs. See our section on molecular epigenetics:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). 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.

Social odors are still called pheromones and we linked the food energy-dependent pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity on Earth via sex differences in microRNAs (pre-mRNAs).
The sex differences in microRNAs will soon be linked to sex differences in healthy longevity and to sex differences in diseases in the context of the cell biology game: “Cytosis.” Next, the game “Subatomic” will teach others how to build an atom.
The fact that this invited review linked energy-dependent changes in atoms to ecosystems may still go unnoticed, since the invited review was returned without review.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
But, for God’s sake, see for comparison: 7/25/13
Jay R. Feierman:

“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.”

Do not ignore the fact that Jay R. Feierman has no understanding of how ecological variation must be linked to energy-dependent ecological adaptation via the pheromone-controlled physiology of reproduction.
See also: December 5, 2016

[MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.]

What I believe about RNA splicing is irrelevant unless someone else links the creation of energy to ATP and the creation of RNA outside the context of energy-dependent alternative splicings of pre-mRNA and the link from energy to the creation of the pre-mRNAs and to energy-dependent biophysical constraints on supercoiled DNA in all living genera.

As Heyn points out, “we still do not fully understand the mechanisms that drive epigenetic variation in populations.”

Natural selection for energy-dependent codon optimality links RNA-directed DNA methylation to all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction. That fact seems to be missing from this representation of a failed paradigm (neo-Darwinian evolution).
Claims that facts about natural selection and epigenetic variation in populations are not fully understood can be viewed in the context of reports by those who understand the facts about Darwin’s “conditions of life.” They are energy-dependent and RNA-mediated
See for example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition and Olfaction Warps Visual Time Perception
It has become obvious to all serious scientists that the sense of smell in bacteria must be linked from mRNA stability to our visual perception of mass and energy in the context of natural selection across the time-space continuum via the pheromone-controlled physiology of reproduction. The complexity of that fact may not be understood by biologically uninformed theorists, but no theorist should claim that the mechanisms of food energy-dependent pheromone-controlled biophysically constrained cell type differentiation are not understood by all serious scientists.
Re: …a strong link between population-specific DNA methylation, mRNA levels, and genotypes.
See also: Methylation Variation Documented Between Human Populations

“Our analysis of five worldwide populations revealed a strong correspondence between population-specific DNA methylation, [messenger RNA] levels, and genotypes,” the authors wrote. “The correlation with genetic divergence was stronger for DNA methylation, and, consistent with this, our results suggest stronger local genetic control of population-specific DNA methylation levels than of mRNA expression levels.”

The strong link and/or strong correspondence between food energy-dependent DNA methylation, messenger RNA levels and genotypes is biophysically constained by the pheromone-controlled physiology of reproduction in all livng genera. See for example: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

Glycolysis and the citric acid cycle appear to provide the free energy for nuclear ATP synthesis and the food-energy-depenent biosynthesis of messenger RNA. If so, all pathology is caused by the virus-driven degradation of messenger RNA, which links mutations but not from ecological variation to ecological adaptations.
See also: Back to Basics: Next-generation sequencing methods and applications (with my emphasis)

…another common NGS application (although one currently more of a research application than a front-line clinical tool) is to examine the transcriptome of a sample—that is, the identity and relative abundance of mRNA transcripts present. Sometimes referred to as “exome sequencing,” this approach is efficient in that it applies resources only to that small portion of the genome which is functionally expressed. Of course, not all significant genetic aberrations occur within coding regions; but by observing levels (or even presence/absence) of transcripts in comparison to reference “normal” conditions, important mutations in non-coding regions such as gene promoters or splice site regulators can be inferred. When such findings are plausibly related to a disease condition, more directed studies to confirm the root cause can then be undertaken as or if needed.

