The tipping point? 50,000 publications (3)

By: James V. Kohl | Published on: May 17, 2016

(click to enlarge)

$121 Million Allocated By White House For Microbiome Study 5/16/16

Excerpt:

The NMI recognizes that it’s important to study the microbiome across multiple ecosystems and organisms, and that the microbiome has an impact on a huge variety of problems in widely diverse areas, such as human health, agriculture, the environment, and weather and atmospheric disruptions.

My comment: Energy-dependent differences in microRNA flanking sequences link the microbiome to metabolic networks and genetic networks of all invertebrates and vertebrates. More than 50,000 indexed publications at PubMed now attest to that fact.

Everything known to physicists, chemists, and molecular biologists links the epigenetic landscape from ecological variation to the nutrient energy-dependent de novo creation of G protein-coupled receptors. The link from quantised energy to the creation of the receptors also links sensory input from the innate immune system to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy.

The NMI will force all serious scientists to acknowledge the fact that the bull sperm microRNAome links energy-dependent RNA-mediated amino acid substitutions, which differentiate all cell types in all living genera, to microRNAs in breast milk that alter infant brain development. Typically, the transgenerational epigenetic inheritance of the innate immune system is linked to healthy longevity. Alternatively, it is linked from virus-driven energy theft to mutations and all pathology.

The NMI is the logical extension of the Precision Medicine Initiative, which has already led to discoveries that link nutritional epigenetics to pharmacogenomics.

See my invited review of nutritional epigenetics, which I submitted for a special issue of the journal “Nutrients” Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

The discoveries show Dobzhansky (1973) was right, and they also show that all neo-Darwinian theorists have always been wrong.

See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

Excerpt:

…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 (p. 127).”

My comment: The differences in amino acid substitutions are examples of energy-dependent ecological adaptations that protect organized genomes from virus-driven entropy. The differences are not examples of mutation-driven evolution, or of natural selection for anything except food. Most neo-Darwinists, however, do not know the difference between an energy-dependent RNA-mediated amino acid substitution and a mutation. They still link the selection of nutrients from the innate immune system to mutations and all pathology at a time when all serious scientists are starting to acknowledge the fact that we are what we eat. That’s because what we eat is the energy source that fuels the physiology of reproduction.

Published on 3 May 2016 (~10 minutes)

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.

Published on 13 May 2016 (~60 minutes)

The White House Office of Science and Technology Policy, in collaboration with Federal agencies and private-sector stakeholders, is launching the National Microbiome Initiative to advance the current understanding of microbiome behavior from descriptive to predictive by investigating the fundamental principles that govern microbiomes in all ecosystems.

My comment: I think that this is the key phrase: “…investigating the fundamental principles that govern microbiomes in all ecosystems.” Why haven’t the fundamental principles that link metabolic networks to genetic networks via the microbiome in all invertebrates and in all vertebrates already been investigated? Who has been funding research that has not been based on the fundamental principles that link metabolic networks to genetic networks in species from microbes to humans?
Watch the last few minutes of this presentation to learn more about the waste of billions of research dollars, after someone asks about viruses.

What about the epigenetic effects of antibiotics on cattle, which extend from the use of manure as fertilizer to epigenetic effects on the water supply, and also extend from epigenetic effects of manure left out to dry to the altered microbiomes of the air we breath? Is the link from viral blooms to the microbiome evidence of biologically-based cause and effect, or is it a correlation? How will it be portrayed in a peer-reviewed published work, and why hasn’t anyone mentioned cause or correlation in a published work that made national news?

In the last few minutes, the dialog takes us back to the time when Sinclair Lewis won (but refused to accept) a Pulitzer Prize for publishing “Arrowsmith.” In the same year (1925), the Scopes trial in Dayton, TN led the way for neo-Darwinists to prevent all the scientific progress that could have been made if researchers had linked viruses from energy theft to all pathology.

The press conference ends and we are left with questions about Eugene Koonin’s claim: “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…“

Is this a predator-prey problem? Is the problem due to a concept stolen from physicists (who know nothing about molecular biology)? Did the viruses come from Mars? Do others really know little about the virome?

See “The Darwin Code” and ask Greg Bear what he has known or suspected about viruses for more than 30 years. Please help serious scientists stop the pseudoscientific nonsense. Ecological adaptation is energy-dependent and viruses steal the energy. That’s why dogs can be trained to sniff out cancer. They detect the difference in the pheromone-controlled physiology of energy-dependent reproduction in bacteria. Simply put, they can be trained to detect virus-driven energy theft. Do you have any idea what that fact means when it is placed into the context of the Precision Medicine Initiative? If not, ask a medical laboratory scientist to explain what is currently known to all serious scientist about the links from RNA-mediated amino acid substitutions to energy-dependent hydrogen-atom transfer in DNA base pairs in solution, like those that are measured in blood gas analyses.

The function of the innate immune system links nutritional epigenetics to healthy longevity via measure of pH that link stress from the replication of viruses to all pathology via critical care testing of other blood gas analytes such as pCO2, pO2, Sodium, Potassium, Chloride, Calcium, Glucose, Lactic Acid, and Hematocrit.

See: Stat Profile Prime CCS Blood Gas Analyzer from Nova Biomedical

Excerpt:

…we show how the information contained in cfDNA fragmentation patterns, effectively the foot-prints of protein-DNA interactions, can be used to infer contributing cell types without relying on genotypic differences. To the extent that cfDNA composition is impacted by cell death consequent to malignancy, acute or chronic tissue damage, or other conditions, this method may substantially expand the range of clinical scenarios in which cfDNA sequences comprise a clinically useful biomarker.

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

Reported as: Researchers Detail How to Control Shape, Structure of DNA and RNA

Excerpt:

“…if the nanoparticles and nucleic acid are in solution, you can change the charge by changing the pH of the solution.”

Excerpt:

The ecological monitoring of the environment has to include the determination of the genotoxicity of anthropogenic and other operating factors, which may lead to changes in the hereditary material. Such an assessment is extremely important because the analyzed indicators are directly related to the disruption of the vital activity of any organism.

Here are some examples of youtube videos on “cell type differentiation“

This video links cell type differentiation from transcription factors via hemoglobin

This video links cell type differentiation to the stability of organized genomes

This video links the sun’s biological anti-entropic virucidal energy from hydrogen-atom transfer in DNA base pairs in solution to all cell type differentiation in all individuals of all species.

This video links virus-driven energy theft to all pathology