Evolutionary theories of epigenetic drift (3)

By: James V. Kohl | Published on: September 21, 2017

Researchers unite in quest for ‘standard model’ of the brain

Modelled on big physics projects, the International Brain Lab will bring together some of the world’s pre-eminent neuroscientists to probe a single behaviour.


The IBL will aim to generate and test unifying theories about how the brain encodes and computes information – seeking to come up with the equivalent of physicists’ standard model.

See also: microRNA foraging

Most serious scientists know that ecological adaptation is food energy-dependent. Some of them seem vaguely aware that quantum physics and classical physics must be linked from the creation of light energy as information to chemistry and to biology. If not, models of top-down causation cannot be linked from foraging behavior and the physiology of pheromone-controlled reproduction to survival of the species.
For example, the weekend resurrection of the bacterial flagellum is an energy-dependent example of how “life finds a way” in P. fluorescens, which fluoresces with exposure to ultraviolet (UV) light. If the species could not collectively regain the nutrient energy-dependent pheromone-controlled ability to forage and find food, the species would become extinct. Instead, these researchers reported it found a way:
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
They inadvertently linked the conserved molecular mechanisms of light energy as information-dependent survival of the species from microbes to mammals via the ability of sperm cells to find the ova. The ability to find the ova is compromised by virus-driven energy theft.
See: The Breadth of Viruses in Human Semen
See for comparison: A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success
See also: The zinc spark is an inorganic signature of human egg activation
The speed of light on contact with water has been linked from the weekend resurrection of the bacterial flagellum to to zinc spark as an indicator of energy-dependent pheromone-controlled reproduction in species from microbes to humans via chromosomal inheritance.
The virus-driven energy theft of quantized energy has been linked to all pathology.
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
In that context I will compare the works of Justin A. Shapiro to James A. Shapiro in an attempt to show how the despicable behavior of neo-Darwinian theorists has caused the unnecessary suffering and premature death of millions.
James A. Shapiro will be used as an example of someone who knows he has been caught touting ridiculous theories. He is trying to save face by refuting neo-Darwinian theories without his supporters knowing it.
See (Justin A. Shapiro and TA Wencewicz, 2017): Structure-function studies of acinetobactin analogs

Pathogenic Acinetobacter baumannii excrete the siderophore pre-acinetobactin as an iron-scavenging virulence factor. Pre-acinetobactin is a 2,3-dihydroxy-phenyl oxazoline that undergoes pH-dependent isomerization to the isooxazolidinone form acinetobactin in order to expand the pH range for iron acquisition by A. baumannii. In this study we establish important structure-function relationships for the kinetics of isomerization, iron(iii) binding, and siderophore utilization by A. baumannii. We showed that electronic properties of the phenyl oxazoline influence isomerization kinetics and iron(iii) binding. We found that iron(iii) chelation was directly correlated with A. baumannii utilization. Our studies provide important structural and mechanistic insight for understanding how pathogenic A. baumannii uses pre-acinetobactin as a 2-for-1 iron-scavenging siderophore virulence factor.

The structural and mechanistic insight that leads to the understanding how pathogenic A. baumannii uses scavenges the iron the stabilizes the organized genomes of all living genera is linked from bacteriophages to the virulence of viruses via the ability of the bacteriophage to substitute at least one food energy amino acid substitution that organized its genome at the expense of its host.
That fact has been placed into a model of the stability of conformational states that underlie energy-dependent systems biology at the nucleotide level.
See:  Model-based design of RNA hybridization networks implemented in living cells

These networks are ultimately coupled to the control of gene expression. We relied on a thermodynamic model of the different stable conformational states underlying this system at the nucleotide level.

Reported as: Cells programmed like computers to fight disease

Cells can be programmed like a computer to fight cancer, influenza, and other serious conditions — thanks to a breakthrough in synthetic biology.

The synthetic biology links natural selection of energy-dependent codon optimality programs the cells to fight against all pathology in all living genera. In mammals, for example, see (1994) [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]. — in Russian

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See also: (1996) Cytogenetic Effect of Pheromones on Bone Marrow Cells of Male House Mice Mus musculus L. — in Russian

Effects of volatile components of the urine (VCU) of mature male and female CBA/LacStoRap mice on proliferating bone marrow cells in young females of the same line were analyzed. To estimate the effects of VCU, cytogenetic analysis of mitotic disturbances in anaphase-telophase cells was performed. The overall frequency of mitotic disturbances such as chromosome bridges, fragments, retarded chromosomes, and multiple rearrangements was assessed. The overall frequency of mitotic disturbances in young female mice treated with VCU from mature females for 2 h significantly increased 24 h after exposure. The spectrum of mitotic disturbances was also affected by the VCU treatment. After exposure to VCU from mature males, no significant variation of parameters analyzed was detected in young female mice. The possible mechanisms and role of specific effects of VCU from animals of different sexes on young female house mice are discussed.

Clearly, the physiology of pheromone-controlled reproduction biophysically constrains viral latency at the level of germ cells and somatic cells in mammals. That fact links the physiology of pheromone-controlled reproduction in insects from bacteria to mammals, but not within the ridiculous context of any evolutionary origins of top-down causation or biodivesity.
Ask a serious scientist if any experimental evidence of biologically-based cause and effect supports the claim that insect pheromones evolved.
See: Evolutionary origin of insect pheromones

Many studies have investigated cuticular hydrocarbons that have evolved a communicative function, although examples of pheromones exist that have arisen from defensive secretions, hormones or dietary compounds. We summarize and discuss the selective pressures shaping the pheromone during signal evolution.

