Amino acid modification FA_Epigenetics_Table1

Eutrophication and phosphorylated biodiversity

In Chinese philosophy, yin and yang (also yinyang or yin yang, 陰陽 yīnyáng “dark–bright”) describe how seemingly opposite or contrary forces may actually be complementary, interconnected, and interdependent in the natural world, and how they may give rise to each other as they interrelate to one another.

Last night I dreamed that someone added color to this symbol and represented it as a spinning disk (in a publication from the Nature publishing group).  The specifics of the dream helped me to complete this accurate representation of biophysically constrained viral latency.
See for comparison: Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions
Reported as: Scientists find potential ‘missing link’ in chemistry that led to life on Earth

“It reminds me of the Fairy Godmother in Cinderella, who waves a wand and ‘poof,’ ‘poof,’ ‘poof,’ everything simple is transformed into something more complex and interesting,” Krishnamurthy said.

In the context of energy-dependent Biblical Creation or Chinese philosophy, the speed of light on contact with water links the Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism to a cleansing Flood of Biblical proportions. After-the-Flood, eutrophication probably stimulated the growth of aquatic plant life.
That speculation helps to explain the rapid re-population of the Earth via the “the process by which a body of water becomes enriched in dissolved nutrients (such as phosphates)…
For comparison, Krishnamurthy’s ‘poof,’ ‘poof,’ ‘poof’ theory of how increasing complexity initially arose twice — before and after the extinction of many different species, will always be placed into the context of a “Fairy Tales.”  Serious scientists can use what is known about biophysically constrained viral latency to link eutrophication from phosphorylation and oligomerization to what has been referred to as the Cambrian Explosion — the rapid diversification of most major living animal body plans (phyla) in the fossil record.
However, serious scientists can also link the facts about eutrophication, phosphorylation and oligomerization to all food energy-dependent pheromone-controlled biodiversity on Earth via the weekend resurrection of the bacterial flagellum.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
See also: A communal catalogue reveals Earth’s multiscale microbial diversity reported as: Mapping the Microbiome of…Everything
The funding includes money from the John Templeton Foundation, which in the past seems to have ensured that all results would be reported in the context of randomness and evolution. But, even with millions of dollars spent trying to support that dogma, efforts are doomed to fail.
Eugene Koonin said it best: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
That fact is readily linked to the ‘poof,’ ‘poof,’ ‘poof’ theory of how increasing complexity arose, because the theory does not include any information on how the virus-driven degradation of messenger RNA has since been linked to all pathology.
Indeed, the fossil record may be the best example of how the viral hecatomb links the virus-driven degradation of messenger RNA to calcification of tissues and to ossification of the tissue that neo-Darwinian theorists claim is evidence that our ancestors evolved into us. Their ridiculous claims have not been supported by any experimental evidence of biophysically constrained biologically-based top-down causation.
If serious scientists allow the ‘poof,’ ‘poof,’ ‘poof’ theory, the pseudoscientists may continue to prevail against all odds. In the world of science, their theories would never be considered. Instead, it seems that biologically uninformed science idiots can suggest anything.When they continue to repeat their suggestions, the uninformed masses may believe them — rather than attempt to learn anything about eutrophication, phosphorylation, or food energy-dependent pheromone-controlled feedback loops, ecological adaptations, and biodiversity.
For instance, in the context of energy-dependent top-down causation, physics and chemistry can be linked from molecular epigenetics to supercoiled DNA in organized genomes via Histone methylation and amino acid substitutions.​​

Lysine methylation of H3 and H4 is implicated in both transcriptional activation and repression depending on the methylation site, while arginine methylation promotes transcriptional activation1.

Methylation is food energy-dependent and RNA-mediated in species from microbes to humans. That fact and all facts about supercoiled DNA, which prevents the virus-driven degradation of messenger RNA, can be placed into the following two representations of cause and effect — or represented as a spinning yin-yang symbol.
The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.
See this black and white representation of energy-dependent biodiversity.
See for comparison, this 3-D imagery:

My comment on Inching toward the 3D genome has not been removed.

