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

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.
rp_levels-of-organization.jpg

Neo-Darwinism failed in 1995

We replaced neo-Darwinian theory with what was known about the nutrient-dependent pheromone-controlled physiology of reproduction in The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)

See also: The Darwin Code by Greg Bear

Evolution rising from the grave

The pioneering thinkers of yesterday are the devoted traditionalists of today. New ideas enter science grudgingly. New paradigms are resisted with a vengeance.

Living with the Neanderthals

…the preposterous ideas of yesterday are the unshakeable dogmas of today, and the ancient superstitions of tomorrow. Science is driven by politics, and politics by fear.

My comment: What could possibly be the purpose of this forthcoming conference?

New trends in evolutionary biology: biological, philosophical and social science perspectives (November 2016)
The trendsetters have failed to present anything new during the past 20 years. Their perspectives are as useless and ridiculous as they have always been.

See for review: Neo-Darwinism has failed as an evolutionary theory May 19, 1995

Excerpt: … far from concentrating on the development of theories of organisms and ecosystems, Neo-Darwinism concentrates on genes as the fundamental entities in biology.

…Neo-Darwinism is not only prone to misleading rhetoric and inadequate science, but its applications may result in ecologically dangerous agricultural applications.

See also: Physics: Material to meaning

Excerpt:

Carroll demonstrates the absurdity of adding to the Core Theory to explain the possibility of things such as an afterlife or a transcendent underlying purpose. These are easy targets. The narrative begins to get awkward when it comes to, say, conscious experiences. These, Carroll writes, are “not part of the fundamental architecture of reality”; they are emergent, a handy way of talking about what brains do. Like entropy, he argues, consciousness is a concept that “we invent to give ourselves more useful and efficient descriptions of the world”. He calls his approach “poetic naturalism”.

My comment: Weekend resurrection of the bacterial flagellum was reported last year in Science Magazine. Ranier Friedrich’s group has since linked energy as information flow from quantum physics the de novo creation of G protein-coupled receptors and zebrafish olfaction to neuronal networks in humans that others have linked to consciousness.
See also:

Excerpt:

One exception would be a small number of pages about the multiverse, which he contrasts with religion, ending with (referring to religion)This is the problem with theories that are not well-defined.

He’s got the problem right, but doesn’t notice that it applies equally well to this particularly dubious bit of “science”.

My comment: No matter how many times that physicists are told their ‘religion’ is based on nothing but theory, they refuse to link energy as information from top-down causation to biologically-based cause and effect. Like neo-Darwinists, they fail to include energy-dependent cell type differentiation, which means they fail to link virus-driven energy theft to all pathology.That’s the magic of how the big bang cosmology industry and evolution industry are linked. Their religion requires no experimental evidence of biologically-based cause and effect to support their ridiculous claims. But they established the popularity of their claims and have not realized that explaining healthy longevity compared to virus-driven pathology on Earth has nothing to do with their religious beliefs or the beliefs of any others.Serious scientists have linked energy-dependent changes from angstroms to ecosystems and virus-driven energy theft to all pathology. Young earth creationist are not the only scientists who have done that.

See also: Site-selective and stereoselective functionalization of unactivated C–H bonds

Reported 5/11/16 as Chemists find ‘huge shortcut’ for organic synthesis using C-H bonds

Excerpt: 
The handedness of a molecule is important in organic chemistry, since this 3D shape affects how it interacts with other handed molecules. When developing a new drug, for instance, it is vital to control the chirality of the drug molecules because biological molecules recognize the difference.
My comment: Substitution of the only achiral amino acid, glycine, at position 6 in the GnRH decapetide links the nutrient-dependent pheromone-controlled physiology of reproduction from the innate immune system to supercoiled DNA in all vertebrates. Supercoiled DNA protects all organized genomes from virus-driven entropy.
Why would any theorist continue to think for 20 years that their ridiculous theory could stand the test of time in the context of experimental evidence of biologically-based cause and effect that has continued to come from serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera?
Filtering light through a prism to identify tissue type

RNA-mediated physics, chemistry, and molecular epigenetics (3)

Summary of the metabolic pathways altered in cancer that are described in this review

Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism

My comment: Metabolic networks are linked to genetic networks by the normal metabolic landscape, which is linked to healthy longevity. Virus-driven energy theft links changes in the metabolic landscape to changes in the physical landscape of supercoiled DNA, which typically maintains healthy longevity across the lifespan by preventing virus-driven entropy. When no consideration is given to facts about virus-driven entropy, you are stuck with theories about brain evolution.
See for example: Metabolic acceleration and the evolution of human brain size and life history 5/4/16 reported as: Humans have faster metabolism than closely related primates, enabling larger brains

My comment: Place that claim into this regression.

Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum 1/15/16
My comment: Copy number variation is nutrient energy dependent
Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants 2/28/16
My comment: MicroRNA flanking sequences link hydrogen atom transfer in DNA base pairs in solution to nutrient energy-dependent copy number variation.

An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers 4/1/16
reported 4/14/16 as: Scientists document rare DNA transfer between animals and plants
My comment: “Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals. For example, ingested plant microRNAs influence gene expression across kingdoms (Zhang et al., 2012). In mammals, this epigenetically links what mammals eat to changes in gene expression (McNulty et al., 2011) and to new genes required for the evolutionary development of the mammalian placenta (Lynch, Leclerc, May, & Wagner, 2011) and the human brain (Zhang, Landback, Vibranovski, & Long, 2011).” — Kohl (2012)
My comment: Place all claims (above) that link nutrient-dependent ecological adaptations into the context of healthy longevity. Place all claims (below) into the context of  virus-driven energy theft and all pathology.
Wolbachia Blocks Currently Circulating Zika Virus Isolates in Brazilian Aedes aegypti Mosquitoes 5/4/16

reported 5/4/16 as: Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing 5/3/16

reported 5/1/16 Australia to spend over $11mn to eradicate carps by releasing herpes virus into rivers

My comment: Place all claims about nutrient energy-dependent cell type differentiation and all claims that link virus-driven energy theft into the context of physics and chemistry linked to the conserved molecular mechanisms of cell type differentiation in twin studies. For example,  NASA’s Twins Study Explores Space Through You: Videos Highlight Omics  4/20/16

What does it take to detect entanglement with the human eye?
reported 5/3/16 as  An experiment seeks to make quantum physics visible to the naked eye

RNA splicing is a primary link between genetic variation and disease 4/29/16

3/31/16 Carl Zimmer Episode 5: Everything you thought you knew about the shape of DNA is wrong

4/24/16 Sea Slug Senses 1/15/13 The sea slug that eats the sun (video)

Saturation of recognition elements blocks evolution of new tRNA identities 4/29/16

reported 5/2/16 Discovery of a fundamental limit to the evolution of the genetic code

Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity and Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPRmt

reported 5/2/16  Genetic switch could be key to increased health and lifespan

The Role of Correlation and Solvation in Ion Interactions with B-DNA 1/19/16

delayed reporting till 5/3/16 A new model for simulating DNA’s ‘atmosphere’ of ions

5/3/16 Part I: Epigenetics: Why Your DNA Isn’t Enough C. David Allis

5/3/16 Part II: Epigenetics in Development and Disease C. David Allis

Genomic instantiation of consciousness in neurons through a biophoton field theory 6/13/14
4/18/16 Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb and 5/1/16 Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy 
collectively reported 5/2/16 as Unraveling complex neuronal networks
My comment: The de novo creation of G-protein coupled receptors (GPCRs) links the epigenetic landscape to the physical landscape of supercoiled DNA via olfaction and the innate immune system.

Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons. Delgado-Peraza F, Nogueras-Ortiz C, Acevedo Canabal AM, Roman-Vendrell C, Yudowski GA. Methods Cell Biol. 2016;132:25-33.
Chapter 1 – Localization and signaling of GPCRs in lipid rafts

Chapter 2 – Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons
Chapter 4 – Single-molecule resolution of G protein-coupled receptor (GPCR) complexes
Chapter 13 – Resonance Energy Transfer-Based Approaches to Study GPCRs
My comment: Place everything known about nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation into the context of virus-driven energy theft and cancer.

