fruit-dove

Happy Darwin Day (2017)

My series of blog posts about the refutation of theistic evolution by George Church led him to contact me via email.

  1. He asked why he would get credit for or against the refutations
  2. He claimed he was trained in quantum physics.
  3. He claimed that he has authored peer reviewed papers on protein folding, biodiversity, supercoiling, etc.
  4. He wanted to know more but did not know enough about my target audience to realize why I included information about the viral hecatomb.
  5. He also claimed to have written more on what is known about endogenous RNA interference than on exogenous RNA interference.

I invited him to discuss this further on my FB group, or on this domain. He declined. That was a great end to my 2017 Darwin Day.
See Evolution-guided optimization of biosynthetic pathways, which was co-authored by George Church and published December 1, 2014.
There is no such thing as evolution-guided optimization. Natural selection for energy dependent codon optimality is the only link from ecological variation to ecological adaptation in all living genera. That means we can move forward without George Church and still place his comments into the context of “Trust me, I’m a biologist.
I think that most serious scientists agree that you can’t trust evolutionary theorists For comparison, you can trust Darwin’s “conditions of life.”
Darwin’s “conditions of life” link the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera. Can you trust anyone who claims evolution did that?
See: RNA-Guided Human Genome Engineering 

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Nutrient energy-dependent microRNAs link natural selection for energy-dependent codon optimality to viral latency and protection of organized genomes from endogenous viral elements. Targeting endogenous viral elements with RNA-mediated amino acid substitutions is the key to biophysically constrained cell type differentiation. Fixation of amino acid substitutions prevents problematic nearly identical copies. There is no need for uncontrolled copies if there is no need to find another energy source. Uncontrolled copies link virus-driven energy theft from mutations to all pathology in all genera.
For example, energy theft from bacteria links messenger RNA degradation to morphological and behavioral phenotypes of archaea. Similarly, messenger RNA degradation in humans links the transgenerational epigenetic inheritance of Zika virus-damaged DNA to craniofacial morphology and brain development in infants.
Taken together with what is known about differences in energy-dependent endogenous RNA interference in nematodes, all ridiculous misrepresentations of Darwin’s works must be reversed to show the truth about what virus-driven energy theft does. It links RNA-mediated cell type differentiation from the energy-dependent creation of bacteria to the energy-dependent creation of humans and it links virus-driven energy theft to all pathology.
Riding the Evolution Paradigm Shift With Eugene Koonin

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

Is Eugene Koonin joking about what was left out? If not, big bang cosmologists and neo-Darwinian theorists have never tried to support their ridiculous theories with any experimental evidence of biologically based cause and effect. They never examined the role of energy-dependent microRNAs or virus-driven energy theft. Instead, they invented gene-centric theories of mutation-driven evolution.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.

A 16 page monograph with 12 pages of citations is an unparalleled achievement for anyone who is not a polymath or someone who has not already linked physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation in all living genera via fixation of nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA.
None of the cited works appear to link what is known about virus-driven energy theft to all pathology. Again, it is time to move forward.
See: Charles Darwin’s Ocean Upwelling

It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory [natural selection]. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Changes in coral reefs are nutrient energy-dependent and controlled by the physiology of reproduction. De vries defined “mutation” in 1902, which means that Darwin could not have had a transmutation theory. Also, Darwin repeatedly asserted the claim that his “conditions of life” must come before any claims about natural selection.
Darwin Day 2017 may become known as the day George Church refused to publicly discuss evolution or to admit there is no such thing as evolution outside the context of virus-driven energy theft and the evolution of  pathology. On the same day, The Smithsonian National Museum of Natural History blog site published a post that misrepresented everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and healthy longevity.  Who could ask for a better Darwin Day than one during which Darwin’s “conditions of life” clearly triumphed over the ridiculous claims made by neo-Darwinian theorists and others who refuse to admit to the facts that link energy-dependent changes in chirality from autophagy to endogenous RNA interference and to supercoiled DNA, which prevents virus-driven energy theft from causing the mutations that all serious scientists have linked to all pathology?
 

Alternative splicing of pre-mRNA

Autophagy: from pre-mRNAs to microRNAs, enhancers, QTLs et al.

Nothing known to serious scientists links anything except energy-dependent changes in chirality to autophagy and biodiversity via RNA-mediated amino acid substitutions that differentiate all cell types in all living genera. That fact forces pseudoscientists to invent new terms to confuse the biologically uninformed masses who were taught to believe in the neo-Darwinian pseudoscientific nonsense of mutation-driven evolution.
Autophagy in the liver: functions in health and disease 
See the section: Regulation of autophagy by amino acids

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt from our section on molecular epigenetics.

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 family members and friends of Robin Williams might be appalled to learn that death from Parkinson’s and death from Lewy Body Disease both include instances of suicide that is caused by untreated virus-driven energy theft. The virus-driven energy theft also is the cause of all pathology in species from archaea to humans. It is manifested as energy-dependent changes in alternative splicings of otherwise identical genes.

The prevention of unnecessary suffering and death could be as simple as restoring the balance of amino acids and sugar to prevent all pathology via RNA-mediated cell type differentiation.

That’s not going to happen without some discussion of what is known to serious scientists about the links from angstroms to ecosystems. All of them are energy-dependent. So, “go ahead,  make my day!”

Ask your professors where the energy came from and how it is linked to the changes in pH that predict when difference in healthy longevity become differences in the types of pathology via links from autophagy to supercoiled DNA or to negative supercoiling.

See also: Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end

This review suggests the term “pre-mRNA” changed to “microRNA” as serious scientists learned more about how energy-dependent cell type differentiation was biophysically constrained.

We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.

This was ~20 years after we linked alternative splicings of pre-mRNA to all cell type diversity via the pheromone-controlled physiology of reproduction in yeasts at the advent of energy-dependent sexual reproduction.

See also: Implications of polyadenylation in health and disease

This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3′ end formation.

Watch as researchers continue to invent new names for the molecular effectors in attempts to obfuscated the facts about biophysically-contrained protein folding chemistry that have been known to all serious scientists since Schrodinger (1944) linked the anti-entropic energy of the sun to all biodiversity.

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

Abstract excerpt:

Eusocial insects organize themselves into behavioral castes whose regulation has been proposed to involve epigenetic processes…

Research article summary excerpt:

…behavioral plasticity can be manipulated in the ant C. floridanus by pharmacological and genetic tools that target chromatin regulatory enzymes to stimulate, inhibit, and reprogram behavior. These findings reveal the epigenome as a likely substrate  underlying caste-based division of labor in eusocial insects.

Conclusion:

…our ability to alter a canonical altruistic behavior in a truly social organism by experimental perturbation of a single gene suggests that the application of increasingly versatile reverse genetic approaches in eusocial insects will allow us to expose the general organizational principles underlying complex social systems (10).

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
All general organizational principles underlying complex social systems are nutrient-dependent and pheromone-controlled in the context of the regulation of gene expression that enables the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.

‘Mysterious’ non-protein-coding RNAs play important roles in gene expression

Berger and Daniel Bose, PhD, a postdoctoral fellow in her lab, study the regulation of gene expression from enhancers, non-coding regions of the genome more distant from protein-coding regions.

The only mystery should focus on why they thought they could continue to suppress the facts by referring to natural selection for energy-dependent codon optimality in terms like “enhancers.” Since 2013, everything known to serious scientists about nutrient-dependent microRNAs has been linked to all healthy longevity and virus-driven energy theft has been linked to to all pathology. Serious scientists are not using the term “enhancer.” See for example any of the 56,000 published works that use the term “MicroRNA

Ask why Phys.org / Medical Xpress must report old news from 2013 in the context of unpublished research by two people who cannot be found on the PubMed indexed list of research that links sunlight from chirality to autophagy and chromosomal rearrangements to all biodiversity via energy-dependent changes in the microRNA/messenger balance, which link supercoiled DNA to the protection of all organized genomes from virus-driven entropy.