See also: microRNA “exome sequencing Items: 1 to 20 of 55 There is no need to infer that splice site regulators are not food energy-dependent and yet that is what biologically uninformed neo-Darwinian theorists have consistently done with their claims about Mutation-driven evolution. For comparison, all serious scientists are Combating Evolution to Fight Disease.
See also: Global Epigenomic Reconfiguration During Mammalian Brain Development July 4, 2013

DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Finally, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain, and that CG demethylation at these hmC-poised loci depends on Tet2 activity.

See also: Inherited chromosomally integrated human herpesvirus 6 genomes are ancient, intact and potentially able to reactivate from telomeres, which was reported as: “Study of inherited herpes virus finds links to ancient humans” August 30, 2017

We used molecular dating methods to compare, for example, the inherited HHV-6B genomes in five individuals from Sardinia, Orkney and England, and estimated that the most recent common ancestor with the inherited HHV-6B existed 24,500 ±10,600 years ago.

The molecular dating methods are evaluated outside the context of what is known about energy-dependent pheromone-controlled feedback loops, which have been linked from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum. But, rather than repeat myself, I will simple support my claims with a link to: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, which was reported in January, 2013, as: Past 5,000 years prolific for changes to human genome. The changes can be place into the context of exome sequencing, but not mutation-driven evolution.
The recent origin of most human protein-coding variants can be linked from food energy-dependent changes in exomes that are biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. The recent origin of the variant can also be linked from the virus-driven degradation of messenger RNA to all pathology.

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

See also: Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans (2013)
I repeat:

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.Kalevi Kull
Cytosis

Host-derived creation of all pathology (2 of 2)

Summary: All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.

See for comparison: Jay R. Feierman: “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.”

A Bacterial Messenger Molecule Extends Healthspan

…indole, a molecule produced by commensal bacteria, extends “healthspan” not only in mice but in the nematode worm Caenorhabditis elegans and in fruit flies as well. Taking away the bacterial production of the molecule ablated these anti-aging gains.

Does anyone need to repeatedly be reminded that food energy is required for the production of any molecule associated with nutrient-dependent pheromone-controlled anti-aging gains? The epigenetically effected gains are consistently manifested in the survival of species via the physiology of reproduction.
The food energy-dependent production of indole is the obvious link from nutrient-dependent pheromone-controlled feedback loops to biophysically constrained viral latency and ecological adaptation in all living genera. Testing for indole is used to determine the ability of an organism to split (deaminate) the amino acid tryptophan.  Indole contributes to fecal odor and it is a chemical messenger that has been indirectly or directly included in detailed representations of biologically-based pheromone-controlled energy-dependent cause and effect like these.
See: Feedback loops link odor and pheromone signaling with reproduction (2005)
There is a model for that! See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans biophysically constrains the virus-driven degradation of messenger RNA. That fact links constraint-breaking mutations to all pathology in all living genera. A test protocol established that fact in the context of this book chapter, which links the test for indole to differences in the microRNA/messenger RNA balance in humans.

For example, the test protocol links the creation of energy as information to all biodiversity via the physiology of reproduction and links the virus-driven degradation of messenger RNA to all pathology. The complexity of the testing can be reduced via the focus on the energy-dependent creation of microRNAs.

See the abstract:

Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety…

MicroRNAs are identified and monitored through the use of locked nucleic acid (LNA)™-based detection probes. The LNA™ technology enhances the sensitivity and specificity of target binding for short, highly similar, microRNA sequences, which help to differentiate cell types in the context of everything known to serious scientists about how to link physics and chemistry from molecular epigenetics to all biodiversity via fixation of RNA-mediated amino acid substitutions.

