From nitrogen atoms to ecosystems in all living genera

By: James V. Kohl | Published on: December 27, 2017

(click to enlarge)

Summary: The “tiny machines” that “massacre viruses” link the creation of the anti-entropic virucidal energy of sunlight to the pheromone-controlled physiology of reproduction in all living genera via the nitrogen-dependent weekend resurrection of the bacterial flagellum in P. fluorescens.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

The nitrogen-dependent weekend resurrection of the bacterial flagellum was placed into the context of Evolutionary Rewiring. This comment appears in the Editor’s Summary of the article: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway.

The claim that an evolutionarily related regulator normally controls nitrogen uptake, which controls flagella biosynthesis has not been supported by experimental evidence of biologically-based cause and effect. That fact may explain why a a caveat was expressed in the context of the absurdity about the de novo origination of new functions in nature. Simply put, the de novo origination of new functions in nature was reported to be an understandable adaptive process. The energy-dependent adaptive process has been detailed at every level of examination. There is no such thing as de novo origination of new functions in nature.
See: Dicer uses distinct modules for recognizing dsRNA termini

…blunt dsRNA is locally unwound and threaded through the helicase domain in an ATP-dependent manner. Our studies reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for discovery of helicase-dependent functions in other Dicers.

Reported as: Meet the tiny machines in cells that massacre viruses

For the first time, this study shows that this single machine processes dsRNA from viruses using a completely different mechanism.

All molecular mechanisms are energy-dependent. In the context of genotypes and phenotypes all serious scientists have traced, in real time, the food energy-dependent pheromone-controlled rewiring of gene networks that links the creation of nitrogen from energy-dependent changes in base pairs to fixation of amino acid substitutions. The amino acid substitutions link nitrogen atoms in modified/phosphorylated NtrC′ to ecosystems in all living genera.
The energy-dependent change in base pairs links the EBP gene ntrC to the creation of a novel regulatory function in the context of a highly repeatable two-step pathway. The two-step pathway is obviously food energy-dependent and pheromone-controlled in the context of the physiology of reproduction in P. fluorescens, and the same food energy-dependent pheromone-controlled adaptations reportedly often recur in independent lineages.
The overwhelming ignorance of theorists who claim that energy-dependent changes in adaptive processes link creation to evolution can be view in the context of this pseudoscientific nonsense:
A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

The creation of an energy-dependent adaptive process has repeatedly been placed into the ridiculous context of the evolution of proteins by biologically uninformed theorists. The theorists probably don’t know any more than the biologically uninformed science idiots who publish papers about protein evolution.
The universal trend (above) requires the creation of energy and the adaptive process links biophysically constrained ecological variation from changes in nitrogen atoms to ecological adaptations in all living genera. That fact has been clear to all serious scientists for more than a decade.
See: Optimal nitrogen-to-phosphorus stoichiometry of phytoplankton (2004)

Competitive equilibrium favours greater allocation to P-poor resource-acquisition machinery and therefore a higher N:P ratio; exponential growth favours greater allocation to P-rich assembly machinery and therefore a lower N:P ratio. P-limited environments favour slightly less allocation to assembly than N-limited or light-limited environments. The model predicts that optimal N:P ratios will vary from 8.2 to 45.0, depending on the ecological conditions.

See also: The Strange Link Between the Human Mind and Quantum Physics (2017) by Philip Ball

The phosphorus nuclei have a quantum property called spin, which makes them rather like little magnets with poles pointing in particular directions. In an entangled state, the spin of one phosphorus nucleus depends on that of the other.

The fact that the entangled state of two phosphorous nuclei links ecological variation to food energy-dependent pheromone-controlled ecological adaptations in all living genera is missing from this 2017 article by Philip Ball:
Quantum common sense

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

How does a science journalist turn the requirement for the creation of an environment full of stuff such as subatomic particles into something that involves a Universe that is always looking. Why don’t others ask him to explain himself?
See for comparison: Proteins in shark teeth could hint at what they eat

1) They found the ratio of nitrogen isotopes were very similar in muscle and teeth for all amino acids except for one – phenylalanine. Phenylalanine is an amino acid that, through biological pathways, gets converted into certain neurotransmitters like dopamine and epinephrine.

All biological pathways are energy-dependent and microRNA-mediated in the context of the fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all living genera.

