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Innate immunity and multiplexing

Scientists Hope to Cultivate an Immune System for Crops

by Carl Zimmer
Excerpt: The complex microbial world in the soil may protect plants much like our immune system protects our bodies.
My comment: The speed of light on contact with water links the sun’s quantized anti-antropic virucidal energy from the de novo creation of nucleic acid precursors to biophysically constrained RNA-mediated protein folding chemistry and supercoiled DNA, which protects all living genera from virus-driven energy theft and genomic entropy.
SeeWhat is Life? (1944)
Excerpt:

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)

See also: Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B
Reported as:
1) Virus uses ‘stolen’ CRISPR to hack its host’s immune system;
2) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
3) Virus Hacks Host Genome, Steals CRISPR to Protect Itself
4) Viruses Hack Their Host’s Genome with CRISPR
5) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
6) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
This ridiculous claim is found in all reports:

“Bacteria and their viruses have a shared evolutionary history stretching for billions of years,” says Suttle. “So at some point along the way N1 stole a defensive CRISPR array from Nostoc or a close relative.”

Someone at the LABROOTS Genetics & Genomics site is removing my posts about this attempt to include viruses in neo-Darwinian theory, which links them to billions of years of co-evolution.
On June 15, 2016 the Genetics & Genomics site reported this:

In the past decade, humans have adopted CRISPR as a genetic editing system, derived from a mechanism bacteria use to remember the pathogens they come across. It turns out that humans are not the only ones who want to “steal” the CRISPR idea – a new study uncovered a virus with a CRISPR DNA sequence.
“This is the first evidence we’ve seen that a virus can donate an immunity system via CRISPR. This is like a hacker compromising a computer system, and then immediately patching it to ensure other hackers can’t break in.”

My comment: Everything in their report is a ridiculous misrepresenation of what is known to serious scientists about biophysically contrained protein folding chemistry and RNA-mediated cause and effect, which links the energy-dependent creation and maintenance of all innate immune systems in all cell types of all living genera to ecological adaptation, or from virus-driven energy theft to all pathology.
Epigenetics and Genetics of Viral Latency
Excerpt:

viral latency is responsible for life-long pathogenesis and mortality risk…

My comment: The innate immune system biophysically constrains cell type differentiation by forcing viruses to wait for stress-induced changes in pH to enable the energy theft that facilitates viral replication. The systems complexity is beyond the grasp of most science journalists and all neo-Darwinian theorists. “Big Bang” cosmologists must learn something about biochemistry and RNA-mediated cell type differentiation before adding more pseudoscientific nonsense for the biologically uninformed masses to regurgitate.
See for example:  How Can Physics Underlie the Mind? Top-Down Causation in the Human Context
See for comparison: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
Excerpt:

we identified a core set of more than 1000 responsive enhancers in the human genome. This TP53 cistrome is invariably used between cell types and experimental conditions, whereas differences among experiments can be attributed to indirect nonfunctional binding events.

Reported as: Cancer-preventing protein finds its own way in our DNA
Excerpt:

It’s a known fact that genes are activated when a protein binds to a specific sequence on our DNA. But how does this protein find its way in our extraordinarily complex DNA? Scientists have thus far been assuming that one protein could never locate the exact DNA sequence to activate a specific gene all by itself – at least not in human beings. However, Professor Aerts and his colleagues from the Department of Human Genetics at KU Leuven, Belgium, have now shown that some of these proteins are in fact capable of locating their targets autonomously. Furthermore, the composition of some DNA switches turns out to be unexpectedly simple.

My comment: The simplicity can be compared in the context of the forward by Roger Penrose to the reprint edition of Schrodinger (1944) What is Life?

“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?”

My comment: The energy links hydrogen-atom transfer in DNA base pairs in solution to RNA methylation and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

See for example: One Tiny RNA Could Break the Cycle of Arterial Thrombosis  (Labroots)
Excerpt:

…a specific type of microRNA called miR-181b regularly balances the impact of both acute and vascular inflammation.

See also:  Color vision helps birds find good food and the right partner

Excerpt:

The researchers have established that chickens — just like people — have colour constancy. For birds, this means that they, in different environments and under different lighting conditions, recognise the colour of, for instance, berries and can thereby distinguish those that are ripe from those that are not. Without colour constancy, they would not be able to rely on their colour vision — they would simply see the berries in different colours as the light changed. They would certainly also not be able to recognise their own kind of species.

