The natural success of RNAi and failed treatment

By: James V. Kohl | Published on: October 21, 2016

see my other blog posts on m6A

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection


…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

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


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

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

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: | 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

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

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

… 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


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

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