What energy source do proteins prefer?

By: James V. Kohl | Published on: May 5, 2017

(click to enlarge)

Quantized energy as information is the anti-entropic virucidal source of healthy longevity. All pathology is caused by virus-driven energy theft.
Impact of cytosine methylation on DNA binding specificities of human transcription factors

…many developmentally important proteins display preference for mCpG-containing sequences.

How do proteins display a preference for anything except food and codon optimality?

Natural selection for quantized food energy-dependent codon optimality links the structure and function of supercoiled DNA to protection from virus-driven energy theft.

That fact was obfuscated in this report: Scientists reveal how epigenetic changes in DNA are interpreted

…some ‘master’ regulatory proteins can activate regions of the genome that are normally inactive due to epigenetic changes. Their findings contribute to a better understanding of gene regulation, embryonic development and the processes leading to diseases such as cancer.

Don’t miss the claim that links epigenetic changes from normally inactive genes to cancer. See also the section on molecular epigenetics from this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes…

If you were an inherited protein in an organized genome, would you prefer to protect yourself from virus-driven energy theft? If the transgenerational epigenetic inheritance of virus-damaged DNA left you, an organism will a debilitating or deadly form of protein-based pathology, would you consider an attempt to eliminate the virus? How could you do that?

Most people are taught to believe that they have no choice but to accept the virus-caused pathology. They do not know that the way to eliminate the pathology is energy-dependent. That’s what they will learn by playing the game Cytosis.

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

When not enough food energy as quantized information is available to the cell, the virus-driven degradation of messenger RNA prevents the DNA code from correctly building more proteins that are found as enzymes, hormones, and receptors. For example, without the energy-dependent de novo creation of more G protein-coupled receptors, the ability of all cell types that contribute to the physiology of pheromone-controlled reproduction is compromised.
See: Feedback loops link odor and pheromone signaling with reproduction

These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

Even in bacteria, the feedback loops link quantized energy as information from what organisms eat to the pheromone-controlled physiology of reproduction. The fact that achiral glycine in position 6 of the GnRH decapeptide is linked to the stability of all organized genomes in all vertebrates from what is known about invertebrates suggest that mutation-driven evolution is the most ridiculous manifestation of human ignorance that could be imagined by serious scientists who have linked energy-dependent changes from angstroms to ecosystems via supercoiled DNA.
For comparison, the virus-driven degradation of messenger RNA links mutations to loss of function and all pathology in all genera via the transgenerational epigenetic inheritance of biophysically constrained viral latency. In cases where viral latency is not biophysically constrained or when stress links the lack of nutrients and/or ongoing social stress to the virus-driven degradation of messenger RNA, organisms die. The death rate is determined by the nutrient energy-dependent ability of organisms to ecological adapt and reproduce.

The technicalities of accurate representations of biologically-based interactions among the birds and the bees and all other living genera have been established. The sun’s anti-entropic virucidal energy links hydrogen-atom transfer in DNA base pairs in solution to nutrient energy-dependent RNA-mediated DNA repair via protein folding chemistry in the context of amino acid substitutions in supercoiled DNA. Simply put, energy as information is linked to all biodiversity via the physiology of reproduction.

But, as Roger Penrose once asked: 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?

All ecological models that link what organisms eat to biophysically constrained biologically-based RNA-mediated protein folding chemistry and the amino acid substitutions have been validated by all serious scientists who have learned that cell type differentiation is nutrient energy-dependent in all cell types in all individuals of all living genera.

For comparison, all theories that fail to link what organism eat to the ecological adaptations manifested in differences in morphological and behavioral diversity havce been removed from any further consideration whatsoever, except for consideration by pseudoscientists.

See for example:

James V. Kohl:

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.

7/25/13
Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

“This study clearly shows that a virus that is not clinically symptomatic can still do bad things to the immune system and set the stage for an autoimmune disorder, and for celiac disease in particular,” Jabri says. “However, the specific virus and its genes, the interaction between the microbe and the host, and the health status of the host are all going to matter as well.”

Pre-order here: Cytosis: A Cell Biology Game

Cytosis is a worker placement game that takes place inside a Human Cell! Players utilize the organelles within a cell to collect cellular resources such as mRNA from the Nucleus, Lipids from the Smooth E.R., ATP from the Mitochondria, etc. and score points when they use these resources to complete Hormones, Receptors or Enzymes! 2 to 5 Players, Ages 10 +, Plays in 50 to 75 mins – (Shipping Aug/Sept 2017 – US, EU, CA & AU will ship from WITHIN their country / region)

The facts about how nutrient energy-dependent biophysically constrained biologically-based cause and effect controls viral latency via the physiology of pheromone-controlled reproduction have been detailed in the extant peer-reviewed literature during the past century. Most people wonder why they have not been taught to believe in the facts. Simply put, there are too many pseudoscientists who want people to believe in the pseudoscientific nonsense touted by neo-Darwinian theorists, and too few who have joined the serious scientists who are: Combating Evolution to Fight Disease
For a recent example of those who are fighting to keep disease, see these comments, which were removed from an attempt to discuss ecological models of top-down causation and biophysically constrained RNA-mediated healthy longevity for comparison to virus-driven pathology.
See also: Your comment on ‘No, epigenetics and environmental responsiveness don’t undermine Darwinian evolution’ has been removed.

What is life when it is not protected from virus driven entropy https://www.youtube.com/watch?v=K35THJtlhoE

Published on 30 Mar 2016

Poster: The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

What experimental evidence of biologically-based cause and effect suggests that it might take a thousand generations? See for comparison: Transgenerational transmission of environmental information in C. elegans https://science.sciencemag.org/content/356/6335/320

Clearly, others have placed the facts about transgenerational epigenetic inheritance into the context of chromosomal inheritance via energy-dependent endogenous RNA interference across life-history transitions. See: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans https://www.genetics.org/content/early/2017/01/25/genetics.116.195438?papetoc

Is there a model organism that you would like to compared to Caenorhabditis elegans, or do you ignore it and others that do not support theories about mutation-driven evolution?

As a medical laboratory scientist who linked the anti-entropic virucidal energy of sunlight to all biodiversity via the potential of hydrogen (pH), I viewed people like you with suspicion.

If you cannot link the creation of energy to all healthy longevity via the physiology of reproduction in all living genera, you cannot link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology.

But, you earned the title of pathologist, anyway. Congratulations! You show others where demanding their respect for your credentials will lead them. To the grave via evolutionary processes!

You claim to be a “Retired physician-scientist-academic; active tree-grower.”

Do you realize that the production of taxol from the Pacific Yew Tree links the physiology of reproduction in soil bacteria to the treatment of cancer in humans via the conserved molecular mechanisms of energy-dependent cell type differentiation I have detailed?

Simply put, taxol is a link from the anti-entropic virucidal effects of ultraviolet light in plants to changes in the microRNA/messenger RNA balance in all living genera. That fact allowed me to link microRNAs from chirality to autophagy and inhibition of apoptosis via signal transduction and activation of transcription in vascular smooth muscle cells and all other cell types.