An evolutionary theory killer

A reversible TCA cycle in a thermophile (3)

A pathway for mitotic chromosome formation

The combination of nested loops distributed around a helically twisted axis plus dense chromatin packing achieves the 10,000-fold compaction of chromatin into linearly organized chromosomes that is required for accurate chromosome segregation when cells divide.

The compaction of chromatin in the context of hydrophobicity is the topic of: 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.

Differential recognition of proteins clearly involves this link from natural selection for energy-dependent codon optimality to the physiology of reproduction via RNA-directed DNA methylation.
See for comparison: DNA-Methylation: Master or Slave of Neural Fate Decisions?

The involvement of splicing as effector of changes in DNA methylation is an exciting new angle to pursue with more precise epigenetic engineering tools. Distinguishing essential from specific, and causal from secondary marks will be essential for neuro-epigenetics. New approaches promise to answer long outstanding questions and will likely facilitate the discovery that DNA modifications might have new unexpected roles in the brain.

Splicing is not the effector of changes in DNA methylation, energy-dependent changes in the microRNA/messenger RNA balance must be given first consideration. But, this article is part of the Research Topic: Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex

The topic is an example of human idiocy for comparison to this report on alternative splicing, which was linked to energy-dependent biophysically constrained viral latency in the context of:

 Alternative splicing and the evolution of phenotypic novelty and the cell biology game: Cytosis

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

The origins of morphological diversity cannot be evaluated outside the context of the origins of energy-dependent behavioral diversity, which requires that RNA-mediated DNA methylation be linked to differences in cell fate in all tissues of all individuals of all species on Earth. Typically, serious scientists do this by linking the creation of the sun’s anti-entropic viral latency from  subatomic particles to creation of atoms and ecosystems in the context of human brain development via mitotic chromosome formation.

See for instance: The Excitable Mitochondria and The vibrational theory of olfaction for the win by John Hewitt.
If he did not believe that “evolution did it” after the emergence of energy, he would not have placed his bets on ridiculous theories and criticized my life’s history of publications and presentations, which he claimed were BS.
See for comparison to his claims: Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity
We placed the facts about alternative splicing and increasing organismal complexity into the context of our section on molecular epigenetics in 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…

The sexual differentiation of all cell types in species from yeast to humans was presciently placed into the context of what was known about pre-mRNA mediated biophysically constrained viral latency in 1996. Food energy-dependent pre-mRNAs are now referred to as microRNAs (miRNAs). The creation of the miRNAs links the anti-entropic virucidal of the sun to all biodiversity via the physiology of reproduction,  and our details from 1996 have been extended across species via this recently published work:
Reproductive role of miRNA in the hypothalamic-pituitary axis

The hypothalamic-pituitary-gonadal (HPG) axis plays a critical role in regulating reproductive function. Gonadotropin-releasing hormone (GnRH), which is secreted by the hypothalamus, acts on pituitary gonadotrophs to stimulate luteinizing hormone (LH) and follicle-stimulating hormone (FSH) synthesis and secretion, ultimately affecting the animal’s fertility. MicroRNAs are small, non-coding RNAs that are widely expressed throughout the brain and can fine-tune gene expression post-transcriptionally. Recently, growing evidence has unveiled the central position of miRNAs within a key regulatory process involving GnRH secretion and subsequent activation in the pituitary. Although transcriptional regulation of reproduction has been well studied, the post-transcriptional processes are less well understood. In this review, we elaborate comprehensively on the critical role of miRNAs in the reproductive process, including both temporal and spatial aspects. A better understanding of how miRNAs impact the neuroendocrine system may improve our knowledge of reproduction and provide novel targets for therapeutic development.

For comparison, see: No Missing Link: Knowledge Predicts Acceptance of Evolution in the United States

Using a new demographically representative survey (N = 1100) that includes a detailed measure of evolution knowledge, we find that knowledge predicts level of acceptance, even after accounting for the effects of religion and politics. These results demonstrate that Americans’ views on evolution are significantly influenced by their knowledge about this theory and therefore might be amenable to change.

Reported as: Better knowledge of evolution leads to greater acceptance of the concept

…actual knowledge of the science seems to play a role, and we’ve documented that here for evolution for the first time in a representative population.”

If that claim was true, we would not see so many examples of people in other countries who have replaced the teaching of ridiculous evolutionary theories with facts that their students learn about ecological variation and ecological adaptations.
For example: Israeli Middle Schools School to Include Theory of Evolution (2014)

…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.

See also: Turkish schools to stop teaching evolution, official says (2017)
If you are willing to consider the facts about why many countries do not teach humans to believe in ridiculous theories, please see:
Subatomic: From thermophiles to humans (in prep)

 
 
 

diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

Biology to a Physicist

Measuring energy vs human idiocy (social science)

Summary:
The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the energy-dependent assembly of cell types with fixed amino acid substitutions that link natural selection for energy-dependent changes in base pairs from atoms to ecosystems in all living genera.

Richard Feynman complains about all the different units that are used to measure the single concept of Energy in this snippet  from one of his lectures in the series “The character of Physical Law.”

For an example of how the anti-entropic virucidal energy of sunlight can be measured and linked to the creation of microRNAs, see: Universal Ratiometric Photoelectrochemical Bioassay with Target-Nucleotide Transduction-Amplification and Electron-Transfer Tunneling Distance Regulation Strategies for Ultrasensitive Determination of microRNA in Cells

…using microRNA-141 (miRNA-141) as target model, the constructed biosensor demonstrated favorable accuracy and excellent sensitivity down to femtomolar level. Impressively, the proposed assay overcame the heavily dependence of target on photoactive materials in current ratiometric PEC assay, and demonstrated admirably universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins by merely two different photoactive materials

The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the food energy-dependent assembly of cell types with fixed amino acid substitutions that link changes in base pairs from atoms to ecosystems in all living genera.
There is a model for that: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See for comparison: A step-by-step microRNA guide to cancer development and metastasis

We propose that the balance between oncogenic versus tumor suppressive miRNAs acting within transcription factor-miRNA regulatory networks, influences both the multistage process of neoplastic transformation, whereby normal cells become cancerous, and their stress responses.