Deletion of Amino Acid Transporter ASCT2 (SLC1A5) Reveals an Essential Role for Transporters SNAT1 (SLC38A1) and SNAT2 (SLC38A2) to Sustain Glutaminolysis in Cancer Cells (4/26/16)
reported on 5/5/16 Starving cancer the key to new treatments
Excerpt:

The research team blocked gateways through which the cancer cell was obtaining the amino acid glutamine and found the cells almost completely stopped growing.

My comment: They prevented the viruses in the cancer cell from adapting. Otherwise, energy theft enables amino acid substitutions in the virus that would link ecological variation to healthy longevity when nutrient-stress or social stress is biophysically constrained. Links from the epigenetic landscape to the physical landscape of supercoiled DNA biophysically constrains energy-dependent RNA-mediated cell type differentiation. They have been placed into the context of mutation-driven evolution by theorists who have killed millions with their ridiculous theories.

See for comparison:

reported 5/2/16 We are pleased to announce that today marks the formal release of our latest title: Amber Palaeobiology by Dr David Penney.

Filtering light through a prism to identify tissue type

RNA-mediated physics, chemistry, and molecular epigenetics

RNA-mediated physics, chemistry, and molecular epigenetics

Genetics and Genomics May 11-12, 2016


Published on 3 May 2016  See the full size poster displayed on Figshare.com

Abstract:

Olfaction and the innate immune system link energy as information from the epigenetic landscape to the physical landscape of supercoiled DNA. The sun’s biological energy is the source of the information that links angstroms to ecosystems via physics, chemistry, and molecular epigenetics.

RNA-mediated protein folding chemistry and amino acid substitutions link the anti-entropic quantized energy of sunlight from the virucidal effects of ultraviolet (UV) light to healthy longevity via biophysically-constrained energy-dependent hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation.

Biomarkers link energy-dependent differences in base pairs and amino acid substitutions to biosignatures across the healthy life span. RNA-mediated amino acid substitutions also reveal the increasing complexity of interactions among cell types as pathology progresses. For comparison, successful reproduction links energy from supercoiled DNA to protection of all organized genomes from virus-driven energy theft and pathology.

This model links the sun’s biological energy from top-down causation in microbes to the most recent model of bottom-up gene activation and cell type differentiation in vertebrates. Citations to extant literature provide examples of what is currently known about how ecological variation leads to biophysically constrained cell type differentiation in the context of nutritional epigenetics and Precision Medicine, which clearly link metabolic networks and genetic networks to pharmacogenomics.

Content:
Physics:  Quantum theory links ecological variation and food odors from the supply of specific nutrients to climate change and stress-effected differences in human brain development. [1-3] [1] A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
[2] Climate warming is predicted to reduce omega-3, long-chain, polyunsaturated fatty acid production in phytoplankton
[3] Maternal choline intake alters the epigenetic state of fetal cortisol-regulating genes in humans
Chemistry:  Quantized energy from the sun links ultraviolet (UV) light on contact with water to hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated DNA repair via amino acid substitutions. [4-9] Cryo-electron tomography (cryo-ET) [10-11] and cryo-electron microscopy (cryo -EM) [12] link electron density from angstroms to ecosystems in the context of transgenerational epigenetic inheritance of energy-dependent RNA-amino acid substitutions and/or virus-driven pathology. For example ~10 amino acids surround the Asn154 glycosylation site of the Zika virus. Remarkably similar findings were confined to one generation of mass die-offs in a species of fish. [13] Transgenerational effects of the Zika virus link the nutrient-dependent RNA-mediated immune system and the physiology of reproduction in vertebrates to supercoiled DNA, which typically prevents virus-driven entropy in all organized genomes. [14-17] Outside the context of the non-linear links from physics and chemistry to biologically-based cause and effect, the differences in the Zika virus and all living organisms are typically placed into the context of neo-Darwinian evolution via master genes that drift to fixation in the host population. [18-19] For contrast, everything known about nutrient energy-dependent cell type differentiation links viruses in gut microbes from metabolic networks and genetic networks to invertebrate and vertebrate biodiversity. [20-23]