The availability of this testing was predicted in: Energy as information and constrained endogenous RNA interference (7-min video)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also: The phylogenetic utility and functional constraint of microRNA flanking sequences
See also: From Fertilization to Adult Sexual Behavior (1996)
See for comparison: Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption (2017)

There is no such thing as transgenerational epigenetic inheritance of morphological or behavioral phenotypes outside the context of feedback loops that link food odors from the metabolism to pheromones and biophysically constrained viral latency. The consumption of choline by bacteria links food energy to protection from viral latency via the test for indole. The virus-driven theft of quantized energy can be linked from reduced amount of choline that link viruses in the bacteria to their ability to overwhelm the immune system. The effects of virus-driven energy theft link the CRISPR-Cas9 technology of gene-editing to DNA repair via exogenous RNA-interference because energy-dependent endogenous RNA-interference protects all organized genomes from virus-driven entropy.
Corporate America is not willing to tell the truth about that. You will probably suffer unnecessarily and die prematurely because the goal of every corporation is to make more money.

See also: Americans Are Dying Younger, Saving Corporations Billions

Absent a war or an epidemic, it’s unusual and alarming for life expectancies in developed countries to stop improving, let alone to worsen. “Mortality is sort of the tip of the iceberg,” says Laudan Aron, a demographer and senior fellow at the Urban Institute. “It really is a reflection of a lot of underlying conditions of life.”

Darwin’s “conditions of life” were food energy-dependent. Serious scientists have since learned that all “conditions of life” also are fixed in the organized genomes of all living genera via the physiology of reproduction. Without the link from ecological variation to ecological adaptation via fixation of amino acid substitutions in supercoiled DNA, natural selection for energy-dependent codon optimality would link mutations to evolution instead of linking mutations to all pathology.

Instead, the reality of cell type differentiation was reported as: Microbes compete for nutrients, affect metabolism, development in mice

 …new research that shows mice that harbor high levels of microbes that eat choline are deprived of this essential nutrient.
 

I placed that fact into the context of this excerpt from my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.

The result of this synergy is (1) a liver enzyme that oxidizes trimethylamine to (2) an odor that causes (3) species-specific behaviors. Thus, the complex systems that biology required to get from nutrient acquisition and nutrient metabolism to species-specific odor-controlled behavior is exemplified by adaptive evolution of an attractive odor to mice that repels rats (see for review Li et al., 2013).

Addendum: Fish odor syndrome is the link from the virus-driven theft of quantized energy. The odor links ecological variation to failed ecological adaptation and all pathology when there is insufficient food energy. Any scientist who does not already know that based on the facts known to every medical laboratory scientist is an example of “human idiocy” (Feynman) or a biologically uninformed science idiot (Kohl).

Serious scientists have begun to effectively use energy-dependent microRNAs to the prevention of all virus-driven pathology. That fact is being reported in the context of gene therapy using ‘junk DNA’  at a time when all serious scientists realize there is no such thing as ‘junk DNA.’

Gene therapy using ‘junk DNA’ could lower risk for heart disease

The LeXis gene belongs to a unique group of genes that until recently were considered “junk DNA” because scientists believed they served little purpose. However, evidence from the human genome project led to the discovery that genes like LeXis are actually active. The study of these genes, now referred to as long noncoding ribonucleic acids, or lncRNAs, is a rapidly evolving area in biology.

Long Noncoding RNA Facilitated Gene Therapy Reduces Atherosclerosis in a Murine Model of Familial Hypercholesterolemia

Long noncoding (lnc) RNAs form the vast majority of transcriptionally active regions and are arbitrary defined as transcripts >200 bps that biochemically resemble mRNA and yet do not template protein.2

Diet and drug-induced changes in LeXis link energy as information to liver X receptor activation of genes via the “promoter binding of RNA-binding proteins.” That fact supports the claim that a transcriptional coactivator for genetically predisposed cholesterol biosynthesis in the mouse liver links promoters, enhancers, quantitative trait loci, et al., to the transciptional coactivator referred to as “Rally” without mention of energy-dependent changes in the microRNA/messenger RNA balance.
If you believe that the long noncoding ribonucleic acids (RNAs) are genes, you may be convinced that mutations in RNA are the same as mutations in genes. But mutations are the cause of all pathology. Linking mutations in RNA to pathology outside the  context of energy-dependent healthy longevity allows others with no expertise in laboratory testing to continue to believe that mutation-driven evolution is the link from natural selection to the origin of new species. That belief is probably common among others who believe that the Universe itself may be conscious.