See: Enhancer RNAs alter gene expression: New class of molecules may be key emerging ‘enhancer therapy’

Enhancers are sequences in the genome that act to boost or “enhance” the activity or expression of nearby genes. They “often behave in a cell-specific manner and play an important role in establishing a cell’s identity and functional potential,” said Christopher Glass, MD, PhD, a professor in the department of Medicine and Cellular and Molecular Medicine at UC San Diego and principal investigator of one of the papers.

Although enhancers have been recognized for more than 25 years, scientists have labored to fully flesh out the breadth and complexity of what enhancers do and how they do it. In 2010, it was discovered that enhancers directed expression of RNA on a broad scale in neurons and macrophages, a type of immune system cell. Dubbed eRNAs…

I do not know any serious scientists who accepts the term invented to replace pre-mRNAs after the term microRNAs was introduced at the turn of this century and more than 56,000 published papers now use the term microRNA in the context of links from metabolic networks to genetic networks in all living genera via non-coding RNAs..

SnapShot: Non-coding RNAs and Metabolism

In recent years, understanding the crucial role played by cellular homeostasis in disease initiation and progression became the focus of scientists and clinicians. This SnapShot sketches the involvement of both short microRNAs and long ncRNAs in the major metabolic pathways altered in diseases.

Functional Importance of eRNAs for Estrogen-dependent Transcriptional Activation Events

Who do they think does not know that the functional importance of microRNAs and the functional difference of eRNAs is the same. eRNAs are the term theorists use for microRNAs.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See also: SPECIAL ISSUE—THE ZIKA VIRUS GLOBAL PANDEMIC: THE LATEST EMERGING INFECTION
Placental Pathology of Zika Virus: Viral Infection of the Placenta Induces Villous Stromal Macrophage (Hofbauer Cell) Proliferation and Hyperplasia

It is still not well understood what role(s) the Hofbauer cell has in facilitating or inhibiting transplacental transmission of infectious agents such as the Zika virus. However, based on the demonstration in this communication of proliferation and prominent hyperplasia of Hofbauer cells in the placenta from a microcephalic fetus infected early in gestation, the identification of residual Zika virus in villous stromal cells, using an RNA probe, and the previously published results of in vitro infection and replication of Zika virus in human Hofbauer cells, it appears highly probable that the Hofbauer cell has an important, or even primary, role in those cases where transplacental transmission of the Zika virus does occur. The unexpected absence in placental tissues of any necrosis or leukocytic response by the mother or fetus to transplacental Zika virus infection is also interesting and of unknown significance.

The absence of a response in the organized genomes of the host clearly indicates ecological adaptation to the virus has already occurred and the supercoiled DNA of the host helps to protect a host from DNA damage. The infants are comparatively unprotected. If they survive to reproduce, and their bones turn up in what a future paleontologist thinks is a fossil record that spans hundreds of thousands of years, the paleontologist would almost undoubtedly claim to have found a new species of non-human primate.
For comparison, all serious scientists known that energy-dependent autophagy is the link to supercoiled DNA, which protects all organized genome from virus-driven energy theft and genomic entropy.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

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

Alternative splicing of pre-mRNA

Energy-dependent coulombic, autophagic, polycombic healthy longevity

Mitophagy is the selective degradation of mitochondria by autophagy.
See also this excerpt:

Disorders in energy creation by mitochondria can cause cellular degeneration…

Mitochondria do not create energy.  They link the creation of the sun’s anti-entropic virucidal energy to RNA-mediated cell type differentiation via biophysically constrained DNA repair. Energy-dependent autophagy links mitophagy to supercoiled DNA via the innate immune system and RNA-mediated repair of damaged DNA.
Repair is nutrient-energy dependent. Separating mitophagy from autophagy is one way to prevent people from realizing how energy-dependent viral latency and healthy longevity is typically achieved outside the context of ridiculous neo-Darwinian theories. Mitophagy and autophagy are two terms used to describe the same energy-dependent molecular mechanisms. In this case, we see the claim that energy creation by mitochondria obfuscates the fact that energy cannot be created or destroyed in the context of what is known about how quantum physics must be linked from quantized energy to biologically-based cause and effect.
Selective removal of deletion-bearing mitochondrial DNA in heteroplasmic Drosophila
Re:  mtDNA deletion (mtDNAΔ) in adult Drosophila muscle.
Excerpt:

Stimulation of autophagy, activation of the PINK1/parkin pathway or decreased levels of mitofusin result in a selective decrease in mtDNAΔ.

Conclusion:

A key question is whether occasional manipulations of cell physiology that promote mtDNA quality control, in otherwise healthy individuals, can bring about a more general ‘housecleaning’ that keeps the frequency of mutant DNA below the threshold for causing cellular dysfunction in diverse tissues without incurring other organismal costs.

My comment: The innate immune system links selective removal of dysfunctional mitochondria to nutrient energy-dependent healthy longevity via the physiology of reproduction in all living genera. Everything known to all serious scientists about energy-dependent thermodynamic cycles of protein biosynthesis and degradation should not lead to the “key question” above. It is too obvious that virus-driven energy theft stimulates autophagy, which typically allows natural selection for nutrient energy-dependent codon optimality to repair damaged DNA.
For example, energy-dependent changes in base pairs link single nucleotide polymorphisms (SNPs) to fixation of RNA-mediated amino acid substitutions in supercoiled DNA via successful reproduction. Fixation of the amino acids substitutions in different cell types of different species is the hallmark of successful reproduction. For contrast, de Vries (1902) defined the term “mutation” in the context of what he claimed were sudden “jump-like” changes in energy. His definition became the basis for the invention of neo-Darwinian pseudoscientific nonsense, which has prevailed among the biologically uninformed.
For comparison, serious scientists have learned that virus-driven energy theft prevents fixation of the amino acid substitutions in host populations. Energy theft facilitates fixation of amino acid substitutions in viruses. For example, fixation via energy-dependent viral replication contributes to the stability of the viral genome via a single amino acid substitution in the influenza virus.
See: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
The increasing instability of the human host’s organized genome can be viewed in the context of accumulated mutations caused by virus-driven energy theft. That instability eventually leads to all virus-driven pathology. The innate immune system is compromised by virus-driven energy theft, and that biological fact also is a historical fact.
See: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Excerpt:

Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.

My comment: No experimental evidence of biologically-based cause and effect suggests that mutations are purged by selection. Natural selection for energy-dependent codon optimality clearly shows that virus-driven energy theft is biophysically constrained. The biophysical constraints link viral latency to healthy longevity in species from microbes to humans. Bacteria are more ecologically adapted than archaea, for example.
See: Virus-mediated archaeal hecatomb in the deep seafloor
Concluding sentence:

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.

My comment: Virus-human interactions clearly play the central role in the history of all life-sustaining cycles of protein biosynthesis and degradation. The transgenerational epigenetic inheritance of Zika virus-damaged DNA is the only proof of that fact that any serious scientist needs.
See for example: Small non-coding RNAs associated with viral infectious diseases of veterinary importance: potential clinical applications (April 4, 2016)
Excerpt:

The emerging correlation between miRNA expression and disease pathogenesis and outcomes suggests the potential use of miRNAs as biomarkers.

See also: MicroRNAs in the Host Response to Viral Infections of Veterinary Importance (October 17, 2016)
Excerpt:

Viruses, particularly DNA viruses [Marek’s disease virus (MDV), bovine herpesvirus] and even retroviruses (e.g., bovine leukemia virus), can also encode their own miRNAs, but due to space limitations, this topic is not emphasized in this review, and we refer the reader to excellent existing reviews [e.g., Ref. (8, 9)].