See for comparison: Feynman on social science
See also: Quantum common sense

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

Amino acid modification FA_Epigenetics_Table1

Thinking about energy is not radical re-thinking

The brain: a radical rethink is needed to understand it

…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.

Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.

Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness.
The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell.
A Fear of Pheromones (1971)
On Smell (1980)

The act of smelling is remarkably like the act of thinking itself.

See also:

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

In 1991, Roger Penrose, summarized what was known about all the mysteries in his forward to the reprint of Schrodinger’s “What is Life?”

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?

For comparison, see this comment by “Sonny” Williams to the International Society for Human Ethology’s yahoo group:

The empirical evidence is overwhelming that the brain is composed of highly specialized regions, whose neuronal members are unique in their cytoarchitecture (down to the molecular level).  Moreover, empirical evidence reveals that genes have directed these neural variations during corticogenesis; that is, most specialized neurons are differentiated early during development and directed to their place in the brain by intrinsic cues, and not activity-dependent cues.  This fact does not preclude later “rewiring,” or changes that are activity-dependent (plasticity), but this range of plasticity is constrained by the genetically derived regions.

Thus, the metaphor that the brain is “modular” is as accurate as any other metaphor.  HOWEVER, “modular” and functionally specialized regions has always included the fact that functional outcomes require a widely distributed network of specialized regions.  That is, modules do not exist in isolation, as islands of specialized function, but rather there existence as a specialized region is predicated upon their iterative communication with many other equally specialized regions.

I cannot recall any comment by Clarence “Sonny” Williams that might ever have made sense to a serious scientist. He is, in my opinion, a biologically uninformed science idiot. I once wondered who could have taught anyone to believe what biologically uninformed people believe in, or why they think what they were taught makes sense to serious scientists.
Then, I tried to discuss what I know about the energy-dependent links from angstroms to ecosystems in all living genera with the senior author of Complex Spike Patterns in Olfactory Bulb Neuronal Networks by Alister U Nicol, Anne Segonds-Pinchon, and Magnus S. Magnussen. It was also published as a book chapter in Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Background:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

CONCLUSIONS:

We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My summary: They link everything known to serious scientists about energy as information to non-randomly recurring patterns of biophysically constrained RNA-mediated protein folding chemistry and “…characterize these patterns in light of their putative role in processing sensory information.”
They ignore the fact that sunlight is the anti-entropic virucidal source of the energy that prevents genomic entropy via the pheromone-controlled physiology of reproduction in all living genera.
Apparently, like other biologically uninformed theorists, they did not realize what Dobzhansky (1973) did when he linked the light of evolution to all biophysically constrained biodiversity via the nutrient energy-dependent pheromone-controlled physiology of reproduction.
Dobzhansky was one of the first self-declared Creationists to level the playing field with his joke about evolution as if it occurred over billions of years.

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.

Anyone who followed Dobzhansky’s works probably got the joke. He knew there was experimental evidence of God’s Creation. For example, he linked sensory input from what organisms eat and their physiology of reproduction to amino acid substitutions that differentiate all cell types in all living genera. He also knew that theorists had not found experimental evidence of biologically-based cause and effect that supported their claims about millions to billions of years of evolution.
All serious scientists were made aware of Dobzhansky’s rabbinical form of debate in 1964. He began by referring to theorists as bird-watchers and butterfly collectors.  A rather well known form of rabbinical begins with: “Thou fool….”
Dobzhansky was far less damning when he started his address with this:

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Dobzhansky probably was referring to himself in the third person when he made the claim about the unidentified Professor of Zoology. Still, to avoid ridicule by biologically uninformed theorists, he tempered the claim.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Clearly, Dobzhansky knew that his claims about amino acid substitutions would be accepted by serious scientists and rejected by pseudoscientists, who have continued to reject the claims of all serious scientists. That’s what pseudoscientists have always done.
See for instance:

3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.

3/17/17 Jay R. Feierman [NEW]: We are adaptively configured to the current environment because we are the most successful mammal on earth by any measure. There are 7 billion of us and we inhabit every continent on earth. We accomplished this by Darwinian natural selection adaptively influencing the structural design features we call genes and the proteins they make as well as the extra-genetic structural design features developed through our creativity and ingenuity where we pass the instructions on how to make them across generations by social learning. An iPhone is an example today and an obsidian arrow head was an example in the past.

My comment:  After attempts to discuss energy-dependent biophysically constrained RNA-mediated cause and effect with Magnus S. Magnusson, I was not surprised to find support for some of Feierman’s claims about human adaptations in:

Complex spike patterns in olfactory bulb neuronal networks

Indeed, adaptations occur. But, in the same article, they failed to support Feierman’s claims that the adaptations randomly occur.

Abstract excerpt:

BACKGROUND:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

Conclusion: We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My conclusion: People like Jay R. Feierman should try to support their assertions about adaptations with experimental evidence of biologically-based cause and effect like the evidence that was cited in the article linked above.