See for comparison: Scientists Now Believe the Universe Itself May Be Conscious

For the behavior of subatomic particles and the systems they constitute promises to be fully explained by physics and the other physical sciences.

 See for comparison: Subatomic

Subatomic is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic enabling players to pay energy to shuffle through their deck quicker, or to offset the cost of more powerful deck building cards.

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking
 

The question arises: “Who needs this kind of nonsense?” Does anyone at any level of examination believe that “the Universe is always looking” is the best representation of what we can expect from a “Conscious Universe?”

See for comparison: 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!

 Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy was reported on the Exiqon FB page. Exiqon is a biotechnology company that specializes in RNA products and services. I recommend that they purchase this domain (RNA-mediated.com) in an attempt to promote their products, which obviously link energy-dependent healthy longevity to all biodiversity and also link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: ‘Chromatin modifiers and remodellers in DNA repair and signalling’ The fact that food energy as information must be linked from ecological variation to ecological adaptation via the pheromone-controlled physiology of reproduction in all living genera appears to be the focus of this Theme issue.

But wait: Here is one of the articles from  the Theme issue:

Nucleosome remodelling, DNA repair and transcriptional regulation build negative feedback loops in cancer and cellular ageing

Nucleosome remodelling (NR) regulates transcription in an ATP-dependent manner, and influences gene expression required for development and cellular functions, including those involved in anti-cancer and anti-ageing processes. ATP-utilizing chromatin assembly and remodelling factor (ACF) and Brahma-associated factor (BAF) complexes, belonging to the ISWI and SWI/SNF families, respectively, are involved in various types of DNA repair.

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

McEwen et al., knew that “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” That statement of fact was the beginning of the abstract from 1964. When he told me my model could not be validated unless I started with energy-dependent gene activation in gonadotropin releasing hormone (GnRH) neurons, I had no reason to doubt him. When I learned that Robert L. Moss had already linked pheromones to energy-dependent gene activation in GnRH neurons, I continued to pursue top-down causation as if it was energy-dependent — because it obviously is energy-dependent.

I never considered that my model of food energy-dependent pheromone-controlled biophysically constrained gene activation would not be accepted by theorists. See for comparison:

Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males (1992)

See also: Gonadotropin releasing hormone and human sexual behavior (1991) in Neuropeptides and Psychiatric Disorders (1991)

Is anyone else interested in linking the facts from our 1996 Hormones and Behavior review From Fertilization to Adult Sexual Behavior or from any other works I have published before Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) to what is known about all biophysically constrained biologically- based cause and effect?
If so, see: Worldwide patterns of human epigenetic variation

We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity…

All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.
See for comparison: 7/25/13
Jay R. Feierman: 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.
See for comparison: Quantum Biology: An Introduction (video) by Philip Ball and Quantum common sense

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

See also these restricted and unrestricted articles: ARTICLES 

Cytosis

Your indifference is killing you and others (3)

Summary: The speed of light on contact with water links the creation of microRNAs to Optical control of membrane tethering and interorganellar communication at nanoscales MicroRNA flanking sequences are linked to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. The physiology of reproduction links energy-dependent changes in the microRNA/messenger RNA balance to the fixation of amino acid substitutions in supercoiled DNA. Supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA.
See also: Combating Evolution to Fight Disease
See also: Biblical Genesis
…in the Garden of Eden but instructs them not to eat the fruit of the tree of knowledge of good and evil.

Tree of the knowledge of good and evil

…when God forbids the man to eat from that particular tree, he says that if he does so, he is “doomed to die”.
I am fascinated by the facts that link the Biblical metaphors from eating a virus-infected “fruit” to the death of everyone who will ever live and die.  That fact can be placed into this context: Past 5,000 years prolific for changes to human genome.