See also this invited (unpublished) review of nutritional epigenetics. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems  (It was returned without review.)

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: Turning back the aging clock

Most people start off life with some level of heteroplasmy, and the levels of mutant mtDNA increase throughout life. When a critical threshold level of mutant mtDNA is passed, cells become nonfunctional or die.

The accumulation of mutant mtDNA over a lifetime is thought to contribute to aging and degenerative diseases of aging such as Alzheimer’s, Parkinson’s, and sarcopenia—age-related muscle loss and frailty. Inherited defects in mtDNA are also linked to a number of conditions found in children, including autism.

My comment: Virus-driven energy theft is clearly linked from changes in the nutrient energy-dependent microRNA/messenger RNA balance to all pathology. The most recent example of this was reported a few days ago in the context of autism: Shared epigenetic changes underlie different types of autism.
See also: Energy-dependent purifying selection / autophagy (2)
See also: Controlled amino acid treatment of all pathology

Alternative splicing of pre-mRNA

Did evolution autophosphorylate your kinases? (3)

Did evolution autophosphorylate your kinases? (1)
Did evolution autophosphorylate your kinases? (2)
See also:

N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

Reported as: Chemical tags affect ability of RNA viruses to infect cells

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

Reported as:  Zika virus infection alters human and viral RNA

My comment: Virus-driven hecatombic evolution of all pathology is linked from the failure of energy-dependent phosphorylation to biophysically constrain the RNA-mediated damage to DNA via fixation of amino acid substitutions in the cell types of all living genera.

It is now perfectly clear to all serious scientists that evolution did not autophosphorylate their kinases.

See how nutrient energy-dependent phosphorylation must occur to regulate transcription in the context of chromatin remodeling, linked to supercoiled DNA and to chromosomal rearrangements that link RNA-mediated amino acid substitutions to all biodiversity via differences in energy-dependent morphological and behavioral phenotypes.

For example: Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription
Excerpt:

Chemical inhibition of MSKs selectively targets inducible transcription

My comment: Even C. David Allis has been forced to admit to the facts about chemical ecology that I placed into the context of this model.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model

THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology.

Everything published by serious scientists since then attests to the facts that link polycombic ecological adaptations from our 1996 review with its section on molecular epigenetics.
See: From Fertilization to Adult Sexual Behavior
Unfortunately, pseudoscientists and supporters of the evolution industry have tried to prevent the dissemination of accurate information about nutrient-dependent RNA-mediated cell type differentiation in the context of the pheromone-controlled physiology of reproduction in species from microbes to humans.
Others went so far as to invent the term oncohistone in an attempt to link virus-driven hecatombic evolution to beneficial mutations rather than admit that virus-driven energy theft is the link to all pathology in all living genera.
See: Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape
Reported as: Gene regulatory mutation linked to rare childhood cancer
Excerpt:

Because the DIPG mutation always changed the same amino acid in the same location in the histone gene, Lewis knew something was special about it.

My comment: Unfortunately, Lewis did not seem to know that energy-dependent changes in RNA-mediated amino acid substitutions are linked to healthy longevity in all living genera or that virus-driven energy theft links amino acid substitutions in viruses to all pathology.

rp_levels-of-organization.jpg

The natural success of RNAi and failed treatment

see my other blog posts on m6A

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

Excerpt:

…ZIKV infection alters m6A location in mRNAs, methylation motifs, and target genes modified by methyltransferases. Our results identify a mechanism by which ZIKV interacts with and alters host cell functions.

Reported as: Zika virus infection alters human and viral RNA
Excerpt:

When Zika virus infects a human cell, Rana’s team found, the cell modifies viral RNA with m6A as a means to get rid of the infection. RNA tagged with m6A is a beacon for human enzymes that come along and destabilize it. In addition, they found that this host response to Zika viral infection also induced specific m6A modifications on human RNA. These human RNA changes were not present in the absence of Zika virus.

My comment: Energy-dependent cell type stability is RNA-mediated and linked from supercoiled DNA to protection from virus-driven energy theft in all living genera. The RNA-mediated cell type stability is consistently reported in the context of RNA interference.

RNA interference

Excerpt:

RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon.

My comment: All biological processes are nutrient-energy-dependent and controlled by the physiology of reproduction.

  1. Everything attributed to energy-dependent RNAi phenomenon has been linked from changes in base pairs and changes in the microRNA/messenger RNA balance to healthy longevity.
  2. Everything linked from virus-driven energy theft to changes in the microRNA/messenger RNA balance has been linked to all pathology.

Those 2 facts fact show that neo-Darwinian theorists and atheists know nothing about RNAi in the context of energy-dependent biologically-based cause and effect. Like all theorists, pseudoscientists have been forced to invent new theories about evolution that are even more ridiculous than the one Masatoshi Nei detailed in 2013 in his book “Mutation-driven evolution.”
On page 144 (see Figure 6.1), Nei wrote:

The expression of a gene is controlled by several other elements or factors such as microRNAs, transcribed small RNAs, and epigenetics.

On page 199, Nei concluded: 

In other words, genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.

My comment: The conserved molecular mechanisms of gene expression are nutrient energy dependent and pheromone-controlled in species from microbes to humans. Constraint-breaking mutations are the link from controlled energy-dependent gene expression to all pathology.
See for example: Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
Excerpt:

In the absence of the antibiotic, transcription is terminated prematurely by the ribo-regulator. However, upon exposure to lincomycin, drug-inhibited ribosomes stall over a conserved three-amino-acid upstream open reading frame found within the ribo-regulator, thus triggering a conformational change in the transcriptional terminator and inducing the expression of the full-length mRNA that encodes the resistance gene.

Reported in the context of neo-Darwinian nonsense by Ruth Williams | August 1, 2016 as Wanted: Transcriptional Regulators
Excerpt:

Nature has evolved a staggering array of mechanisms for regulating gene expression, but few are so simple and elegant as the riboswitch.

My comment: How could Nature evolve an energy-dependent three-position switch? The claim that the three position switch could be activated by exposure to lincomycin links everything known about autophagy from the innate immune system to supercoiled DNA, which prevents virus-driven energy theft from causing entropy in the organized genomes of all living genera. No matter how much effort is made to place new experimental evidence back into the context of neo-Darwinian pseudoscientific nonsense, the efforts will be ridiculed by serious scientists. But, the pseudoscientists may still cause the death of us all.
Another report on this same research claimed that

In order to describe the diversity of life, science differentiates, for example, between the plant and animal kingdoms.

See: Phys.org | October 20, 2016: Research delivers ground-breaking insights into evolution by studying transcription termination in archaea

Bacteria only have a very short end sequence, after the part responsible for coding the proteins. This study shows that Archaea, in contrast, have a long end sequence after the part responsible for coding the proteins in their mRNA similar to Eukarya. The supposedly uninvolved ends of the mRNA could also potentially contribute to gene regulation in Archaea. The scientists were also able to prove that over 30 percent of the genes in Archaea could be regulated by a series of consecutive alternative termination signals for transcription. Therefore, different lengths of end sequences are generated in response to environmental conditions.

My comment: No serious scientist ever suggested that the molecular mechanisms of cell type differentiation vary with domains-of-life or any species-specific level in any species of plant or animal. Instead, all serious scientists have linked energy-dependent changes from angstroms to ecosystems in species from soil bacteria to mammals via autophagy, supercoiled DNA, and chromosomal rearrangements that link feedback loops from odors and pheromones to the physiology of reproduction to the transgenerational epigenetic inheritance of healthy longevity or Zika virus-DNA damage manifested in craniofacial morphology and brain development in human infants.
If the conserved molecular mechanisms of Transcriptional Regulators could not be linked from transcription termination in archaea to transcription termination in human infants there would be no logical basis for claims about RNAi in the context of gene editing.
See for comparison: Gene Editing: From Roots to Riches
Excerpt:

The technique involved sandwiching an altered copy of a gene between two regions of code identical to those flanking the endogenous gene, which would be swapped out for its engineered counterpart.