[4] Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water
[5] Serial interactome capture of the human cell nucleus
[6] Pado, a fluorescent protein with proton channel activity can optically monitor membrane potential, intracellular pH, and map gap junctions
[7] Dissipation Bounds All Steady-State Current Fluctuations
[8] Physicists prove energy input predicts molecular behavior
[9] Metabolic Regulation of Histone Post-Translational Modifications
[10] Architecture of the symmetric core of the nuclear pore
[11] Structural diversity of supercoiled DNA
[12] The 3.8 Å resolution cryo-EM structure of Zika virus
[13] Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia.
[14] Force distribution in a semiflexible loop
[15] Mammalian elongation factor 4 regulates mitochondrial translation essential for spermatogenesis
[16] The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
[17] Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk
[18] From Mosquitos to Humans: Genetic Evolution of Zika Virus
[19] Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes
[20]  A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans
[21] Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota
[22] Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways
[23] Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

Molecular epigenetics
It has become clear to all serious scientists that nutrient-dependent microRNA flanking sequences link RNA-mediated amino acid substitutions to  ecological adaption via protection against virus-driven energy theft, which links a single amino acid substitution to increased virulence of viruses. [24 -28] The role of the nutrient-dependent substitution of the achiral amino acid glycine in position six of the gonadotropin releasing hormone (GnRH) decapeptide, established GnRH secretion as the link from the gut microbes of invertebrates to all vertebrate biologically-based cause and effect. GnRH secretion links hormone-organized and hormone-activated behaviors from invertebrates to vertebrates via olfaction and the innate immune system. [29] This representation of epigenetically-effected genome organization can be compared to theories about mutations in the context of facts about RNA-mediated amino acid substitutions and energy-dependent cell type differentiation. The nutrient-dependent amino acid substitutions differentiate all cell types in all individuals of all genera via what is currently known about biophysically constrained RNA-mediated protein folding chemistry.

[24] Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses;
[25] Nutrient-dependent/pheromone-controlled adaptive evolution: a model
[26] The phylogenetic utility and functional constraint of microRNA flanking sequences;
[27] Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
[28] Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
[29] From Fertilization to Adult Sexual Behavior

Microbiomes, Metabolism, Mitochondria, Mechanisms, and Molecular diagnostics
What is known about  Microbiomes, Metabolism, Mitochondria and Molecular diagnostics links any energy-dependent systems approach from -omics to Precision Medicine via the innate immune system. [30] All phenotypic expression starts with the energy-dependent creation of nucleic acids and the creation of G protein-coupled receptors. The receptors allow nutrients to enter cells. For example, see [31] The energy-dependent creation of olfactory receptor genes links metabolism and mitochondrial function to stress-driven changes in neuroendocrine, metabolic, inflammatory, transcirptional responses and to differences in behavior. [32-33] Expression of c-fos links gene expression in GnRH neurosecretory neurons from the first step to the final steps of cell type differentiation all vertebrates. [34-36] Nutrient stress and social stress link changes in hydrogen-atom transfer in DNA base pairs in solution from pH and virus-driven energy theft to mutations and all pathology.[37] GnRH secretion links nutrient energy-dependent RNA-directed DNA methylation to the stability of organized genomes RNA-mediated amino acid substitutions. [38]  See also: [39]

[30] Endolysosomal trafficking of viral G protein-coupled receptor functions in innate immunity and control of viral oncogenesis
[31] An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
[32] Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
[33] Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
[34] Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity
[35] Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males,
[36] Stimulus-specific combinatorial functionality of neurona c-fos enhancers
[37]  Allosteric switch regulates protein–protein binding through collective motion
[38] Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus,
[39] Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Conclusion:
Nutrient energy-dependent changes in base pairs link olfaction and c-fos expression from microRNAs to changes in the innate immune system via microRNA flanking sequences and energy-dependent DNA methylation that varies with stress.[40] In mammals, DNA methylation and microRNA activity link gene activation from olfaction to hormone-organized and hormone-activated behaviors via the secretion of hypothalamic gonadotropin releasing hormone (GnRH) and downstream effects on the hypothalamic-pituitary-gonadal (HPG) and HP-adrenal (HPA) axis. [41] One base pair change and a single RNA-mediated amino acid substitution link the stability of viruses to the stability or the instability of metabolic networks and genetic networks in the organized genomes of all living genera. Energy-dependent RNA-mediated amino acid substitutions are inappropriately called mutations. [42-48] Mutations are linked from emergence to evolution by theorists who may not know anything about RNA-mediated biophysically constrained protein folding chemistry. Many theorists seem to know nothing about the conserved molecular mechanisms of healthy longevity and biodiversity in all living genera. See [49]

