Hydrogen-atom transfer in DNA base pairs (7)

By: James V. Kohl | Published on: February 10, 2016

(click to enlarge)

February 9, 2016 at 9:45 pm

James, if you think you have a solution then fill out a proper prize submission and show that you have met the specification.
My comment: There is no prize submission form and I repeatedly requested the Non-Disclosure Agreement. I think that Perry Marshall knows I will win the prize, and simply doesn’t want the challenge to his claims that I would provide in my submission. For example, I would include citations and explanations like the ones below.

Scientists Demonstrate Basics of Nucleic Acid Computing Inside Cells

Excerpt:

Cells, of course, already know how to sense toxic molecules and the development malignant tendencies, and to then take action. But those safeguards can be turned off by viruses or cancer cells that know how to circumvent natural cellular processes.

My comment: They seem unwilling to tell others how the proliferation of viruses links energy theft to the viral microRNAs in cancer cells and in other pathological cell types via alternative splicings.
See for comparison: Mobile small RNAs regulate genome-wide DNA methylation
Excerpt:

RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses.

My comment: They established the fact that RNA-directed DNA methylation and RNA mediated events link supercoiled DNA in organized genomes to protection against virus-driven entropy in all living genera. A few days later, others report that evidence is weak that nutrient-dependent pheromone-controlled RNA-directed DNA methylation links caste-specific RNA-mediated DNA methylation to the social behavior of insects.
See also: Robust DNA Methylation in the Clonal Raider Ant Brain
Excerpt:

Evidence for caste-specific DNA methylation in social insects is weak.

My comment: How did this evidence suddenly become weak? What other experimental evidence of biologically-based cause and effect links hydrogen-atom transfer in DNA base pairs from ecological variation to ecological adaptation in all living genera via cell type differentiation in all individuals of all species?
Reported as: New study challenges popular explanation for why a social insect becomes a worker or queen
Excerpt:

…this finding could be really important for those who want to understand the evolution of social behavior and the function of DNA methylation in insects.

My comment: No experimental evidence of biologically-based cause and effect links anything to the evolution of social behavior. Social behavior is nutrient-dependent and pheromone-controlled in species from microbes to humans.
See also: 5 things we learned about the brain in 2015

IMMUNE SYSTEM IS DIRECTLY TIED TO MENTAL FUNCTION

Researchers at the University of Virginia found a direct connection between the immune system and brain function that, until now, was unknown. What they found was a network of lymphatic vessels in the brain that were previously thought to only exist at the base of the skull. Dr. Jonathan Kipnis said, “”When we discovered the lymphatic vessels, we were very, very surprised, because based on the textbooks — these vessels do not exist.”

3. DIRECT CORRELATION IN BRAIN HEALTH AND GUT HEALTH

Researchers discovered that by balancing the healthy bacteria in your gut, certain symptoms of depression and anxiety could be lessened, or even treated. The results were based on a study that involved people eating fermented foods to increase healthy gut bacteria, and the impact the gut bacteria had on anxiety and depression. One of the co-authors of the study, Dr. Matthew Hilimire said, “It is likely that the probiotics in the fermented foods are favorably changing the environment in the gut, and changes in the gut in turn influence social anxiety. I think that it is absolutely fascinating that the microorganisms in your gut can influence your mind.
See also: RNA-mediated degradation of microRNAs: A widespread viral strategy?
Desires of Microscopic Shrimp Illuminate Evolutionary Theory
Reveling in the Revealed
Considerations: Recent research has revealed how DNase?I’s cutting bias may limit the method’s usefulness for the identification of DNA footprints. Analyzing supposed binding of 36 different transcription factors, the researchers showed that DNase-seq data were not useful for illuminating footprints for many of them (Nat Methods, 11:73-78, 2014).
Because where the enzyme cuts is sequence-dependent, researchers should use naked DNA (i.e., DNA with no associated proteins) as a control in DNase-seq (also, in ATAC-seq) footprint analysis, says Clifford Meyer, research scientist in X. Shirley Liu’s lab at Harvard University and a coauthor on the Nature Methods study. “If you see a pattern in the naked DNA, then you know it’s got nothing to do with transcription-factor binding,” he adds.
My comment:

“If you see a pattern in the naked DNA, then you know it’s got nothing to do with transcription-factor binding,” he adds.

Is he claiming that hydrogen-atom transfer in DNA base pairs cannot be linked to the patterns neo-Darwinists assumed linked mutations to evolution?
If so, what does that tell serious scientists about the assumptions the neo-Darwinists made?
Without those assumptions, is there a way for a new species to evolve via an accumulation of mutations? If not, who will be the first neo-Darwinian teleophobe to tell the others that they were taught to believe in pseudoscientific nonsense?

See also: Description:

Biophysicist Hubert Yockey has determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. He states that the maximum amount of time available for it to originate is 6.3 x 10^15 seconds, and that Natural Selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal, which amount to one trillion times the 15 billion years of the imagined age of the universe for natural Selection to have created the genetic code, and therefore, the genetic code cannot have been produced by evolutionary processes. He states also that the genetic code posesses characteristics which could only have been a product of intelligence.

See for comparison: Researchers observe one of the world’s fastest chemical reactions for the first time
Excerpt:

Our DNA contains the bases adenine, guanine, cytosine and thymine. The chemists used ultra short blasts of light to shoot base pairs guanine and cytosine which were stimulated with UV light. They were only able to reveal the protective molecular mechanism using this method of femtosecond spectroscopy, because the process happened within a few quadrillionths of a second.

My comment: Energy-dependent UV light links ‘one of the world’s fastest chemical reactions’ from hydrogen-atom transfer in base pairs to DNA repair via amino acid substitutions in supercoiled DNA. If it did not, there would be no virus protection in organized genomes. Virus-driven entropy would destroy all life on earth via mutations and pathology.
The virus-driven entropy is biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding. RNA-mediated amino acid substitutions link ecological variation to biophysically constrained ecological adaptations via the physiology of reproduction in all living genera. If you are still not sure where nucleic acids came from and can’t confirm the validity of my other claims, you can still be sure of this: VIRUS-DRIVEN MUTATIONS AND PATHOLOGY ARE NOT BENEFICIAL.
See also [link opens pdf]: A DNA-Based Archival Storage System, ASPLOS (2016).
Excerpt:

…time is ripe for computer architects to consider incorporating biomolecules as an integral part of computer design. DNA-based storage is one clear example of this direction. Biotechnology has benefited tremendously from progress in silicon technology developed by the computer industry; perhaps now is the time for the computer industry to borrow back from the biotechnology industry to advance the state of the art in computer systems.

My comment: It is time for all serious scientists to recognize the limits of their current knowledge. Stop making unsupported claims about DNA outside the context of epigenetic links to its energy-dependent RNA-mediated stability.
Serious scientists have already reported this:

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report.
On average, 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

My comment: Obviously, each of us may be carrying around more harmful mutations than our ancestor did a few thousand years ago. If you think your ancestors arose from a species of primate that mutated and became human, remember what Dobzhansky (1973) said:

…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)

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Hydrogen-atom transfer in DNA base pairs (7)

Scientists Demonstrate Basics of Nucleic Acid Computing Inside Cells

3. DIRECT CORRELATION IN BRAIN HEALTH AND GUT HEALTH

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