My comment: The technique can be placed into the context of natural information processing and codon optimality, which links energy-dependent changes from hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated DNA repair via microRNA flanking sequences, which prevent messenger RNA degradation in the context of virus-driven energy theft during autophagy.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences
Excerpt:

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest.

My comment: Every aspect of energy-dependent RNAi links virus-driven energy theft to all pathology via conserved molecular mechanisms in species from microbes to humans. If that fact was not known to all serious scientists, pseudoscientists could continue to tout RNA-guided human genome engineering as if it would lead to the cure for most if not all virus-driven pathology.

All pathology is biophysically constrained by nutrient energy-dependent changes in cell types that allow all living organisms to adapt to the presence of viruses.

See for instance: Epigenetics and Genetics of Viral Latency
Excerpt:

… viral latency is responsible for life-long pathogenesis and mortality risk…

My comment: The deliberate misrepresentation of biologically-based cause and effect is clear, since (I reiterate):

All pathology is biophysically constrained by nutrient energy-dependent changes in cell types that allow all living organisms to adapt to the presence of viruses. 

See also: Alnylam Pharmaceuticals: RNAi Failure Could Catch Monsanto Investors Off Guard?
Excerpt: It’s clear from the mistakes above that they really do not know and fully understand everything there is to know about how the genetic code works and our increase[d] understanding of epigenetic gene expression is proving that every single day.
My comment: Let’s place that into the context of Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy  and this claim Last month, one of the top intelligence officials in the United States warned that genome-editing technology is now a potential weapon of mass destruction.
Co-suppression, post-transcriptional gene silencing, and every other aspect of biophysically constrained energy-dependent cell type differentiation can be placed into the context of:

How to Track Translation in Living Cells

Excerpt:

This domain, which the team dubbed “the spaghetti monster,” binds multiple FLAG-specific fluorescent antibodies that are injected into the cell, while the mRNA binds its own fluorescent antibodies. Thus, both the mRNA and its newly forming protein are observable at once (Science, 352:1425-29, 2016).

My comment: It’s as if serious scientists who are tracking translation in living cells are ridiculing theorists who chastise creationists for their belief in what theorists call the “flying spaghetti monster.” The theorists learned nothing about the complexity of RNA-mediated autophagy and joked about the creationist’s flying spaghetti monster.
See: The Flying Spaghetti Monster

…noticed that the Board only specified “Intelligent Designer” and not the specific name of any one known deity. This inspired Bobby to protest the proposal by creating the fictional deity named “Flying Spaghetti Monster.” In May of 2005, Henderson posted an open letter to the Kansas school board on his website[2], in which he addressed his opinion that intelligent design was no more valid than the belief that a Flying Spaghetti Monster created the universe.

My comment: How can any serious scientist enter into a debate with atheists who know nothing about biologically-based cause and effect; nothing about physics, and nothing about chemistry?
electra navarone wrote:
Ok, so from reading the contents of your site you are trying to communicate cellular processes that occur within all living beings called ‘autophagy’ that essentially involve recycling of nutrients within the being by breaking down old things and using them to build new things. Ok good. Now what do you want? Like · Reply · 29 mins
My reply: Nothing. It would be nice to have everyone else who is dying from virus-driven energy theft realize that we included every aspect of biophysically constrained RNA-mediated cell type differentiation in our 1996 Hormones and Behavior review — in a section on molecular epigenetics.  What we included has since been linked from autophagy to all healthy longevity or to all virus-driven pathology.
But I don’t care if pseudoscientists acknowledge that fact. Biologically informed serious scientists have already cited it our review, and my other works.

See also: Autophagy Pioneer Wins Nobel

October 3, 2016

…autophagy, the process by which a cell recycles unnecessary components. “His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection…

My comment: How much more can be done without claiming that the energy-dependent changes link natural selection to codon optimality and codon optimality links fixed RNA-mediated amino acid substitutions to the stability of all cell types in all living genera via supercoiled DNA. The supercoiled DNA links ecological variation to ecological adaptation via the physiology of reproduction, which is the only way I know to prevent virus-driven energy theft from being transgenerationally inherited as it is with the Zika virus.

October 20, 2016

Research delivers ground-breaking insights into evolution by studying transcription termination in archaea
From the title above, would anyone recognize that this is a second report on the research reported in The Scientist on August 1, 2016 as Wanted: Transcriptional Regulators
The journal article was published on April 8, 2016. See Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
Conserved molecular mechanisms of energy-dependent autophagy are obviously the link from virus-driven nutrient-dependent pheromone-controlled antibiotic resistance in bacteria to supercoiled DNA, which protects human infants from the transgenerational epigenetic inheritance of Zika virus damage.
But, in Research delivers ground-breaking insights into evolution by studying transcription termination in archaea we are told that…

In order to describe the diversity of life, science differentiates, for example, between the plant and animal kingdoms.

What differences does science introduce to remove the molecular mechanisms of autophagy from archaea before linking them to cell type differentiation in all other living genera?
See for comparison: Biologists first to observe direct inheritance of gene-silencing RNA
also reported as: RNA-mediated gene regulation across generations
 

Physics

Light 'drives' adaptation; nothing 'drives' evolution

Embedded Image

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

Abstract: Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences transcript decay. Codon composition shapes maternal mRNA clearance during the maternal-to-zygotic transition in zebrafish, Xenopus, mouse, and Drosophila, and gene expression during homeostasis across human tissues. Some synonymous codons show consistent stabilizing or destabilizing effects, suggesting that amino acid composition influences mRNA stability. Codon composition affects both polyadenylation status and translation efficiency. Thus, the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.

See also: Biological causal links on physiological and evolutionary time scales

Excerpt:

Occam’s Razor – the problem solving principle in philosophy that suggests that the theory with fewest assumptions should be preferred at first – could be helpful here in judging each potential causal direction. For example in the gene duplication and genetic dispensability problem presented above, the evolutionary causal effect requires the extra assumption that dispensable genes are more likely to undergo gene duplication during evolution; this is non-trivial.

My comment: Pseudoscientists have trivialized the link from the speed of light on contact with water to the de novo creation of nucleic acids and all biodiversity, which links the creation of the innate immune system to supercoiled DNA.  Science journalists report the trivialization in articles like this.

See: Do genomic conflicts drive evolution?

My comment: Nothing “drives” evolution across two billion years. Pennisi is in rare form.

She reports this:

Two billion years ago, an early cell swallowed an energy-producing microbe, giving birth to the mitochondria that are the hallmarks of all eukaryotes, from protists to people. Evolutionary biologists now think that was just the start of the influence that the cell’s “powerhouses” have on the tree of life.

In the same context, she reports:

…evidence that natural selection boosts mutation rates in the nucleus, apparently to keep up with mitochondrial evolution.

See for comparison: Virus-driven energy theft has been linked  to all pathology in Epigenetics and Genetics of Viral Latency.

Excerpt:

…viral latency is responsible for life-long pathogenesis and mortality risk…

My comment: All serious scientists know that ecological variation must be linked to nutrient energy-dependent RNA-mediated ecological adaptation via biophysically constrained protein folding chemistry in all living genera. Only pseudoscientists and science journalists continue to report results in the context of two billion years of mutations, natural selection, and evolution.

See also: Inching toward the 3D genome; All in the (bigger) family — both articles were written by Pennisi, and the links are to my comments on the articles

See also: Combating Evolution to Fight Disease

My comment: Science journalists like Pennisi are supporting neo-Darwinian nonsense each time they report research in the context of two billion years of evolution.