My comment: Species recognition is nutrient-dependent and the pheromone-controlled physiology of species specific reprodution in all vertebrates has been link linked to chromosomal rearrangements in birds and to morphological as well as behavioral diversity.  See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

See also: DNA in ‘unbiased’ model curls both ways

Excerpt:

“Think of the chromosome at mitosis as a bit like what would happen to a piece of sewing thread if you doubled it up and rolled it between your finger and your thumb,” he said. “Depending on how you rolled your fingers, you would get right- or left-turning structures.”
The thread itself has a helical arrangement of even smaller fibers, though the twist at one scale doesn’t necessarily determine the twist at the larger scales. “But bundles of threads usually get twisted somehow,” Wolynes said.
That “somehow” remains one of the mysteries, he said.

My comment: The fact that someone like Wolynes thinks that details of biophysically constrained RNA-mediated protein folding, supercoiled DNA, and energy-dependent chromosomal rearrangements have left us with any mysteries is a mystery. It’s as if he cannot link physics to chemistry, and stalls before linking protein folding chemistry from RNA methylation to supercoiled DNA. If he were not attempting to explain biologically-based cause and effect, he might readily explain why there is no mystery to how energy is created in physical systems.
See:Scientists using sunlight, water to produce renewable hydrogen power
Excerpt:

Hydrogen also can be made using electrolysis, which requires electricity and highly purified water to split water molecules into hydrogen and oxygen. Although this is a sustainable process (assuming the electricity is produced from a renewable energy source), the cost of materials associated with the system are expensive—a major barrier to the affordable production of renewable hydrogen.

My comment: All life on earth is hydrogen powered. Hydrogen-atom transfer in DNA base pairs in solution links the sun’s anti-entropic virucidal force to the de novo creation of receptors that link olfaction from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. What prevents serious scientists from grasping the facts that must link quantized energy to physical systems or to biophysically constrained cell type differentiation?

See: Engineers discover light can stamp out defects in semiconductors for better solar panels and LED bulbs
Excerpt:

The team discovered that if you add light while firing the material in a furnace at high temperatures, the light generates extra electrons that can change the composition of the material.

My comment: The energy-changing properties of light and its effects on the composition of materials is linked from the speed of light on contact with water to the de novo creation of nucleic acid precursors and all biodiversity via supercoiled DNA.
See also: Biosensor Chip Flawlessly Detects Genetic Mutations
Excerpt:

The future of this technology is as vast as scientists’ understanding of the genetic mutations that cause certain diseases. If they know the SNP that causes a certain autoimmune disease, they can create the complementary strand and attach it to a biosensor chip to be sent into a patient suspected to have the disease or has a family history of the disease.

My comment: If they know how biophysically constrained energy-dependent RNA-mediated cell type differentiation occurs, they can link viruses from energy theft to the changes in SNPs that are link mutations to all pathology. But, even people who know that are not going to tell anyone until after their plans to make money from potent cures are secured by patents like this one.

RNA-Guided Human Genome Engineering

Excerpt:

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

My comment: They know that energy-dependent RNA-mediated protein folding chemistry is the cure for all virus-driven energy theft and pathology. When do you think they’re going to tell you that?

See also: Pregnant women’s high-fat, high-sugar diets may affect future generations
Excerpt:

“Our data are the first to show that pregnant mouse mothers with metabolic syndrome can transmit dysfunctional mitochondria through the female bloodline to three generations,” Moley said. “Importantly, our study indicates oocytes – or mothers’ eggs – may carry information that programs mitochondrial dysfunction throughout the entire organism.”

My comment: That fact has been known to all serious scientists for at least two decades. See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior
See also: Alzheimer’s Disease: The Role of Presenilin 2
Excerpt:

Why exactly this is the case is unclear, but Ralph Nixon at NYU (who was unaffiliated with this study in Cell), suggests that it might be because the aggregation-prone Aβ42 is more resistant to the acidic environment in the lysosomes so it accumulates instead of being degraded like Aβ40.

My comment: Nutrient stress and social stress cause the pH changes the favor viral replication in specific tissue types.

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