 [40] Rapid Down-Regulation of Glucocorticoid Gene Expression in the Dentate Gyrus after Acute Stress in vivo: Role of DNA Methylation and microRNA Activity
[41] Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders
[42] Molecular requirements for a pandemic influenza virus: An acid-stable hemagglutinin protein
[43] Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
[44] The SNP rs1625579 in miR-137 gene and risk of schizophrenia in Chinese population: A meta-analysis
[45] COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia
[46] Reduced protein synthesis in schizophrenia patient-derived olfactory cells
[47] Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
[48] Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
[49] Essential role for a novel population of binucleated mammary epithelial cells in lactation

Chemistry

Energy is INFORMATION

Hydrogen atom transfer in DNA base pairs in solution

Photosynthesis

Nutritional epigenetics

base pair substitutions

microRNA flanking sequence

miRNA/mRNA balance

RNA/DNA Methylation

 RNA-mediated amino acid substitutions

Thermodynamic cycles of nutrient-dependent cell type differentiation

Quantum and Classical Physics

innate immune system

de novo creation of nucleic acids

microRNA (miRNA) biogenesis

alternative splicings / pre-mRNA

G protein-coupled receptor gene creation

Molecular Epigenetics

Olfactory receptor genes

 Food odors & Pheromones

 Feedback  loops

 Physiology of Reproduction

 RNA-mediated DNA repair

 Supercoiled DNA

 HHHealthy longevity

Excessive STRESS

 changes in pH

Virus-driven energy theft

ENTROPY

 Altered Brain development

 Altered Learning and memory

 Altered Life history transitions

 Altered Feedback loops

 Altered Reproduction & Aging

 Transgenerational epigenetic inheritance

 Virus-perturbed neural circuitry, odor hedonics, mood, memory, motivation, expressions of affect, cognitive behavioral state, and potentiating responses to other stimuli link energy theft from stress  to mutations and all pathology.