See: Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution’s null hypothesis

Excerpt:

…we interpret the striking similarities in organismal morphology, community structure, habitat, and evident physiology between the ancient and modern sulfur-cycling biotas as evidencing stasis resulting from adaptation to a physically quiescent subseafloor environment that has remained essentially unchanged over billions of years.

See for comparison: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Excerpt:

A central process in evolution is the recruitment of genes to regulatory networks. We engineered immotile strains of the bacterium Pseudomonas fluorescens that lack flagella due to deletion of the regulatory gene fleQ. Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway.

My comment: Compare the bacteria that recruited genes to re-evolve their flagellum via a two-step evolutionary process to the lack of any evolutionary process in the bacteria living in ocean sediments.  What was the two-step evolutionary process that was required for the weekend evolution of the bacterial flagellum? Why did nothing change in the other bacteria for ~ 2 billion years? If you ask answers to the right questions, you will find that theories about mutations, natural selection, and evolution have no explanatory power.

See: Mutation-Driven Evolution

Conclusion: 

genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).

My comment: In that view of evolution, there is no need to consider anything except the ridiculous conclusion, which can be placed into the context of what serious scientists can see. Occam’s razor suggests that all serious scientists should view ecological variation in the context of observed ecological adaptation. If they cannot see that their observations should be placed into the context of what is known  about biologically-based cause and effect, they may need to start looking under the light.

See for example: Gen9 “Our Founders

The founders of Gen9 include people who are likely to know that femotosecond blasts of UV light are linked to RNA-mediated DNA repair of all virus-driven pathology via energy-dependent changes in base pairs and RNA-mediated amino acid substitutions. Unfortunately, most people cannot see how that fact is connected to this fact:

Amino acid composition also influences mRNA stability in vertebrates.

My comment: Perhaps people should open their eyes; look up; and see the light. Quantized energy is difficult to ‘see’ if you live and die in the dark. Schrodinger (1944) and Dobzhansky (1973) reported what they saw. The links open the pdf of Schrodinger’s book “What is Life?” and Dobzhansky’s classic Nothing in Biology Makes Any Sense Except in the Light of Evolution.
In the forward to the reprint of “What is Life?” Roger Penrose asks:

“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?”

Others still report that learning more about mutations and natural selection is the key to understanding how evolution occurs across millions of years — even after the report on weekend evolution of the bacterial flagellum in Pseudomonas flourescens which fluoresces when exposed to UV light. It seems that neo-Darwinian theorists and other theorists are not interested in linking Darwin’s “conditions of life” from Schrodinger’s claims about sunlight to Dobzhansky’s claims about the light of evolution. Do the theorists intend to keep ignoring everything known to serious scientists about the energy-dependent links from angstroms to ecosystems?
See: Structural diversity of supercoiled DNA
Excerpt:

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.

My comment: The differential structure features of DNA are RNA-mediated. Energy-dependent amino acid substitutions link angstroms to ecosystems in all living genera, and virus-driven energy theft links mutations to all pathology.
See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
My comment: For details on the conserved molecular mechanisms that link RNA-mediated amino acid substitutions to cell type differentiation in all cell types of all individuals of all species, see my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract excerpt:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: This protein designer aims to revolutionize medicines and materials

Excerpt:

Baker’s team has all but solved one of the biggest challenges in modern science: figuring out how long strings of amino acids fold up into the 3D proteins that form the working machinery of life.

Conclusion: Protein designers have shed nature’s constraints and are now only limited by their imagination. “We can now build a whole new world of functional proteins,” Baker says.”

My comment: RNA-mediated protein folding chemistry is biophysically constrained by nutrient energy-dependent microRNA flanking sequences, which link the details in our section on molecular epigenetics from our 1996 Hormones and Behavior review to all morphological and behavior diversity in all living genera via RNA-mediated amino acid substitutions.

Baker fails to mention that quantized energy is the link to energy-dependent changes and all links from angstroms to ecosystems via RNA-mediated protein folding chemistry in all living genera. That fact requires the ‘design’ of an innate immune system that protects all organized genomes from virus-driven energy theft and genomic entropy so that organisms can reproduce when enough food is available. If not enough food or energy is available to support the physiology of reproduction, metabolic networks cannot be linked to genetic networks via RNA-mediated amino acid substitutions and protein folding. But virus-driven energy theft can clearly be linked from the Zika virus to differences in craniofacial morphology and brain development by smaller skull size in victims of the transgenerational epigenetic inheritance of the virus.

The facts about the Zika virus-damaged DNA link virus-driven pathology to every aspect of development during life history transitions that are altered by the energy theft. Plasticity associated with olfactory input in this example, and many others, can be examined in the context of what is currently known to serious scientists, or it can be placed back into the context of the pseudoscientific nonsense touted by neo-Darwinian theorists.

See: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

See also:


See also: Light ‘drives’ adaptation; nothing ‘drives’ evolution (2)
 

rp_levels-of-organization.jpg

Virus altered thermodynamic stability

Mechanisms of Zika Virus Infection and Neuropathogenesis and Flavivirus infection requires specific host genes

Excerpt:

The researchers identified 9 genes that… are associated with the cell’s endoplasmic reticulum, where viral translation, replication, and assembly of viral particles takes place. Six of the genes also reduced infection of Zika, dengue, Japanese encephalitis, and yellow fever viruses when removed from human cells. Most showed similar effects when absent from insect cells tested for West Nile and dengue virus infections.

My comment: They linked virus-driven theft of quantized energy to a single amino acid substitution in the virus but do not appear to know that virus-driven energy theft is linked to all pathology by the conserved molecular mechanisms of biophysically constrained energy-dependent RNA-mediated protein folding chemistry in all living genera.

See: Structure of the thermally stable Zika virus

Excerpt: The Ala340 insertion in the C strand of DIII allows the CD-loop to stretch further towards the five-fold vertex compared to DENV2 (Fig. 3a). Gln350 of the CD-loop from one DIII could potentially form a hydrogen bond with Thr351 from another CD-loop in the neighbouring DIII, and thus may create a hydrogen bond network between the five DIIIs (Fig. 3a and Extended Data Fig. 6). In comparison, in DENV2, there is a lack of interaction between the DIIIs in this region (Fig. 3a). The possible hydrogen bond network around the five-fold vertex of ZIKV could be responsible for the rotation of the E protein molecule

Reported as: Cracking the Zika Mystery

…the Zika virus is more thermally stable than the dengue virus, and is also structurally stable even when incubated at 40 degrees Celsius, mimicking the body temperature of extremely feverish patients after virus infection.

Energy-dependent biodiversity (3)

Amino acids and virus penetration

rp_levels-of-organization.jpg

Energy-dependent RNA methylation (7)

“…viral latency is responsible for life-long pathogenesis and mortality risk…” – Lieberman (2016)

My comment: Energy-dependent RNA-mediated amino acid substitutions are responsible for life-long healthy longevity and decreased mortality risk.

See for comparison: How cancer was created by evolution

Excerpt 1)

But even though it is evolutionary processes that have made cancer such a problem, it is also evolutionary thinking that is now leading to pioneering treatments that could stack the odds against cancer and in favour of our health.

Excerpt 2)

Genetic diversity is “the spice of life, it’s the substrate upon which natural selection acts”, says Swanton. By this he means evolution by natural selection, first proposed by Charles Darwin in 1859.

See for comparison:

Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.” — James V. Kohl (7/24/13)

My comment: Thinking about evolutionary processes in the context of cancer pathology, which is obviously a problem that arises in the context of virus-driven energy theft, is like not thinking at all.

See for comparison:  Engaging epigenetics experts

The comments represent the only success I have had with attempts to explain what is currently known about RNA-mediated cell type differentiation in any FB group.