Any claims about how a population becomes adaptively configured to the current environment are not true outside the context of what is known about energy as information and biophysically constrained RNA-mediated protein folding chemistry. If those ridiculous claims were true, the experimental evidence of top-down causation that theorists think support the claims could be used to convince serious scientists that something besides natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction could replace facts to support theories about mutation-driven evolution.

See also 3/18/17: [MODERATOR NOTE: I’m posting this submission even though it misquotes Feierman, who did not ever say or imply that “adaptations randomly occur.” jrf]
See alson 3/18/17: [MODERATOR NOTE: Adaptations and mutations are not synonyms. An adaptation is a mutation acted upon by natural selection to configure a population to the current environment. It would be an oxymoron to say that “adaptations randomly occur.” By definition, adaptations are mutations that have been acted upon by natural selection by which their frequency is increased in a population over time in a specific environment. jrf]

Alternative splicing of pre-mRNA

Theistic evolutionists fight back and lose (2)

For a historical perspective on the amount of ignorance theistic evolutionists and atheists have repeatedly displayed as they ignored everything known about the energy-dependent RNA-mediated de novo creation of genes, see:
The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels (1982)
Thirty-five years later, there is another clear indication that theorists and atheists will never consider the fact that there must be an anti-entropic virucidal source of energy.
See for example: HSP90 Shapes the Consequences of Human Genetic Variation (2017)
Reported as: Researchers uncover a role for HSP90 in gene-environment interactions in humans

…uncovered a role for HSP90 in humans, not only as a modifier of the effects of mutations, but as a mediator of the impact of the environment on the function of mutant proteins. And these effects of HSP90 can alter the course of human diseases.

Serious scientists placed the effects of HSP90 and all other heat shock proteins into the context of thermodynamic cycles of microRNA-mediated protein biosynthesis and degradation. The fine-tuned cycles link virus-driven energy theft from the degradation of messenger RNA to all pathology via degrees of increasing genomic entropy in species from bacteria to Zika-virus infected humans.
Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. 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.

The metabolic processes are energy-dependent. See also: Functional Metabolic Analysis in Live Cells

The role of metabolism in cellular and physiological processes is well established, with many diseases now linked to metabolic dysfunction or reprogramming.

See also: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Reported as Researchers find new code that makes reprogramming of cancer cells possible

with my comments, such as this one:

Oct 14, 2015
“By administering the affected miRNAs in cancer cells to restore their normal levels, we should be able to re-establish the brakes and restore normal cell function,” Dr. Anastasiadis says.
This suggests nutrient-dependent microRNAs can stop the progression of virus-proliferation that links viral microRNAs to cancer pathology.
The suggestion comes from experimental evidence of how biophysically constrained nutrient-dependent RNA-mediated cell type differentiation occurs in the absence of viral proliferation, which young earth creationists have linked to all pathology.
For comparison, evolutionary theorists would probably tell you that the progression of cancer is inevitable via ongoing processes that link accumulated mutations to pathology except when beneficial mutations are linked to the evolution of a new species.
But, I can’t really attest to what theorists might say, and don’t really care what they claim. They are biologically uninformed.

See also:

See for comparison: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer (October 13, 2015)
The only thing that has emerged from any evolutionary theme is the failure to predict outcomes of treatments, which is due to the ignorance of theorists who refuse to consider experimental evidence of energy-dependent biophysically constrained biologically-based cause and effect.
See: Viral and cellular messenger RNA targets of viral microRNAs and 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.

Theorists continue to ignore the fact that energy-dependent biophysically constrained protein-folding chemistry, which is manifested in endogenous RNA interference, is the link from sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Sunlight, for example, is the source of anti-entropic virucidal ultraviolet (UV) light that clearly links the nutrient-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens.
See also: Energy as information and constrained endogenous RNA interference (2/15/2017)

See also: A third of Americans don’t believe in evolution (January 1, 2014)
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.
See the claims of PZ Myers and his idiot minions for comparison: One crank dies, another rises to take his place

Alternative splicing of pre-mRNA

Dobzhansky 1973 and precision medicine (4)

See: Dobzhansky 1973 and precision medicine (3)
Evidence-based medicine has been hijacked: a report to David Sackett
Fake news

See for comparison: Sugar Gliders, Flying Squirrels, and How Evolutionists Explain Away Uncooperative Data

…contradictory evidence drives evolutionists to embrace irrational just-so stories. Natural selection cannot “adapt” anything. Natural selection kills off the bad designs. It cannot influence the random mutations that must, somehow, come up with such amazing designs. This is the hard reality, but in order to rationalize the evidence, evolutionists must resort to this sort of teleological language, personifying and endowing natural selection with impossible powers. As often happens, a distinctive grammatical form — “for similar lifestyles” — is a dead giveaway. Natural selection becomes a designer.

Creationists shoot themselves in the foot each time they fail to mention the fact that natural selection for energy-dependent codon optimality is obviously the link from the sun’s anti-entropic virucidal energy to ecological adaptations manifested in all biodiversity. See:
Most of the proponents of Intelligent Design still seem to be fighting against the concept of energy as information. Some of them seem to hate the fact that virus-driven energy theft has been linked to all pathology. I suspect their hatred is inspired by their ignorance. They never learned that sunlight is the anti-entropic energy source for all life on Earth.

If energy is not equal to information, where does the life sustaining information come from that links physics and chemistry to molecular epigenetics? And where does the energy go after death or after the extinction of a species?
See also: Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms

One way to influence extracellular metabolites is through active modification or degradation by other organisms (7–9).

…this reaction is reminiscent of reduced flavin acting as the electron donor in its own destruction in vitamin B12 biosynthesis (30).