Re: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”
Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.
Life is physics and chemistry and communication —
The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and the conserved molecular mechanisms of communication in species from microbes to man.
Until nutrient-dependent protein folding is linked via the conserved molecular mechanisms of amino acid substitutions and pheromone-controlled DNA stability in organized genomes, which links the epigenetic landscape to the physical landscape of DNA, researchers must take a piece-meal approach to integrating the requirements for life and successful life history transitions — despite the fact that life history transitions have been detailed in the context of the honeybee model organism. See: Honey bees as a model for understanding mechanisms of life history transitions

Gene Robinson is the senior author of this report on phosphorylation in the honeybee model organism. See: Socially responsive effects of brain oxidative metabolism on aggression

Despite ongoing high energetic demands, brains do not always use glucose and oxygen in a ratio that produces maximal ATP through oxidative phosphorylation. In some cases glucose consumption exceeds oxygen use despite adequate oxygen availability, a phenomenon known as aerobic glycolysis. Although metabolic plasticity seems essential for normal cognition, studying its functional significance has been challenging because few experimental systems link brain metabolic patterns to distinct behavioral states. Our recent transcriptomic analysis established a correlation between aggression and decreased whole-brain oxidative phosphorylation activity in the honey bee (Apis mellifera), suggesting that brain metabolic plasticity may modulate this naturally occurring behavior.

Elekonich and Robinson (2000) cited our 1996 Hormones and Behavior review:

The development of species-typical and sex-specific adult behaviors in vertebrate animals is influenced by gonadal steroid hormones, non-gonadal hormones, and non-hormonal factors working on the underlying neural circuitry (reviewed in Diamond et al., 1996; Kawata, 1995; Schlinger, 1998).

The facts that link the creation of sunlight from the creation of ATP to the creation of RNA have been known since 1964.
See: 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.

The facts about Honey bees as a model for understanding mechanisms of life history transitions have been ignored.
See also: Feedback loops link odor and pheromone signaling with reproduction
What can be said about the amount of willful ignorance that has been displayed by theorists, since “What is Life?” was published in 1944?

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

In the reprint edition, Roger Penrose (8 August 1991) wrote:

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?

See also my comments on: Methyldynamics behind virtually all pathologies?

Vast Complexity of Chromatin 3D Shapes
N6-methyladenosine marks primary microRNAs for processing
Our 1996 Hormones and Behavior review linked pre-mRNAs (microRNAs) to RNA-mediated cell type differentiation in species from yeasts to mammals via what was known about the conserved molecular mechanisms of nutrient-dependent RNA-mediated protein folding and the pheromone-controlled physiology of reproduction.
From Fertilization to Adult Sexual Behavior
See also:
Unraveling the secrets of RNA-mediated events

It is difficult for me, as a medical laboratory scientist, to understand how others who are involved in diagnostic medicine seem to have accepted ridiculous theories that cannot be linked to results reported from testing in the medical laboratory.
See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels

Mutations in the period (per) gene of Drosophila melanogaster affect both circadian and ultradian rhythms. Levels of per gene product undergo circadian oscillation, and it is now shown that there is an underlying oscillation in the level of per RNA. The observations indicate that the cycling of per-encoded protein could result from per RNA cycling, and that there is a feedback loop through which the activity of per-encoded protein causes cycling of its own RNA.

What have other medical laboratory scientists and medical professionals been taught to believe about the underlying oscillation that have since been linked from cryo-EM to all energy-dependent biophysically constrained viral latency? Is there any model of biologically-based cause and effect that links anything except food energy-dependent feedback loops from the physiology of pheromone-controlled reproduction to all biodiversity? If not, help stop the nonsense.
Play the cell biology game: Cytosis: A Cell Biology Board Game

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

Stop playing the games of theorists.

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