Excerpt:

I don’t see a lot of research on the role of ‪#‎epigenetics‬ in suppressing endogenous retroviruses, so I was intrigued by this one. The investigators in this article in Development turn off the gene Setdb1, a histone methylator, and let slip the dogs of MLV. I’m certain one of our regular visitors will find this interesting.
Working on mouse cells, the team of researchers from Germany’s Ludwig Maximilians University and elsewhere discovered that releasing Setdb1’s hold on endogenous retroviruses definitely allows murine leukemia virus (MLV) to ramp up protein production, ultimately killing the host cells. Of course.

See for comparison:  Creationism and Creationism

My comment: Many people seem more interested in arguing about the religious beliefs of others compared to learning about energy-dependent cell type differentiation for comparison to virus-driven energy theft and pathology.

See also: Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

Excerpt:

…global demethylation is, contrary to previous assumptions, a consequence of neither loss of de novo methylation nor active Tet-dependent demethylation but caused by impaired maintenance methylation.

My comment: Maintenance methylation is energy-dependent and it is RNA-directed.

See: RNA directed DNA methylation and cell types or Google rna-directed dna methylation or search PubMed rna directed dna methylation

RNA-directed DNA methylation is a conserved molecular mechanism that typically prevents transgenerational epigenetic inheritance of damage due to virus-driven energy theft. It is like a reset button on your router, or initiating “restart” on your computer after the problem with virus-driven energy theft of programming information has been corrected. In all living genera, “restart” works wll until the efficiency of energy transfer to the information in programming has been corrupted by the accumulation of viruses and mutations in your ancestors.

The only way to prevent the damage your ancestors knew about was to follow the laws of biology that link virus-driven energy theft to pathology across generations of people who failed to follow those laws. Now, some offspring are susceptible to Zika virus energy theft, which causes craniofacial abnormalities and brain damage in infants — but not always.

There are clear links from nutritional epigenetics that predict when damage is most likely to be transgenerationally (epigenetically) inherited. Anatagonist Sean Ovis (Sirius Cyantis),  put them into God’s plan to kill us all via the creation of viruses, which means he linked the viruses to craniofacial abnormalities and brain damage in infants via the same model — as if God’s intent was to start killing his Creation from the time of birth.

See also: Creationism

My comment: That’s the clearest example of hate-mongering I have seen in this group, so far. And he twisted my model of virus-driven energy theft to do it. Group members wanted a definition of virus-driven energy theft. They refused to accept the fact that it has been linked to all pathology in my model and in the accurate representations of biologically-based cause and effect by all other serious scientists. However, some of the scientists who failed to make the obvious connection are trying to link what is known from a loss of function mutation to the creation of new oncohistones.

Neo-Darwinin theories about mutations, natural selection, and evolution have lost nearly all their appeal among serious scientists. Facts replaced theories about human brain development and the National Microbiome Initiative predictably will undoubtedly continue to be linked to the Precision Medicine Initiative in all publications — except those published by theorists.

Within the next year or two, we should see the mutation-driven evolution approach that theorists have linked to the development of the human brain and behavior become recognized as the theory that is the source of all preventable pathology. Serious scientists continue to make progress, and they will enlist others who are “Combating Evolution to Fight Disease.”
The only researchers left fighting against scientific progress will be the neo-Darwinian theorists, and they may be subjected to something akin to the Spanish Inquisition, or the Salem Witch Trials. “What caused you to keep thinking your magical thoughts about cell type differentiation, you witch?”
See for comparison: Regulation of prefrontal cortex myelination by the microbiota

Excerpt 1)

“… we believe we demonstrate for the first time that the microbiome is necessary for appropriate and dynamic regulation of myelin-related genes with clear implications for cortical myelination at an ultrastructural level. The microbiota is therefore a potential therapeutic target for psychiatric disorders involving dynamic myelination in the PFC.”

My comment: I believe everything that is reported in the context of the belief that it has been demonstrated for the first time should be placed into the context of a model of biologically-based cause and effect. If the model links what is known about RNA-mediated amino acid substitutions and cell type differentiation in all living genera, it could be used to predict what would be demonstrated next for the first time and demonstrated next for the first time after that, ad infinitum.

Eventually, everyone who has ever demonstrated for the first time that the microbiome is the key component of what they have demonstrated for the last time may link the microbiome from metabolic networks to genetic networks via the physiology of energy-dependent reproduction in all living genera and demonstrate for the last time that all other demonstrations linked from virus-driven energy theft to pathology have shown the same thing.

No one has ever shown anything else besides that fact that cell type differentiation is energy-dependent and that RNA-mediated fixation of amino acid substitutions occurs in the context of the physiology of reproduction linked to supercoiled DNA by the innate immune system.

Excerpt 2)

Studies utilizing approaches such as monocolonization in either GF or microbiota-depleted animals using antibiotics would allow deciphering whether specific bacterial strains have the capacity to normalize the observed altered myelination patterns in these animals.

My comment: Those studies could be linked from pattern recognition in other species to demonstrate for the last time that all pathology is caused by virus-driven energy theft, which alters everything known about how metabolic networks are linked to genetic networks by biophysically constrained RNA-mediated protein folding chemistry. Physics and chemistry link quantized energy from angstroms to ecosystems via the physiology of reproduction and biologically-based cause and effect in all living genera.

Summary: Unique microRNAs (miRNAs) appear to link the nutrient-dependent pheromone-controlled life history transitions of bees to RNA-mediated metabolic networks and genetic networks in all genera via base pair substitutions and amino acid substitutions that differentiate all cell types in all living genera. Jon Lieff continues to present what is known about cell type differentiation in articles that an educated audience can understand. I’ve added more technical representations from the most recently reported sources of information.

See also: Microbes Effect on the Brain in my blog post from May 25, 2015: Pattern recognition: biogeochemical structure and function

See also: Counting viruses and bacteria in photosynthetic microbial mats

My comment: Photosynthesis in the ecological regions at the lowest level of a body of water such as the ocean appears to link the minimum amount of quantized virucidal energy from ultraviolet (UV) light and the maximum amount of water molecules found on Earth. The speed of biologically-based symbiotic interactions has now been measured in the context of femtosecond blasts of UV light, which links RNA-mediated DNA repair to amino acid substitutions and cell type differentiation at every subsequent level of examination. All levels of examination have always required a link from an anti-entropic source of energy. All serious scientists have linked atoms to ecosystems in all living genera, via the physiology of reproduction and supercoiled DNA, which protects all organized genomes from virus-driven entropy.  Only recently have serious scientists linked angstroms to ecosystems in the context of the physiology of reproduction and supercoiled DNA.

The serious scientists that did that appear to be having great fun demonstrating “…for the first time that the microbiome is necessary for appropriate and dynamic regulation of myelin-related genes with clear implications for cortical myelination at an ultrastructural level.”

See for example:


C. David Allis’s group seems to want others to believe cell type differentiation is not all about the base. He may want them to believe it’s all about histones. Others have also suggested that approach.
See: Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus reported as: Social behavior in carpenter ants reprogrammed using epigenetic drugs
Excerpt:

It’s All About the Histone The almost decade-long collaboration between the Berger, Liebig, and Reinberg labs, supported by the Howard Hughes Medical Institute, blends molecular biology with observations of animal behavior to understand how caste-based differences arise in ants.

Allis’s group is now reporting the existence of oncohistones (cancer causing histones). They invented the term.
See: An oncohistone deranges inhibitory chromatin

Missense mutations (that change one amino acid for another) in histone H3 can produce a so-called oncohistone and are found in a number of pediatric cancers. For example, the lysine-36–to-methionine (K36M) mutation is seen in almost all chondroblastomas. Lu et al. show that K36M mutant histones are oncogenic, and they inhibit the normal methylation of this same residue in wild-type H3 histones. The mutant histones also interfere with the normal development of bone-related cells and the deposition of inhibitory chromatin marks.