There should be no need to link vitamin B12 biosynthesis or any other biosynthetic process to biodiversity since all protein biosynthesis and degradation is energy-dependent and biophysically constrained by RNA-mediated protein folding chemistry. Serious scientists have known for several decades how energy-dependent changes in chirality must be linked from sunlight to autophagy by nutrient-dependent pheromone-controlled quorum-sensing in species from microbes to humans. Every aspect of biophysically constrained protein folding chemistry in all cell types of all individuals of all living genera involves thermodynamic cycles of hydrogen-atom transfer in DNA base pairs in solution, which link ecological variation to ecological adaptation via protein biosynthesis and degradation.
The weekend resurrection of the bacterial flagellum in P. fluorescens links its nutrient-dependent pheromone-controlled physiology of reproduction to the  nutrient-dependent pheromone-controlled physiology of reproduction in P. aeruginosa,
See also: Neuroscience of Early-Life Learning in C. elegans Scientists identify the brain circuits with which newly hatched nematodes form and retrieve a lifelong aversive olfactory memory.
My comment:

See also:  Pan-neuronal imaging in roaming Caenorhabditis elegans
Reported as: Watching sensory information translate into behavior

“We have long been recording behavior in worms, but we and others have concluded that, if you want to get physiologically relevant neural activity patterns, you have to look at neurons inside a behaving animal,” Samuel explained. “Only in that context are all feedback loops intact, where behavioral output modulates neural activity which, in turn, shapes behavior.”

As all serious scientists continue to link ecological variation to ecological speciation via nutrient-dependent pheromone-controlled reproduction in species from microbes to humans, my antagonists have all but disappeared.

Clearly, it is time to finally begin discussion of how virus-driven energy theft links hydrogen-atom transfer in DNA base pairs in solution from mutations to pathology instead of from nutrient-dependent RNA-mediated DNA repair via amino acid substitutions to supercoiled DNA, which protects organized genomes from virus-driven entropy.

My comment to the Scientist led to a warning from senior editor Bob Grant.  I was told not to post anything else about virus-driven energy theft.
See Schrodinger (1944) for his prescient representation of what has since been exemplified in all organisms.

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.)

In the reprint edition, the facts about the extremely well-ordered state of matter in food were placed into the context of this question.

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

See also: American Society for Biochemistry and Molecular Biology “This morning [1/24/16], ASBMB learned that an email went out today to senior NIH officials apparently instituting temporary procedures for correspondence with public officials. The email states that all correspondence must be approved by the Department of Health and Human Services. We contacted NIH to find out what’s going on.”
Here’s what we found: NIH transition – trying to provide clarity

Conclusion: …we, frankly, do not know if this is the beginning of a new phase of more restricted communications, or if everything will go back to normal – whatever that means – after Feb. 3.

We do know, however, that any effort to stop a scientific agency from responding to congressional, federal, state and local inquiries has a chilling effect.  As we told the Huffington Post, peer-reviewed science should remain free of politicization, and we support the NIH and all federally funded scientific agencies in their efforts to continue on their missions without political interference.

The fact that they told the Huffington Post anything makes the American Society for Biochemistry and Molecular Biology seem to be in bed with the Demoncrats. Political interference from liberals and theorists has cost billions of dollars that could have been spent on preventative medicine and to implement Precision Medicine based on what has been learned from the National Microbiome Initiative.
See also: The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
They link short, recurring patterns in DNA, which pseudoscientists call sequence motifs to sequence-specific binding sites for proteins. nucleases, transcription factors (TF), and other proteins link energy-dependent RNA mediated ribosome binding, mRNA processing (splicing, editing, polyadenylation) and transcription termination. Serious scientists put the facts about RNA-mediated events into the context of natural selection for energy-dependent codon optimality and healthy longevity. Pseudoscientists fail to link virus-driven energy theft to all pathology because they don’t know enough about physics, chemistry, and molecular epigenetics to integrate the experimental evidence. If they could do that, they would have a model of biophysically constrained biologically-based cause and effect. Instead, they have reputations to protect.
Reported as:Biologists unlock code regulating most human genes

They also discovered that this sequence is located precisely at the start site of more than half of all , underlining the importance of the human Initiator in the human genome.

The human Initiator in the human genome is of no importance whatsoever unless it can be linked from natural selection for energy-dependent codon optimality to healthy longevity, and from virus-driven energy theft to all pathology.
See: Dobzhansky 1973 and precision medicine (5)

rp_levels-of-organization.jpg

Happy biophysically constrained Thanksgiving (in the USA)

Is there any other holiday in the world that celebrates biophysically constrained cell type differentiation in all living genera?
The availability of amino acids and proteins in new genes is nutrient energy-dependent. The de novo creation of genes is biophysically constrained by the innate immune system and the physiology of reproduction. That fact was detailed for a general audience in Biblical Genesis.
Today, all of us can be thankful that the pseudoscientific nonsense of neo-Darwinian theory was replaced earlier in the month with experimental evidence of how new genes are created in the context of energy-dependent hydrogen-atom transfer in DNA base pairs in solution, single nucleotide polymorphisms, microRNA flanking sequences and RNA-mediated amino acid substitutions that stabilize the naturally fluorescent supercoiled DNA in all organized genomes.
We had this: “…insight coming from re-analyses of translated transcripts in yeast that suggested that de novo gene evolution could even be more prevalent than gene duplication-divergence processes [13]
The energy-dependent de novo creation of genes in the context of duplication and divergence was accurately portrayed like this: “…the exact network of interactions between the nuclear lamina and the genome depends on the protein components of the nuclear envelope, the epigenetic state of the genome, and the availability of specific proteins that interpret these epigenetic signals and mediate interactions with the nuclear lamina.
Naturally occurring DNA fluorescence in bacteria and dinosaur osteocytes proves that the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution is the basis for the creation of all biodiversity on Earth.