 
Youtube Narrative:
My name is James Kohl. I’m a medical laboratory scientist.
Physicists, chemists, and molecular biologists have linked energy-dependent changes in DNA base pairs from angstroms to ecosystems and healthy longevity in all living genera.
Energy is information. The innate immune system links the information from the epigenetic landscape to the de novo creation of genes and to the physical landscape of supercoiled DNA. Energy-dependent supercoiled DNA protects the organized genomes of all living genera from virus-driven energy theft.
Energy theft causes the accumulation of mutations that leads to all pathology.
In this presentation, I link ecological variation to energy-dependent RNA-mediated events and ecological adaptation. Chemical ecology links the energy-dependent events from nutrient-dependent microRNA flanking sequences to biophysically constrained protein folding chemistry. RNA-mediated protein folding chemistry links the conserved molecular mechanisms of cell type differentiation to all biodiversity.
Simply put, the sun’s biological energy links what organisms eat to cell type differentiation via the physiology of reproduction. Transgenerational epigenetic inheritance links single nucleotide polymorphisms and RNA-mediated amino acid substitutions, such as COMT Val158Met  and BDNF Val66Met to differences in phenotypes. Fixed amino acid substitutions exemplify differences in the morphological and behavioral phenotypes of all living genera.
The color-coded sections of the model include links to cited works that support the brief representations in the text. The center section of the poster attests to the fact that cause and effect is non-linear. Experience-driven changes link energy from physics and chemistry to molecular epigenetics via RNA-mediated protein folding.
That’s how experience links top-down causation from sunlight to molecular epigenetics and the morphological and behavioral phenotypes of all living genera across their lifespan. All life-sustaining interactions must be integrated during life history transitions and successful transitions are manifested as fixed amino acid substitutions.
The sections in yellow, green, and white link the anti-entropic quantised energy of the sun from the virucidal effects of ultraviolet light to healthy longevity. The citations attest to facts about energy-dependent hydrogen-atom transfer in DNA base pairs in solution. Biophysically constrained protein folding chemistry links hydrogen-atom transfer  from angstroms to ecosystems via pH in the context of cell type differentiation.
Facts about measured analytes in addition to pH link RNA-mediated amino acid substitutions to the energy-dependent physiology of reproduction. All facts about cell type differentiation link biophysically constrained protein folding chemistry to pH and protection from virus-driven entropy.
For contrast, everything in red links excessive nutrient stress and/or social stress from changes in pH and virus-driven energy theft to mutations and all pathology.  If everything in yellow, green, white, and red is not considered in the context of healthy longevity compared to virus-driven pathology, researchers and clinicians are left with theories.
In the context of genetics and genomics all theories are equally irrelevant compared to the facts that link angstroms to ecosystems. Virtually all theories ignore Schrodinger’s claims about the anti-entropic energy of sunlight. And most theories also ignore Dobzhansky’s claims about nutrient-dependent amino acid substitutions and biodiversity.
Facts link chemical ecology from quantum physics to olfaction and facts link the immune system and the sense of smell. The sense of smell is linked from symptoms of neurodegenerative diseases like Alzheimer’s to the hard problem of consciousness. The sense of smell also links the bull sperm microRNAome to microRNAs in human breast milk that are essential to brain development. Brain development occurs in the context of fixation of RNA-mediated amino acid substitutions that stabilize organized genomes.
In the age of Precision Medicine and problems like energy theft by the Zika virus, genomics and genetics must be linked by facts about cell type differentiation. What is known about  Microbiomes, Metabolism, Mitochondria and Molecular diagnostics links this energy-dependent systems approach from the innate immune system to Precision Medicine.  All phenotypic expression starts with the energy-dependent creation of nucleic acids and the creation of G protein-coupled receptors. The receptors allow nutrients to enter cells.
Receptor-mediated gene expression links c-fos in the gonadotropin releasing hormone neurosecretory neurons of all mammals from the first step to the final step of cell type differentiation in all vertebrates. That fact has been known for more than two decades.
MicroRNA flanking sequences link nutrient energy-dependent RNA-directed DNA methylation and histone acetylation to the stability of organized genomes via RNA-mediated amino acid substitutions in all genera. That fact has been known for more than a year.
Conclusion:
Nutrient energy-dependent changes link olfaction and c-fos expression from microRNAs to changes in the innate immune system via microRNA flanking sequences and energy-dependent DNA methylation that varies with stress. In mammals, DNA methylation and microRNA activity link gene activation from olfaction to hormone-organized and hormone-activated behaviors via the secretion of hypothalamic GnRH and downstream effects on the HPG and HPA axis.
One base pair change and a single RNA-mediated amino acid substitution link the stability of viruses to the stability of metabolic networks and genetic networks in the organized genomes of all living genera. Unfortunately, energy-dependent RNA-mediated amino acid substitutions are frequently called beneficial mutations by theorists.
Definitions of mutations and assumptions about what mutations do has biased biodiversity research and patient outcomes since de Vries defined “mutation” in 1904.

amino acid homeostasis

RNA splicing, genetic variation, and disease

More than 600 blog posts on this domain attest to the fact that nutrient energy-dependent RNA-mediated cell type differentiation is the key to healthy longevity in all living genera. Only those who have missed the accurate representations of others who have linked angstroms to ecosystems via the innate immune system, the physiology of reproduction, and supercoiled DNA will continue to place RNA splicing into the context of disease, without acknowledging that RNA splicing is the key to Precision Medicine.

RNA splicing is a primary link between genetic variation and disease

Excerpt:

RNA splicing links genetics to disease

Many genetic variants associated with disease have no apparent effect on any specific protein coding sequence. Li et al. systematically analyzed the effects of DNA variants on the main steps of gene regulation, from the chromatin state through protein function. One-third of expression quantitative train loci (QTLs) are mediated through transcriptional processes, not chromatin. Splice QTLs and expression QTLs are about comparable in their complex disease risk. Posttranscriptional mechanisms therefore play a large role in translating genotype to phenotype.