My comment: By placing the change in the base pair that precedes the energy-dependent change in the amino acid substitution, biologically uninformed researchers will focus on the oncohistones, not the virus-driven energy theft that links all mutations to all pathology. The focus of drug development on histones is on damage control or repair.
Allis’s group can develope treatments for disorders of cell type differentiation that link virus-driven energy theft from base pairs to detrimental amino acid substitutions without mentioning the role of energy-dependent amino acid substitutions in cell type stability in all living genera. Cell type stability is controlled by the physiology of reproduction, which links the amino acid substitution to the histones and supercoiled DNA , which protects all organized genomes from virus-driven energy theft and genomic entropy.
See also: Censorship & Upcoming Royal Society Evo Meeting discussion on the Creationism FB group

rp_levels-of-organization.jpg

Energy-dependent RNA methylation (1)

“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

“We know, for instance, when we eat food nucleic acids can get into our cells. Also, there is a theory that our cells in the body keep sending out nucleic acids and one theory has it that it seems to correct the mistakes that other cells have suffered from mutations. . . .” Mae-Wan Ho (2015)

See also: Study: Up to 90 percent of cancers not ‘bad luck,’ but due to lifestyle choices, environment

My comment: Anyone who claims the cause of morphological and/or behavioral diversity or the cause of cancer remains largely unknown is misrepresenting what is known to all serious scientists about biophysically constrained energy-dependent protein folding chemistry. All morphological and all behavioral diversity exemplifies how  energy-dependent RNA methylation must be linked from RNA-directed DNA methylation and fixation of RNA-mediated amino acid substitutions to all cell type differentiation in all individuals of all living genera. Fixation of the amino acid substitutions links metabolic networks from the innate immune system to genetic networks via the biophysically constrained physiology of energy-dependent reproduction.
If you continue to let theorists mislead you with their misrepresentations of biologically-based cause and effect, you may never link RNA methylation from metabolic networks to genetic networks. You will be of no use to those who are combating evolution to fight disease. Instead, you will be fighting against them on the side of ignorance and ridiculous theories.
Your army of ignorant theorists is being decimated by facts. I have nearly 10,000 citations in my bibliographic reference source to prove that. But everything I have detailed or could detail further is worthless if people do not look at the experimental evidence that already has been reported. Pseudoscientists must learn to incorporate facts into accurate representations of biologically-based cause and effect. That is the only way to compare facts to theories. If you are not willing to do that, do not expect someone else to keep doing it for you.
Instead, continue to revisit information that I have already detailed at RNA-mediated.com or begin to make scientific progress towards your understanding of creation by examining what is already available for comparison and then begin to move on.
See for example: Epigenetic Control of Gene Expression failed to link energy-dependent changes from hydrogen-atom transfer in DNA base pairs in solution to biophysically constrained protein folding via detailed representations of how microRNAs and adhesion proteins link supercoiled DNA to the protection of all organized genomes from virus-driven energy theft and genomic entropy.
The university adds more injury to that insulting perspective on gene expression via this collaboration: The University of Melbourne is excited to announce a new partnership with Monash University to lift commercialisation and collaboration of research and innovation outcomes.
See the new course from the University of Copenhagen: Origins – Formation of the Universe, Solar System, Earth and Life

Excerpt:

The story you are about to hear is mainly based on evidence from meteorites and we would therefore like to show you some particularly interesting examples.

My comment: You will be told a story that makes it appear as if theories about meteorites can be used by serious scientists to link top-down causation from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in soluttion to what is known about metabolic networks and genetic networks in all living genera. What is known must link energy-dependent changes from angstroms to ecosystems and also link virus-driven energy theft to mutations and all pathology.

You will not be told anything about anti-entropic energy or virus-driven energy theft as you are taught to believe that their ridiculous theories are based on scientific evidence.

Excerpt:

In the last set of lectures we will look the modern biodiversity, which is perhaps the most remarkable result of the evolution, which we have described throughout the course.There is an enormous difference between the biodiversity of different types of habitats on our planet – from the equator to the arctic, from deserts to rainforests, and from isolated islands like the Galapagos to large continents.

My comment: What will they teach about genetic entropy?

I’ve spent more time than I could have imagined during the past few weeks attempting to discuss experimental evidence of biologically-based cause and effect with biologically uninformed participants in FB groups. Antagonists refused to discuss the experimental evidence. Instead, secular humanists tried to try to get a consensus of opinions about how to define a creationist. Then someone mentioned they would need prevent anyone from defining evolutionists.

Once evolutionists and creationists were “defined,” it would be clear that secular humanists have nothing on which to base their beliefs. They just believe others have no scientific basis for their beliefs. Creationists do not seem to be much better off, and they are clearly as antagonistic. See, for example:

Well, James Kohl has been an embarrassment for this group, attacking other members calling them ignorant and also trolling other groups, this is not what a Christian is supposed to behave.

I do not attack. I inform. If the people I inform chose to not learn anything about the difference between theories and experimental evidence that establishes fact about biologically-based cause and effect, I typically complain that they are biologically uninformed and can be provoked into referring to them as biologically uninformed science idiots. It doesn’t take much to provoke me. If I ask some one to search PubMed for information to be used in the context of discussion, I usually supply a link from my search strategy.

See for example: m6A and microRNA and m6A microRNA mrna
By adding “mRNA” to the search strategy, this citation is lost:

Novel RNA regulatory mechanisms revealed in the epitranscriptome

Others might never learn that the novel RNA regulatory mechanisms were first mentioned in 2013, and they would probably miss this:

THE ENZYMATIC METHYLATION OF RNA AND DNA. 8. EFFECTS OF BACTERIOPHAGE INFECTION ON THE ACTIVITY OF THE METHYLATING ENZYMES

Excerpt:

The virulent bacteriophage-host cell system is an example of a phenomenon involving recognition by the host of a foreign nucleic acid; in some instances, phage DNA is rapidly synthesized while the host DNA is rapidly degraded. If methylated bases are involved in controlling such a recognition mechanism, then a study of the methylated base content of 7′ DNA’s of various bacteriophages grown in different hosts might provide a clue as to the biological function of the methylating enzymes.

My comment: Until you learn about virus-driven energy theft, this authors’ comment from 2013 would  be meaningless.

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

One of the secular humanists I encountered took that claim and every aspect of RNA-mediated cell type differentiation that I have detailed during the past 20 years, and represented it here:

See: Virus Driven Energy Theft

Conclusion:

If you are a creation scientist, you can take comfort in the fact that as you get older, the control of these viral fragments is considerably weakened, and eventually one or more of these jumping genes will be let loose in your body to wreak havoc on your DNA. When that happens, you can thank God, because they will have brought you closer to him.

My comment: It is difficult for me to imagine how anyone could remain so horribly uninformed or how anyone could become such a hate-monger. For example, virus-driven energy theft is linked to pathology throughout life, not just in old age.

See for example: Maternal Inflammation Disrupts Fetal Neurodevelopment via Increased Placental Output of Serotonin to the Fetal Brain

Excerpt:

SIGNIFICANCE STATEMENT The mechanisms linking maternal inflammation during pregnancy with increased risk of neurodevelopmental disorders in the offspring are poorly understood.

My comment: In the introductory statement of this blog post, I wrote: “Anyone who claims the cause of morphological and/or behavioral diversity or the cause of cancer remains largely unknown is misrepresenting what is known to all serious scientists about biophysically constrained energy-dependent protein folding chemistry.” The significance statement was published with the article in the Journal of Neuroscience and reported as: Flu-like symptoms in pregnant woman could affect baby
Excerpt:

Levels of tryptophan, an amino acid that activates the immune system, increased, causing the placenta to produce more serotonin, which led to higher concentrations of serotonin in the fetal brain.