Simply put, God started with the creation of energy contained in hydrogen atoms as information, which is exactly what the Holy Bible says about His Word and the Light (the quantized anti-entropic virucidal energy of sunlight).Schrodinger (1944) linked it to the works that led to the Nobel Prize in Physiology or Medicine (1933) awarded to Thomas Hunt Morgan for linking inheritance to chromosomal rearrangements. Schrodinger and Dirac shared the prize in Physics that year.

If you remember how your sheets smelled after they had been hung out to dry in the sun, you have already experienced an example of purifying selection for energy-dependent codon optimality, which can be placed into the context of the Nobel Prize-winning works from 1933, or not. You can tell atheists and agnostics about the energy-dependent purifying selection before asking them where they think the energy in a hydrogen atom came from, or not.

When a friend asked me about that, I was forced to learn more about subatomic particles, but what I learned does not matter as much now that the energy has been linked to the creation of new genes. The de novo creation of genes is referred to as the “holy grail” of biology.

However, the energy-dependent protection of the new genes from virus-driven energy theft is also important. If energy-dependent protein folding chemistry is not biophysically constrained and protected from energy theft, life on Earth could not exist.

Thank God, for the anti-entropic virucidal effects of ultraviolet (UV) light, which links femotosecond blasts of UV light to energy-dependent RNA-mediated DNA repair outside the context of claims about emergence and evolution. For comparison, see:

Evolution: Dynamics of De Novo Gene Emergence

Conclusion (with my emphasis):

It has been suggested that the seemingly finite amount of stable protein folds observed across all domains of life is indicative of an early origin of all folds [16–18], possibly under different conditions and functions than the ones today [17]. However, entirely new folds have been shown to arise de novo in viruses [19] and new domains are present in recently acquired regions of old genes, as well as in young genes [20]. Until now, de novo evolved genes are largely underrepresented in structural analyses, and it seems that resolving their structure is a challenge that will provide us precious information about the origin of stable folds, molecular functions and the interaction between genome and environment.

Resolving the issues of virus-driven energy theft, which have been underrepresented in claims about the structure of functional DNA requires all serious scientists to include the role of virus-driven energy theft in the context of protein folding chemistry. There has never been a suggestion made by any serious scientist that the de novo creation of genes could occur outside the context of biophysically constrained protein folding chemistry. That’s why all serious scientists have linked energy-dependent changes from angstroms to ecosystems via the creation of genes and the virus-driven energy theft that links mutations to loss of function manifested in all pathology.

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

Pseudoscientists who make claims like this have never supported them with experimental evidence of biologically-based cause and effect. Why would anyone include such a claim in the same article that proved the de novo creation of genes was energy-dependent and biophysically constrained via supercoiled DNA, which protects all organized genomes from virus-driven energy theft?

Alternative splicing of pre-mRNA

Polycombic ecological adaptation as a science, not a theory (2)

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Conclusion:

… the results here presented indicate that purifying selection is driving not only HBD evolution but also its neighbor pseudogene, HBBP1. In the light of recent advances in the characterization of the β-globin cluster, we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate process of chromatin and protein interactions coordinating the differential expression of genes at the β-globin cluster during development.

My comment: No experimental evidence of biologically-based cause and effect suggests that any locus of genes or any pseudogene has ever evolved. Purifying selection cannot drive evolution. Only energy-dependent variations can can be linked to polycombic ecological adaptation, and only virus-driven energy theft has been linked to the creation of pseudogenes in the context of biophysical constraints on viral latency.

See for comparison: microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Excerpt:

miRNA function is generally limited to cytokine levels in response to RNA viruses

Reported as: Mount Sinai Researchers Use Cellular miRNA-Elimination Tool to Study Viral Infection Dynamics

Excerpt:

…while the loss of miRNAs had a negligible impact on the cell’s immediate reaction to a virus or the short-term biology of the cell, sustained depletion had dramatic results on gene expression that was coupled to a burst of cytokines. The researchers concluded in the paper that miRNA function is limited to modulating the biology of the cell over long periods of time.

My comment: In my model, energy-dependent changes in the microRNA/messenger RNA balance link nutrient energy-dependent changes to all healthy longevity and virus-driven energy theft is linked to all pathology. Over long periods of time, autophagy is the link to polycombic ecological adaptation or virus-driven hecatombic evolution of pathology via energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction. For comparison, virus-driven hecatombic pathology is linked from mutations to all pathology.

Simply put, in my model of polycombic ecological adaptation, differential gene expression is nutrient-dependent and controlled by the physiology of reproduction.

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

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’.

My comment: Claims about RNA-mediated polycombic ecological adaptation were first placed into the context epigenetic imprinting in our 1996 review.

See: From Fertilization to Adult Sexual Behavior

Excerpt:

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.

My comment: Polycombic ecological adaptation appears to link energy-dependent epigenetic effects on hormones (i.e., proteins) to chromatin structure in telomeric regions, which links the effect on transcription and silencing of various genes to hormone-organized and hormone-activated affects on behavior. The hormone-organized and hormone-activated behaviors link the epigenetic landscape of yeasts to the physical landscape of supercoiled DNA in species from bacteria to invertebrates and all vertebrates via the de novo creation of G protein-coupled receptors, which link chemotaxis and phototaxis to all biodiversity.

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] 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.

My comment: The facts about nutrient energy-dependent amino acid substitutions link hemoglobin variants from ecological adaptation to healthy longevity and the facts also link molecular defects from mutations to the pathology of α-, β- or δ-thalassemia, respectively. It would be difficult to include facts about biophysically constrained energy dependent cell type differentiation in the context of any other model that links amino acid substitutions to healthy longevity and links mutations to all pathology in all living genera.