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

See also: Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy
Reported by Exiqon as: Robust one-day ISH protocol for disease microRNA biomarker development

ISH of biopsy material has become routine pathology procedure for monitoring gene expression and sample characterization. This could be of microRNAs which prove excellent as biomarkers for disease diagnosis, patient stratification and treatment efficacy.

A fast and robust microRNA ISH protocol well-suited for clinical biomarker studies has just been published in Methods Mol Biol using DIG or FAM double-labeled microRNA-specific LNA™-enhanced detection probes in formalin-fixed, paraffin-embedded (FFPE) tissue sections.

Monitoring gene expression and sample characterization via natrurally occuring microRNA biomarkers is the key to developing biomarkers for use in “…disease diagnosis, patient stratification and treatment efficacy.”
The microRNAs need only be linked from flanking sequences to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution and the physiology of reproduction, which links energy-dependent changes in the microRNA/messenger RNA balance from the fixation of amino acid substitutions in supercoiled DNA to protection from the virus-driven degradation of messenger RNA.
See: Optical control of membrane tethering and interorganellar communication at nanoscales

All the observed interactions seem to require the presence of at least two consecutive positively charged residues (‘KK’ or ‘KR’). Replacement of a single lysine with alanine in such dyad motifs could lead to pronounced reduction in puncta formation; whereas KK-to-AA substitutions often abrogate the PB-lipid/PM associations (Fig. 4 and S4†). Further structural studies on the interaction between PB domains and PIs will likely provide a definitive answer by pinpointing the exact molecular determinants.

The temporal and spatial control that connects subcellular compartments to interorganellar communication, which links energy-dependent changes from angstroms to ecosystems in all living genera is RNA-mediated and biophysically constrained by the pheromone-controlled physiology of reproduction. The temporal and spacial control is linked to our visual perception of mass and energy via the sense of smell in bacteria and RNA-mediated amino acid substitutions in the organized genomes of all living genera.
See also: Mechanism of metabolic puncta formation and its functional significance

Many metabolic enzymes have recently been shown to assemble into multi-component puncta in cells, and this assembly is though to play some role in controlling metabolic flux. For example, substrate channeling within these structures could play an important role in metabolism, enabling intermediates to be directly fed from one enzyme to another without dilution. Therefore the assembly of enzymes into these puncta could be an important mechanism for cells to manipulate their metabolism in response to different signals. However, the mechanism of formation of these puncta is completely unknown.

If the energy-dependent formation of these puncta was not known to be linked from differences in the microRNA/messenger RNA balance to the pheromone-controlled physiology of reproduction in all living genera, I could not have found the obvious link from food energy to all biodiversity in this PubMed search.
puncta formation microRNA

For example, food energy is the obvious link from changes in chirality to autophagy. Autophagy protects all organized genomes from the virus-driven degradation of messenger RNA. Simply put, biophysically contrained energy-dependent autophagy protects all living genera from the mutations that serious scientists have linked to all pathology.
See also:
MicroRNA-141 Targets Sirt1 and Inhibits Autophagy to Reduce HBV Replication.
C. elegans Dicer interacts with the P-granule component GLH-1 and both regulate germline RNPs.

See also:  Bridging Length and Time Scales in Cell Organization

For comparison, see: “For the past century some people have regarded natural selection as “that secular God.” Now, that title belongs to CRISPR. “— Jay R. Feierman
Feierman has not learned that natural selection for energy-dependent codon optimality links a light-activated endogenous substrate from the innate immune system in bacteria: CRISPR, to the biophysically constrained physiology of pheromone-controlled reproduction in all living genera. That fact is proof of God’s energy-dependent Creation. The claim that the title of “secular God” belongs to CRISPR is as ridiculous as this claim.
7/25/13
Jay R. Feierman: 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.
See also:  7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
CRISPR is the only obvious link from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the theft of quantized information that links mutations to all pathology via the degradation of messenger RNA.
See also: Your indifference is killing you and others (4)