Excerpt (with my emphasis): “The study provides a new molecular pathway to understanding how prenatal insults could program a baby to eventually develop mental diseases. Even mild viral attacks such as the flu or Zika virus, which generally does not require a mother to visit to the doctor’s office, might affect the development of a baby’s central nervous system…”
My comment: The article published in the Journal of Neuroscience did not mention the link between the nutrient energy-dependent amino acid and activation of the immune system. If they had it would suggest that no new molecular pathway has been discovered. Virus-driven energy theft has always been linked via a single amino acid substitution in the virus to all pathology in all living genera.
Getting researchers to report that fact in the context of their findings has been a challenge. Until someone establishes a clear link from energy-dependent RNA methylation to behavior and publishes in a journal such as the Journal of Neuroscience, others may not examine other experimental evidence that clearly links viruses like the Zika virus to changes in morphological phenotypes and behavioral phenotypes via differences in energy-dependent brain development.

terrarium-eco-system

War Games: False Flag Terrorism

Sirius Cyantis (aka Sean Ovis) takes my claims about virus-driven energy theft and pathology outside the context of creationism.  Using his assumed name, he places them into the context of support for evolution. That’s an example of what happens on the “False Flag” Creationism FB group. In the context of combating evolution to fight disease, the war games become more interesting.

Most people in False Flag groups do not know who they are fighting against. In the end it won’t matter. Until then, let’s look at what serious scientists know about virus-driven energy theft, again. This is what the False Flag Creationism FB group has tried to prevent others from learning.

1996 (open access)

Excerpt:

As silencing in both yeast and Drosophila is similarly enhanced by mutations in particular ubiquitin processing enzymes, the regulation of silencing by these enzymes appears to be an evolutionarily conserved process.

My comment: Serious scientists have linked angstroms to ecosystems via what is known about supercoiled DNA, which protects all organized genomes from virus-driven entropy.

For comparison to what is known, see:

2016 (open access)

Excerpt (with my emphasis):

…a mathematical model that is able to accurately estimate 5mC levels and the individual activity of the three main pathways relevant to DNA methylation dynamics (p1, de novo; p2, maintenance; and p3, active demethylation) and predicts with great accuracy corresponding 5hmC kinetics in all instances of global epigenetic reprogramming.”

My comment: Nutrient energy-dependent silencing via RNA-directed DNA methylation and enzymes linked to supercoiled DNA and protection of orgnaized genomes from virus-driven entropy now must occur via three pathways p1, p2, and p3.
p1, is the magical “de novo” pathway. (de novo means they don’t know how to link the energy-dependent pathway from angstroms to ecosystems).

p2, maintenance becomes part of something magical.
p3, demethylation also automagically occurs.

Leave out the energy-dependent biophysically constrained pathway. Start with magic. Stay with it. Leave out out everything known to serious scientists about virus-driven energy theft. What’s left is neo-Darwinism — the antithesis of creationism. Creationism – The Official Page may not be a False Flag group. See if you can tell the difference.

The differences remind me of the movie “War Games.” The game played by the computer was tic-tact-toe. The computer finally ended the simulated war by refusing to play.

Facts about who started the war and/or why computer models are still being used to combat creationism and promote ridiculous theories about mutations and evolution have never been addressed. The only thing certain is that — in the context of creationism — if you continue to play the evolutionist’s game, everyone loses.

Eventually,  virus driven energy theft kills everyone because viruses adapt faster that people do. The superbug crisis is proof of that. It’s the adaptation by viruses in the bacteria that is the biggest threat. Nutritional epigenetics points the way towards eliminating that threat.

See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Excerpt: (with my emphasis):

Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).

Comment: In this case the p1, p2, and p3 pathways are nutrient-dependent and receptor-mediated.

For example, calcitriol is the active form of vitamin D. Its effects on the microRNA(miRNA)/messenger RNA (mRNA) balance appear to protect against perturbed protein folding, which is associated with colorectal cancer. MiRNA-627 targets the mRNA that encodes an enzyme linked to histone demethylation and amino acid substitutions that increase stability of hydrogen bonds in DNA, which are important to protein folding (Padi, Zhang, Rustum, Morrison, & Guo, 2013). Rarely does a week go by without yet another report that details cause and effect in the context of miRNAs (Follert, Cremer, & Beclin, 2014). For example, the potential for therapeutic use of miRNA-126-5p to treat atherosclerosis was reported in time for me to note the importance of miRNAs to cell type differentiation via the circulatory system (Schober et al., 2014). However, in Section One, my focus is on the role of vitamins in nutritional epigenetics. The importance of the miRNA/mRNA balance to protein folding that enables structural and functional differentiation of cell types is detailed further in the Section Two of this review.

My comment: The importance of the link from virus-driven energy theft to pathology in the context of the Precision Medicine Initiative led to the National Microbiome Initiative.  5-hydroxymethylcytosines (5hmCs) link the p1, p2, and p3 nutrient energy-dependent pathways to cell type differentiation and protection of our organized genomes from virus-driven entropy.
Researchers in other countries know that. They will no doubt do everything possible to protect themselves and their countries from threats like the Zika virus and the Ebola viruses. For comparison, look at what happened in the United States of America.
1) Presidential candidate, Dr. Ben Carson was harassed for his young earth creationists beliefs.
2) PLOS one retracted an article for merely mentioning the Creator.
See: Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living [retracted]
Excerpt:

In conclusion, our study can improve the understanding of the human hand and confirm that the mechanical architecture is the proper design by the Creator for dexterous performance of numerous functions following the evolutionary remodeling of the ancestral hand for millions of years. Moreover, functional explanations for the mechanical architecture of the muscular-articular connection of the human hand can also aid in developing multifunctional robotic hands by designing them with similar basic architecture.

My comment: What led to the attacks on Dr. Ben Carson’s religious beliefs? What led to the attacks on my scientific credibility in the FFCg?

These are the people who are playing the False Flag game with everyone:

Raymond Bane

Brandi Bell Fuller

Patrick Dennis

Dan Delane

Charles C. Hall, who plays as: Charles Blaha, Professor of Neurosurgery

Zachary Johnson

Dennis Jones

Jay Lutsky

Herman Mays

Sean Ovis  (as Sirius Cyantis, and too many of his friends to mention)

Christopher Richard Pruett
Dave Prout
Ryan Tipple
A few others deserve to also be mentioned, but first things first. Let them know you will try to stop them. Help other serious scientists who are Combating Evolution to Fight Disease, and help to restrain those who are fighting for the diseases that are destroying your security.
Alternatively, see: Comet contains glycine, key part of recipe for life May 27, 2016

Excerpt:

In addition to the simple amino acid glycine, the instrument also found phosphorus. The two are key components of DNA and cell membranes.

My comment: Instead of combating evolution to fight disease you could fight against the reporting of pseudoscientific nonsense by theoretical physicists.
See: Scientific method: Defend the integrity of physics

…the issue boils down to clarifying one question: what potential observational or experimental evidence is there that would persuade you that the theory is wrong and lead you to abandoning it? If there is none, it is not a scientific theory. The imprimatur of science should be awarded only to a theory that is testable. Only then can we defend science from attack.

My comment: Substitution of achiral glycine in position six of the GnRH decapeptide in vertebrates links all energy-dependent RNA-mediated cell type differentiation from the innate immune system to supercoiled DNA and the stability of organized genomes via the physiology of reproduction. The theorists of physicists and evolutionists have not been supported with experimental evidence of biologically-based cause and effect. Many people have simply been taught to believe that the theories are scientific theories and they are the people that will continue to prevent scientific progress. They may allow virus-driven energy theft to kill us all.