Abstract:

Noncoding variants play a central role in the genetics of complex traits, but we still lack a full understanding of the molecular pathways through which they act. We quantified the contribution of cis-acting genetic effects at all major stages of gene regulation from chromatin to proteins, in Yoruba lymphoblastoid cell lines (LCLs). About ~65% of expression quantitative trait loci (eQTLs) have primary effects on chromatin, whereas the remaining eQTLs are enriched in transcribed regions. Using a novel method, we also detected 2893 splicing QTLs, most of which have little or no effect on gene-level expression. These splicing QTLs are major contributors to complex traits, roughly on a par with variants that affect gene expression levels. Our study provides a comprehensive view of the mechanisms linking genetic variation to variation in human gene regulation.

My comment: MicroRNA flanking sequences link energy-dependent changes in base pairs from hydrogen-atom transfer to the RNA-mediated amino acid substitutions that differentiate the cell types of all living genera. The microRNA/messenger RNA balance links metabolic networks to genetic networks via the innate immune system, the energy-dependent physiology of reproduction and supercoiled DNA. The supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.
Substitution of ‘expression quantitative trait loci (eQTLs)’ in attempts to link RNA splicing only to disease is disingenuous and borders on the absurd given the publication history of Yoav Gilad and/or Jonathan Pritchard. Both of them should know better than to keep trying to support neo-Darwinian nonsense with wordplay in the context of what they portray as new revelations.
See: Epigenetic modifications are associated with inter-species gene expression variation in primates
See: Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency

rp_levels-of-organization.jpg

Molecular Diagnostics: What is unprotected life (4)

Pado, a fluorescent protein with proton channel activity can optically monitor membrane potential, intracellular pH, and map gap junctions

Excerpt:

Nature has developed a vast array of voltage-responsive proteins. To improve our ability to optimize the voltage sensitivity, kinetics, and signal size of GEVIs, an in silico search strategy was developed to identify potential voltage-sensing proteins since new genomes are routinely being sequenced. The use of a conserved amino acid motif in the second transmembrane segment of the voltage-sensing phosphatase (VSP) gene family enabled the identification of distantly related voltage-sensing proteins including voltage-gated calcium channels (Cav), voltage-gated sodium channels (Nav), voltage-gated potassium channels (Kv), and voltage-gated proton channels (Hv).

My comment: Their claim about what “Nature” somehow developed can be compared to what obviously must occur. First, genes must be created.  The de novo creation of G protein coupled receptors, such as olfactory receptor genes,  links energy-dependent changes in base pairs from angstroms to ecosystems via nutrient-dependent RNA-directed DNA methylation and histone acetylation in all living genera. For example, de novo gene creation links the conserved amino acid substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide to the nutrient-dependent pheromone-controlled physiology of reproduction in all vertebrates.

Their conclusion:

…the ability to shift the Hv activity to more negative potentials by increasing the external pH of the bath solution offers researchers a straightforward way to control the internal pH with an immediate, optical feedback.

My conclusion: The link from the sun’s anti-entropic virucidal biological energy and top-down causation will lead to rediscovery of the equally obvious link from virus-driven energy theft to all pathology. The energy theft is clearly linked from lower intracellular pH, which facilitates the replication of viruses in different cell types of different tissues, such as blood. They need only place their current findings into the context of what is known to those who already linked energy-dependent hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated DNA repair and all biodiversity via microRNA flanking sequences, amino acid substitutions, adhesion proteins, and supercoiled DNA.

Alternatively, they could place their findings into the context of what is known about the weekend evolution of the bacterial flagellum in P. fluorescens. In either case, it becomes obvious that virus-driven energy theft causes all mutations and all pathology. That fact will not become less obvious.

For example, a few months ago I suggested to a student in Dr. Rosenberg’s lab at Baylor that virus-driven energy theft could be linked to all pathology in the context of Richard Lenski’s experiments. The ability to measure a virus-driven change in the intracellular pH of E. coli would link a virus-driven change in the fluorescence of P. fluorescens. The virus-driven change in two microbes would be the ultimate neo-Darwinian evolutionary theory killer. It would show that weekend evolution of the bacterial flagellum was biophysically constrained by nutrient-dependent and pheromone-controlled RNA-mediated DNA repair and the physiology of reproduction.