Cytosis

Your indifference is killing you and others (4)

Summary:
I suspect that Subatomic, like Cytosis, will help link atoms to ecosystems via my model of nutritional epigenetics and the pheromone-controlled visual perception of mass and energy, which has been linked from the sense of smell in bacteria across the space time continuum via olfaction.
From 7 years ago.
Published 7 years ago on 15 Aug 2010 by James V. Kohl of Pheromones.com, RNA-mediated.com, and Autophagy.pro
Kohl is the co-author of “The Scent of Eros” and he is the creator of: The Scent of Eros and The Mind’s Eyes human pheromone-enhanced products. This is an excerpt from his presentation at the 2010 Annual Gathering of Mensa (i.e., the “high IQ” society).

Pheromones have since been linked from suicide prevention to the prevention of all neurodegenerative diseases and the prevention of all other pathology, which includes cancer prevention.

See for examples:

 
 
 

Everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and viral latency in the context of quantum physics and the space time continuum will soon be known to everyone older than 10 who plays the game “Cytosis” and the game “Subatomic.”

In less than 3 hours of play-time, it will become clear that the virus-driven theft of quantized energy causes the degradation of messenger RNA, which links mutations to all pathology.

Suzan Mazur: What is your definition of life?

Eviatar Nevo: Our understanding of origin of life is very slim. . . . [First] life didn’t fossilize. The best we can know about origin of life may be from viruses we are looking at. They could have been at the origin of life before they parasitized it, or became symbionts in prokaryotes and eukaryotes. . . .

Young earth creationist / scientists put the virus-driven parasitism of life into the perspective of perfect creation in: Viral Genome Junk Is Bunk

“The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

The fact that viruses got their genes from their hosts became clear in the context of what is known about natural selection for energy-dependent codon optimality.

The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically diverse human RNA viruses. This analysis showed that the overall extent of codon usage bias in RNA viruses is low and that there is little variation in bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Synopsis

Embedded Image

In addition to spelling out protein sequence, mRNA codon triplets contain translation‐dependent regulatory information that influences transcript stability and contributes to controlled turnover of maternal mRNAs in frogs, mice, and flies.

  • Codon optimality forms a regulatory code within the genetic code that controls mRNA stability and translation efficiency.

  • Codon composition shapes maternal mRNA clearance during the maternal‐to‐zygotic transition in zebrafish, frog, mouse, and fly in a translation‐dependent manner.

  • Amino acid composition also influences mRNA stability in vertebrates.

  • Codon optimality correlates with codon bias, suggesting that codon optimality shapes steady‐state mRNA levels in homeostasis.

Excerpt:

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Reported as: A code within a code: how codons influence mRNA stability

The sequence changes in the amino acid optimality code link energy-dependent changes in base pairs to fixation of amino acid substitutions in supercoiled DNA via the physiology of reproduction. The substitutions protect all organized genome from the virus driven degradation of messenger RNA that links mutations to all pathology.

See also: Kinetic Rain | Art + Com

The level of creativity required to link physics to chemistry and the conserved molecular mechanisms that link kinetic energy and food energy to RNA-mediated cell type differentiation via quantum mechanics and amino acid substitutions is exemplified in this moving sculpture and ignored by theorists who might unknowingly attribute all the interactions to mutations and evolution.

See also: The  Critical Thinking Cafe

The group has been archived. No more comments will be added by those who lack the critical thinking skills required to link what organisms eat to the physiology of pheromone-controlled reproduction and all biodiversity.

It should be even clearer that two games “Cytosis” and “Subatomic” will put an end to any theoretical nonsense about mutations and evolution.

I suspect that Subatomic, like Cytosis, will help link atoms to ecosystems via my model of nutritional epigenetics and the pheromone-controlled visual perception of mass and energy, which has been linked from the sense of smell in bacteria across the space time continuum via olfaction.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems