The human virome (revisited)

By: James V. Kohl | Published on: October 23, 2016

(click to enlarge)

From October 2013: Describing the Silent Human Virome with an Emphasis on Giant Viruses

“…viruses infect all domains of life, including bacteria, archaea and eukaryotes, and are found in all ecological niches [2]. This pleiotropic distribution on our planet allows viruses to play the role of ‘natural motors’ that drive global energy and nutrient cycling [3,4].”

My comment: The portrayal of viruses as ‘natural motors’ is made outside the context of the fact that the energy-dependent changes attributed to the ‘natural motors’ is not possible in the context of virus-driven energy theft, which is linked to all pathology — not to the evolution of anything.

See also: (Air date: April 22, 2015) Thanks to Teresa Binstock for calling attention to this: The mammalian virome in genetic analysis of health and disease pathogenesis

Teresa Binstock wrote: This NIH lecture titled, “The mammalian virome in genetic analysis of health and disease pathogenesis,” radically refutes conventional assumptions about the inherent pathogenicity of viruses, illuminating how many latent viruses within the human body (e.g. Herpesviruses) are indispensable to prevent infection by mediating the genotype-phenotype relationship within the host.

As the indispensable role of the human virome in proper immune function comes to light it will be increasingly difficult to maintain the ideologically myopic, if not imbecilic view that “viruses are bad,” must be vaccinated against, and eventually “eradicated” from the face of the earth.

See also: Creating and maintaining the human virome June 5, 2015

Excerpt:

Epistasis is perturbed by viruses, which is why the viruses are linked to pathology. They are not linked to beneficial mutations because there is no such thing as a pathological benefit.

See for comparison: The Human Virome Oct 21, 2016 | Posted by: Carmen Leitch
My comment: Carmen Leitch and other science journalists have repeatedly ignored my Labroots presentations, published works, and my comments on their misrepresentations of what is known to all serious scientists about biologically-based cause and effect. With this post, Leitch sinks to a new low. She is helping others to tout the pseudoscientific nonsense of neo-Darwinian evolution by ignoring this fact:

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Description:

In this talk by Frederic Bushman, PhD, William Maul Measey Professor in Microbiology, Perelman School of Medicine, presented by the American Society for Microbiology, an overview of the human virome – the viruses present in a human body – is presented.

There are many viruses on Earth, with estimates as high as billions. Human harbor many viruses, with some infection most of the population; Herpes simplex, for example, is estimated to infect as much as 80% of people or more if you count both types of the virus. Viruses can also confer benefits, such as in some vaccines.

Improvements in genetic technology have allowed researchers to learn more about viruses and nature. Researchers would like to delve deeper into the study of viruses and questions that surround them such as why the viruses in the human gut are so variable from person to person. Bushman’s lab is working in this area, and he shares some of his results with us.

He claims that “viruses mutate themselves,” and that much of his work is funded by the Human Microbiome Project, which might be another source of funding akin to the more recent National Microbiome Initiative (link opens pdf), which was announced on May 13, 2016.
See for comparison to what is known to serious scientists about energy-dependent polycombic ecological adaptation via nutrient-dependent fixation of RNA-mediated amino acid substitutions for comparison to hecatombic evolution of all virus-driven pathology. Both polycombic ecological adaptation and the hecatombic evolution of all virus-driven pathology can be placed into the context of the Precision Medicine Initiative via links from quantised energy to amino acid substitutions of from the theft of quantised energy to mutations and all pathology.
Until people like Professor Bushman are willing to admit that they have misrepresented the differences between a mutation and an amino acid substitution, scientific progress will be stalled by reporters like Carmen Leitch. She cannot be expected to know anything more about biophysically constrained energy-dependent RNA-mediated protein folding chemistry than what she was taught to believe by professors like Professor Bushman, who have taught her to believe in pseudoscientific nonsense.
See for comparison: What is life when it is not protected from virus driven entropy
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.
See also: The Microbiome Initiative
How much would it cost to fund a Nutrient-dependent Pheromone-controlled “Polycombic Adaptation Inititative”
See also: Beyond the gut bacterial microbiota: The gut virome

Excerpt:

The creation of a “human virome project” just like the human genome project could lay the basis in understanding not only diseases pathophysiology but also to know how viral populations that inhabits the human body could interfere with therapies and vice versa how therapies could change the viral ecosystem.