See for example:  Criticisms of the nutrient-dependent pheromone-controlled evolutionary model 

Excerpt:

…James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.

My comment: The claims of a biologically uninformed undergraduate student reviewer were placed into the context of modern evolutionary theory, which involves Masatoshi Nei’s simple-minded revision of neo-Darwinian pseudoscientific nonsense. Nei does not compare his theory of mutations to the facts about nutrient energy-dependent fixation of amino acid substitutions in supercoiled DNA. The problem appears to be the use of the term “mutation” in the textbook published on the same day as my 2013 review was published.

I linked the energy-dependent fixation of amino acid substitutions to all healthy longevity. Nei’s textbook misrepresentations did not link anything to healthy longevity, but linked mutations to what I claimed are nutrient-dependent pheromone-controlled polycombic ecological adaptations.

I failed to include what is known about energy-dependent codon optimality in the context of polycombic ecological adaptations because there was no experimental evidence of biologically-based cause and effect to support those claims at the time of our 1996 review or my 2013 review. For comparison, there has never been any experimental evidence of biologically-based cause and effect to support claims about mutation-driven evolution. Simply put, nothing known to serious scientists about cell type differentiation suggest that mutation-driven evolution can occur.

For comparison, see: New analysis of big data sheds light on cell functions
Excerpt:

With today’s technology, scientists are able to generate data about a cell’s or organism’s complete set of genes, proteins, RNA profiles, metabolites and much more—known as omic data. Using omic data, scientists can model complex biological interactions and gain a more holistic view of different cellular processes.

See also: Research Topic Multi-omic Data Integration

Excerpt:

Stable, predictive biomarkers and interpretable disease signatures are seen as a significant step towards personalized medicine. In this perspective, integration of multi-omic data coming from genomics, transcriptomics, glycomics, proteomics, metabolomics is a powerful strategy to reconstruct and analyse complex multi-dimensional interactions, enabling deeper mechanistic and medical insight.

My comment: Glycomics, transcriptomics, proteomics, metabolomics and genomics have established fact about the biological basis of complex multi-dimensional interactions that link the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria from quorum sensing to the molecular mechanisms that enable deeper mechanistic and medical insight in the context of the National Microbiome Initiative and Precision Medicine Initiative.

See for example: ‘Oming in on RNA–protein interactions

Excerpt:

…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt:

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…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: Detailed examples of how the interactions between pre-mRNA and alternative splicings create new genes in the fine-tuned energy-dependent functional structure of supercoiled DNA explain how all cell types of all individuals of all living genera are protected from virus-driven energy theft. Energy-dependent RNA-mediated amino acid substitutions are fixed in organized genomes via the physiology of reproduction, which helps to prevent the transgenerational epigenetic inheritance of nearly all pathology by linking innate immune system to supercoiled DNA.

For comparison, viruses steal the energy that is required for cell type differentiation, which is how mutations are linked to all pathology. All differences between healthy longevity and virus-driven human pathology can be explained in the context of how nutrient energy-dependent microRNAs. The nutrient energy-dependent microRNAs are carried by erythrocytes in species with circulating blood.

See: Pitfalls of analysis of circulating miRNA: role of hematocrit

MicroRNAs are are delivered to the cell types on an as needed basis. When too few nutrient energy-dependent microRNAs are available, viruses use the existing energy they steal from cells to replicate. Eventually, the replication of the viruses causes the mutations, which are linked to all pathology. That’s why it is important to revisit the facts presented in the context of this article, which was published on 10/26/16

See: Multi-omic data integration enables discovery of hidden biological regularities
I reported this here as: Polycombic ecological adaptation as a science, not a theory for comparison to Biological evolution as a philosophy, not a science.
Despite several attempts to discuss the difference between science and philosophy, no progress was made.
See for example: Evolutionary assumptions (revisited)
See also the impasse that was reached in this attempt to discuss the anti-entropic virucidal energy of the sun.
It is worth joining The Battlefield FB group to see that others would rather hold on to their theories and opinions despite the overwhelming amount of experimental evidence that I have used to support my claims. For me, it is time to move forward and focus on the rediscovery of hidden biological regularities.
Finally, others have discovered that small intranuclear proteins generate alternative splicing techniques of pre-mRNA, which is how microRNAs link hydrogen-atom transfer in DNA base pairs in solution to the conserved molecular mechanisms of energy-dependent cell type differentiation, and to all cell type differences in all individuals of all living genera.
For comparison, this is an example of how virus-driven energy theft is linked viral replication and to virulence:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

For an example of how nutrient energy-dependent RNA-mediated amino acid substitutions are linked to healthy longevity via the physiology of reproduction, see:

…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 (p. 127).”

My comment: The facts stated above have forced theorists to invent evolutionary cell biology.
See Evolutionary cell biology: Two origins, one objective
Reported as: Why some junk DNA is selfish, but selfish genes are junk
Excerpt:

“A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection.” They point out, for example, that many pathways to greater complexity of both genomes and cells don’t confer any selective fitness.

My comment: Greater complexity requires a link from ecological variation to polycombic ecological adaptation, which links supercoiled DNA to protection from the virus-driven hecatombic evolution of all pathology.
My comment: New theories are worthless if they do not include information on the role of energy in cell type differentiation or the role of virus-driven energy theft in all pathology.
See for comparison the facts about: Detection of hemoglobinopathies and thalassemias using automated separation systems
See also: In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
Excerpt: 

The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration.

My comment: That fact suggests all suffering and death caused by hemoglobin variants is caused by neo-Darwinian theorists who do not know how the variants link ecological variation to polycombic ecological adaptation.

Reported as: Scientists edit gene mutations in inherited form of anemia
Excerpt:

The researchers found that the technique corrected the mutation to such a degree that the mice no longer had symptoms of thalassemia. After 140 days, they tested hemoglobin levels in the animals and found them to be normal.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia,” Glazer said.

My comment: The ability to correct the mutation requires a link from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solutions such as blood. That’s how their IV therapy works. It changes the microRNA/messenger RNA balance and that forces the innate immune system to repair the damaged DNA.
See also:  Two novel loci, COBL and SLC10A2, for Alzheimer’s disease in African Americans
Excerpt:

Two SNPs at novel loci, rs112404845 (P = 3.8 × 10−8), upstream of COBL, and rs16961023 (P = 4.6 × 10−8), downstream of SLC10A2, obtained genome-wide significant evidence of association with the posterior liability.

Reported as: Study Identifies Two New Genes Responsible for Alzheimer’s in African Americans
Excerpt:

In 2013, a genome-wide association study of AD in more than 5,500 African Americans identified two genetic risk factors for AD. This study looked at genetic variants across subjects’ entire genome and compared their frequency in cases versus controls.
By doing so they were able to identify two new genes (COBL and SLC10A2) associated with risk of AD in African Americans.

My comment: The author’s study results link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in the microRNA/messenger RNA balance. The neuroscience news report claims they identified two new genes. The neuroscience news report then links the genes — instead of the energy-dependent changes — to the disease in a human population. Many African Americans are examples of how ecological variation has been linked to polycombic ecological adaptation via hemoglobin variants. The adaptations include amino acid substitutions linked to the stability of organized genomes in populations where malaria is endemic. Failed adaptations are included in examples of virus-driven energy theft linked to mutations and the pathology of Alzheimer’s disease.

My comment: The ability to edit out gene mutations clearly links RNA-mediated amino acid substitutions to supercoiled DNA and all biodiversity.
See also: Inventing neo-Darwinism
See also: Pioneering Geneticist Explains Ambitious Plan to “Write” the Human Genome

Excerpt:

…he notes that with an editing tool like CRISPR, one base out of many can be altered, but with a synthesis approach, a hundred edits could be made. This sort of change, he tells JAMA, could make a cell resistant to multiple viruses.

My comments: All the changes in base pairs may already have been linked from natural selection for codon optimality and energy-dependent changes in RNA-mediated cell type differentiation to supercoiled DNA, which links the physiology of reproduction from the innate immune system to fixation of the amino acid substitutions that differentiate the cell types of all living genera. If so, what might happen to an organized genome when a hundred edits are made?

Will anyone be able to stop the hecatombic evolution of pathology via the polycombic ecological adaptation, which links autophagy to healthy longevity via protection of organized genomes from virus-driven entropy?

See also: Yale scientists edit gene mutations in inherited form of anemia Genetics & Genomics

A new gene therapy is being tested for its ability to treat thalassemia, a form of anemia caused by genetic mutations. So far, scientists have successfully corrected gene mutations causing the disease in mice, and now researchers are interested in seeing if the same approach will work effectively in humans.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia. We demonstrated we have extremely low off-target effects.”

See for comparison:

Product Development Pipeline

Excerpt:

Each microRNA mimic in our pipeline is designed to replicate the activity of a single tumor suppressor miRNA and regulate the expression of key oncogenes across multiple oncogenic pathways which can prevent proliferation and induce apoptosis in cancer cells.

See also: VACRC Projects

Excerpt: Future Projects

 The Influence of Carbon Dioxide Enhancement on Plant Growth
 Thermoregulation in Honey Bees
 Biochemistry and Taxonomy in Pine Trees
 The Formation of Multiple Tree Rings in Bristlecone Pine Trees

The VACRC suddenly seems willing to take everything I have claimed about RNA-mediated cell type differentiation during the past twenty years and begin to investigate the claims. This would have been a desirable outcome 20 years ago, but now it might prevent progress via use of my model. The model links energy-dependent changes from angstroms to ecosystems in all living genera, it and links virus-driven energy theft to all pathology.

The Pacific Yew Tree and production of taxol is an example of how the physi0logy of reproduction in soil bacteria can be linked from plant growth to the honeybee model organism of thermoregulation and behavior, which must be linked to the biochemistry and taxonomy of all species. That becomes meaningful via the explanatory power of a model that links RNA-mediated amino acid substitutions to all energy-dependent biodiversity via the conserved molecular mechanisms of polycombic ecological adaptation we detailed in our 1996 review.

However, when others wait too long to accept a model that may already have led to a paradigm shift, they may also realize it. That fact was addressed by Kaveli Kull in the context of next week’s meeting of the Royal Society.

See: Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt:

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.

My comment: Some work by young earth creationists has been at the cutting edge since 1996, as indicated here: Where do viruses come from?

Excerpt:

‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9

My comment: 9 is Holmes, B. (1996) Who Rules the Waves? New Scientist 152(2054):8-9, supp I have not read it in its entirety but the claim fits into the context of everything else I have learned about physics, chemistry, and conserved molecular mechanisms of RNA-mediated cell type differentiation, which appears to be biophysically constrained in all living genera via their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction.

terrarium-eco-system

Epigenetic (re)programming of behavior

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus

Excerpt:

Our results suggest that behavioral plasticity in animals may be regulated in an epigenetic manner via histone modification.