2) …their research shows that nitrogen isotopes associated with amino acids in teeth can be used to understand a shark’s diet and position in the food web.

The proteins in shark teeth link the nitrogen atom-dependent creation of enzymes from the weekend resurrection of the bacterial flagellum in P. fluorescens to the pheromone-controlled physiology of all genera, which protect organized genomes from the virus-driven degradation of messenger RNA. For examples of how CYP enyzmes and pathways are linked to the stability of organized genomes see: Alpha Genomix profiles. Download a sample report
The need for statins and the response to statins is predicted by Arg112Cys and Cys158Arg, which are food energy-dependent pheromone-controlled RNA-mediated amino acid substitutions. Both substitutions are reported to be mutated and linked from a defect in apolipoprotein E (APOE) to the structure lipoprotein particles that play critical roles in blood lipid metabolism and transport of food energy-dependent microRNAs to all cell types in humans.
See for comparison: Cell-specific and region-specific transcriptomics in the multiple sclerosis model: Focus on astrocytes

Significance

Molecular mechanisms underlying distinct disabilities during neurological diseases may differ based on the neurological pathway involved. Multiple sclerosis (MS) is multifocal, characterized by distinct disabilities affecting walking, vision, cognition, and fatigue. Neuroprotective treatments tailored for each disability may be more effective than nonspecific treatments aiming to reduce a composite of disabilities in clinical trials. Here, we use the MS model to apply a cell-specific and region-specific gene expression approach to discover targets in distinct neuroanatomic regions. Altered cholesterol synthesis gene expression in astrocytes in spinal cord and optic nerve was identified as a potential target for walking and visual disabilities, respectively. This disability-specific discovery approach represents a strategy for finding neuroprotective treatments for multifocal neurodegenerative diseases.

Fig. 8.
Hypothetical effect of reduced cholesterol synthesis in astrocytes during EAE. (A) Peripheral cholesterols cannot enter into the CNS due to the blood–brain barrier; thus, cholesterols in the CNS are synthesized de novo.

On December 26, 2017, John Hewitt tweeted:

Cholesterol, local synthesis.

I responded

Re: “Astrocyte-specific RNAs from various neuroanatomic regions…” Cell type-specific RNAs are energy-dependent and biophysically constrained via the pheromone-controlled physiology of reproduction and autophagy, which prevents the virus-driven degradation of messenger RNA.

See: microRNA multiple sclerosis (Items: 1 to 20 of 312)
The virus-driven theft of quantized energy links changes in the food energy-dependent microRNA/messenger RNA balance that biophysically constrain RNA-mediated cell type differentiation in the context of the pheromone-controlled physiology of reproduction. That fact, so far as I know, has not been mentioned by science journalist, John Hewitt or any other science journalists, besides J.A. Parker.
J.A. Parker helped me to put the facts about virus-driven pathology into the perspective of this interview:

See also: Drosophila active zones: from molecules to behaviour
Nobel Laureate Michael Rosbash linked thermodynamic cycles of RNA biosynthesis to all biodiversity via his works on Drosophila, which led to him sharing the 2017 Nobel Prize for the development of the cryo-EM technology. All serious scientists know how to link energy-dependent changes from electrons to ecosystems via the physiology of pheromone-controlled reproduction and microRNA-mediated enzyme-dependent autophagy.
In our 1996 review of cell type differentiation in species from yeasts to humans we linked alternative splicings of pre-mRNA to all biodiversity via the physiology of pheromone-controlled reproduction. See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

See for comparison: RNA splicing and its connection with other regulatory layers in somatic cell reprogramming

Recent work has added a conserved layer of RNA splicing and other post-transcriptional regulatory processes to the transcriptional and epigenetic networks already known to cooperate in the establishment and maintenance of cell identity.

The fact that alternative RNA splicings are food energy-dependent and that food energy biophysically constrains viral latency seems to have escaped the attention of all biologically uninformed theorists and philosophers who have continued to tout pseudoscientific nonsense as if no one could ever stop them. I wonder what pseudoscientists thought that all serious scientists had been doing during the past two decades. But I also know that pseudoscientists don’t care what serious scientists have been doing to link the creation of energy to all biodiversity via the pheromone-controlled physiology of reproduction and autophagy, which protects organized genomes from the virus-driven degradation of messenger RNA.