No evidence of biophysically constrained signal transduction/transmission suggests that signals evolved. All experimental evidence suggests that food odors and pheromones biophysically constrain biomolecular interactions.
See: Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Nucleotides, amino acids, and sugars are chiral; namely, they do not possess mirror plane symmetry but have symmetry like a “hand” (cheir in Greek).

Glycine is an achiral amino acid. The substitution of the achiral amino acid, glycine in position 6 of the GnRH decapeptide is the beginning of the end to all theoretical pseudoscientific nonsense.
The substitution of glycine in position 6 links energy-dependent changes in chirality from autophagy to the protection of all organized genome is vertebrates by way of these three published works, but two out of three suggest that the energy-dependent pheromone-controlled physiology of reproduction that is required to link RNA-mediated amino acid substitutions from fixation in supercoiled DNA to the organized genomes of all living genera occurs in the context of evolution:
Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity
Handbook of Biologically Active Peptides (2013)
Chapter 106 GnRH (LHRH) Page 794

Figure 2 indicates that substitution at position 6 with glycine or any other D-amino acid stabilizes the folded conformation and increases binding affinity and decreases metabolic clearance. This feature is incorporated in all agonist and antagonist analogs.

Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

The discovery of the fact that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid is, in my opinion, important, fascinating and beautiful.

See also: Copying nature’s lock-and-key system could improve rapid medical diagnostics

Receptors recognise molecules with particular shapes and bind to them in a lock-and-key mechanism.

The receptors do not create themselves and the de novo creation of all receptors is energy-dependent. The virus-driven degradation of messenger RNA causes the loss of function in receptors and the loss of function links virus-driven energy theft from mutations to all pathology.

See also: Scientists find way to remove ‘noise’ from big data in metabolomics study

“It turns out that more than 90 percent of the signals we see in E. coli data are essentially noise,” Mahieu said. “This greatly reduces the number of unknown metabolites that we thought we were detecting.”

“I think this is sort of a wake-up call, a reality check if you will, on what metabolomics suggests about the size of the metabolome,” Patti said. “I believe it is a good thing. It means we’re a lot closer to understanding metabolism than we probably thought we were.”

This is the kind of information that would otherwise link the creation of energy as information to all biodiversity via the physiology of reproduction and feedback loops that link odors and pheromones to biophysically constrained viral latency. Instead, they make no claims about how energy as information was linked from metabolism to the pheromone-controlled biodiversity of E. coli, or to the weekend resurrection of the bacterial flagellum in P. fluorescens. There is also no mention of how increasing organismal complexity has been constrained by the physiology of reproduction in all species.

See for comparison: Complex life evolved out of the chance coupling of small molecules

“Something needed to happen for molecules to reproduce, and thereby starting life as we know it. That something turned out to be the simple ligation of a set of small molecules, billions of years ago,” says Durand.

Conformational landscape of isolated capped amino acids: on the nature of non-covalent interactions

This is what had to happen before the metabolism of food was linked to the pheromone-controlled physiology of reproduction and biophysically constrained viral latency in all living genera. It’s the same thing that has to happen when the weekend resurrection of the bacterial flagellum of P. fluorescens occurs.

Clearly, life finds a way, but it finds it too fast for pseudoscientists to continue to claim that it evolved after energy emerged from nothing. https://www.youtube.com/watch?v=gE8fKOozG40

There is also this perspective: https://3c1703fe8d.site.internapcdn.net/newman/csz/news/800/2017/onebillionsu.png A change in the electron caused it to abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. The electron, as always, ejected its own photon, which was jarred loose by the energy of the incoming photons. But then, the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

That perspective links the biophysically constrained energy of hydrogen atoms to the uranium isotopes that other serious scientists have linked from bacterial metabolism to all pheromone-controlled physiology of reproduction in species from microbes to humans.

If you leave out the fact that energy is required for all interactions that link quantum physics to quantum souls, anything could have kickstarted life. But see: https://www.kickstarter.com/projects/geniusgames/cytosis-a-cell-biology-board-game/?ref=kicktraq

This is a kickstarter.com project. What do you think happened after life was kickstarted to prevent the virus-driven degradation of messenger RNA that serious scientists have linked to all pathology?

Thanks for the link to the Fullerene-Amino Acid Interactions paper from 2008. What was your point? See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/

Brain Bugs Neuropharmacologist John Cryan of University College of Cork in Ireland explains the links between the microbiome and the central nervous system.

John Cryan sneaks up from behind and delivers the details of my model in the same month as the cell biology game Cytosis is scheduled to be delivered to those who pre-ordered it.
They will be among the first to learn that the virus-driven degradation of messenger RNA causes all pathology, which means it is time for Cryan and others to start telling the truth about what has been known to serious scientists for several decades.
See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems or this 7 minute-long video representation.

How Microbes May Influence Our Behavior Researchers are piecing together the links between the gut microbiome and mental health.

…in a group of adults with major depression. They found that one-third of the participants reported a significant improvement in symptoms after 12 weeks on the diet…

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
All serious scientists know that the virus-driven degradation of messenger RNA links mutations to all pathology. John Cryan should already have revealed that fact to theorists, but he may be unwilling to refute all their pseudoscientific nonsense about the emergence of energy and the mutation-driven evolution of all biodiversity.
Thankfully, McEwen et al., (1964) did it in Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

In the early 1990’s Bruce McEwen told me that my model could not be validated unless I started with energy-dependent gene activation (e.g., c-fos expression in GnRH neurosecretory neurons). I had already linked the pheromone-controlled physiology of reproduction to all biodiversity, and he continued to link the epigenetic effects of stress from changes in hormones to the affect of the hormones on behavior.


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