My comment: Experimental manipulation of a single gene changed behavior. The evidence suggests all invertebrate and all vertebrate morphological and behavioral phenotypes can be linked via nutrient-dependent changes in microRNAs, adhesion proteins, and supercoiled DNA.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences
My comment: Nutrient-dependent RNA methylation, RNA-directed DNA methylation, and RNA-mediated amino acid substitutions in the histones link microRNAs and adhesion proteins to supercoiled DNA in the context of chromosomal rearrangements and the physiology of species-specific reproduction linked to the stability of organized genomes in all living genera via protection from virus-driven entropy.
The results from ants extend what is known about how nutrient-dependent pheromone-controlled weekend evolution of the bacterial flagellum occurred via two amino acid substitutions.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt: 

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).

My comment: Neo-Darwinian theorists do not seem to know the difference between the definition of mutation, which is linked to pathology, and how nutrient energy-dependent amino acid substitutions are typically linked to healthy longevity. They bastardized Darwin’s “conditions of life” by placing de Vries “jump-like” changes in energy (i.e., mutations) into the context of natural selection and evolved biodiversity.
Serious scientists have linked atoms to ecosystems within the biophysical constraints of Darwin’s “conditions of life” and everything known about nutrient-dependent pheromone-controlled biodiversity in species from microbes to humans.
See: Structural diversity of supercoiled DNA
Conclusion:

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 deferentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

My comment: I cannot put that conclusion into the context of neo-Darwinian theories. And, neo-Darwinists do not seem willing to address the speed at which weekend evolution of the bacterial flagellum occurred.
As more examples from other species show that experimental manipulation of a single gene changes behavior, other model organisms can be linked to human behavior via as little as a single base pair substitution and single RNA-mediated amino acid substitution. Changes that would typically only occur during life history transitions can be linked from animal models, which are often used to model human physical and mental disorders.
For example: 

The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

The molecular mechanisms continue to be detailed in disparate reports that make evolutionary theorists seem to become more desperate to change their theories each week. They have run out of “wiggle room.”
See also: An Illuminated State of Mind
Excerpt:

“A subsequent study demonstrated that scientists can even implant — we call it ‘incept’ — false memory in the mouse brain,” added Tonegawa. “The challenge is how to extend the information obtained in animal models to human models. The invention of revolutionary noninvasive or low-invasive technologies will be needed, and God knows when that will happen.”

My comment: I wonder how many minds need to be illuminated before everyone accepts the extension of information obtained in animal models to human behavior.
Additional illumination comes from several other articles published today in Science.
Sperm RNA fragments modify offspring metabolism (subscription required)
Excerpt(s)
…two new studies highlight a different class of RNAs, transfer RNAs, carried by sperm.
The effects of the RNA fragments don’t have to be harmful, Chen notes. “If a bad diet can influence us, I think a healthy diet can do it in the same way,” he predicts.
Seeing mTORC1 specificity (subscription required)
Excerpt:

On page 48 of this issue, Aylett et al. (1) help uncover the molecular underpinnings of mTORC1, while on pages 43 and 53, Wolfson et al. (2) and Saxton et al. (3), respectively, make strides in determining how mTORC1 is regulated by the amino acid leucine.

My comment: Nutrient-dependent immune system function is regulated by one amino acid substitution. Researchers seem to have difficulty placing that fact into the context of how ecological variations are linked to ecological adaptations manifested in supercoiled DNA that protects organized genomes from virus-driven entropy.
There seems to be a disconnect between theories and what is know about the theft of nutrient energy by viruses.
For example, I keep reminding people of this claim: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
It replaced this comment, which I fortunately had also posted to The Atlantic before it was removed by Science

See also: “Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution”
The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

 

 

poster-from-jesse

Mutated mitochondrial genes vs Supercoiled DNA

Genetics probe identifies new Galapagos tortoise species

Excerpt 1)

Their paper1, published in PLoS ONE on 21 October, is the culmination of a decade of work. It presents 25 mitochondrial DNA mutations that reliably separate the two groups.

Excerpt 2)

“The species concept is a fuzzy one,” he says. “Call them whatever you want, I don’t care. What is important is that people realize there is hidden diversity.”

My comment: The editors at “Nature” seem to typically support the misrepresentations of the title: new Galapagos tortoise species,  despite accurate claims that “The species concept is a fuzzy one.”
Let’s compare what we see this week in “Nature” to what we see in “Science.”
Is the nature of “Nature” pseudoscience? Is “Systems biology” what’s important to “Science?”

Systems biology (un)certainties

Excerpt:

Models are simplified (but not simplistic) representations of real systems, and this is precisely the property that makes them attractive to explore the consequences of our assumptions, and to identify where we lack understanding of the principles governing a biological system.

My comment: (published to the “Science” site)

Is anything less than this atoms to ecosystems approach to modeling biologically-based cause and effect going to be acceptable from this point forward?
What this article suggests to me is that others must develop models based on nutrient-energy dependent base pair changes, or that their models cannot be validated with experimental evidence.
Structural diversity of supercoiled DNA
Re: “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.”

Summary: Claims that mutations in mitochondrial genes led to the biodiversity manifested in Galapagos tortoise species, or any other species should be evaluated in the context of this question: “Is there a model for that?”
If no model of biologically-based cause and effect links mutations in mitochondrial genes to RNA-mediated gene duplication and RNA-mediated amino acid substitutions, the mutations cannot be placed into the context of anything known about nutrient-dependent RNA-mediated cell type differentiation in species from microbes to man, which is controlled by the physiology of reproduction.
Also, ask yourself, would a serious scientist who understands RNA-mediated gene silencing or any other aspect of RNA-mediated epigenetic regulation of gene expression claim that mutations in mitochondrial genes led to anything except pathology?