Dobzhansky 1973 and precision medicine (3)

By: James V. Kohl | Published on: January 25, 2017

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Dobzhansky 1973 and precision medicine
Dobzhansky 1973 and Precision Medicine (2)
How Do Bacteria Help Cancer

Studying bacterial effects on cancer are very complex, because there is no one clear mechanism

Jon LIeff has again obfuscated the clarity of facts about energy-dependent conserved molecular mechanisms. These are the facts:
1) Closed feedback loops link nutrient energy-dependent pheromone-controlled quorum sensing in bacteria to supercoiled DNA in all living genera.
2) Virus-driven energy theft causes the degradation of messenger RNA in bacteria that is manifested in the morphology and behavior of so-called archaea.
3) Archaea are bacteria with less supercoiling in their DNA. (For comparison to bacteria the so-called archaea are less well-adapted. They must struggle harder to avoid extinction.)
4) Negative supercoiling in the organaized genomes of bacteria has been linked to communication among viruses.
5) Viral signaling pits energy theft against the nutrient energy- dependent signaling that links quorum sensing from ecological variation to ecological adaption in all cell types of all individuals of all species on Earth.
Healthy longevity is linked from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to supercoiled DNA, which prevents the transgenerational epigenetic inheritance of Zika virus-damaged DNA.
To his credit, this is the first time I have seen Jon Lieff attempt to distance himself from ridiculous theories about evolution.
He concludes:

All of these interactions are based on the natural communications between bacteria and human cells.

…Sorek reports in the journal Nature that his team has found the protein that viruses used to communicate. His team has called the protein arbitrium, which is Latin for “decision.”

They conclude with this ridiculous claim about viruses as a primitive life form instead of realistically linking virus-driven energy theft from mutations to all pathology.

Even though viruses are the most primitive form of life, they infect and harm millions of people every year. The possibility of tapping into viral communication has many scientists excited, because it offers new ways to build drugs that could defeat viruses.

Quorum sensing in bacteria is the nutrient energy-dependent pheromone-controlled link from the innate immune system of all living genera to the physiology of reproduction. Ecological variation must be linked to ecological adaptation via conserved molecular mechanisms of RNA-mediated protein folding chemistry in the context of the physiology of reproduction. If the physiology of reproduction is not biophysically constrained by the availability of nutrients, you are left with a ridiculous theory about mutation-driven evolution.
See also: Alternative RNA Splicing in Evolution (2012)
On 10/27/13 Jon Lieff wrote:

I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.

That comment was edited, and now appears as:

Thanks for the current article and information. I very much appreciate your important information and will try to learn more about it.

Another pertinent current article was published in May 2016
See: Spliceosomal intronogenesis
Unfortunately, Jon Lieff and many others have tried to link alternative RNA splicings to the evolution of morphological and behavioral phenotypes outside the context of the energy-dependent physiology of reproduction. Attempts to make viruses the cause of evolution are even more ridiculous, since virus-driven energy theft is the cause of all pathology.
See for comparison: Stromal cues regulate the pancreatic cancer epigenome and metabolome

…these studies raise the possibility that microenvironmental context broadly influences the epigenetic state of tissue-resident cell types under physiological and pathological conditions.

They refuse to admit that the epigenetic state is energy-dependent and RNA-mediated. They must not reveal that virus-driven energy theft is the cause of all pathology. Instread, they claim that “…the mechanistic underpinning of this crosstalk remains poorly understood.”
See for comparison: Communication between viruses guides lysis–lysogeny decisions
Reported as: Do you speak virus? Phages caught sending chemical messages

If you had a molecule that could drive viruses into complete latency, it would be a good drug.

Viral latency is nutrient energy-dependent and it is controlled by the physiology of reproduction. There is no need for a good drug until virus-driven energy theft causes the accumulated mutations that all serious scientists have linked to all pathology. For comparison, all pseudoscientists have linked the mutations to evolution.
Pseudoscientists abandoned every aspect of nutrient energy-dependent healthy longevity and focused on drug development. For a track record of pseudoscientific nonsense, see:
Masatoshi Nei and Naruya Saitou (1986) Genetic relationship of human populations and ethnic differences in reaction to drugs and food

…variant alleles at the pseudocholinesterase locus seem to be maintained by the balance between mutation and weak selection.

Naruya Saitou, JC Stephens and Masatoshi Nei (1985) Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species.

Naruya Saitou and Masatoshi Nei (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data.

29 years later we have:
IA Babarinde and Naruya Saitou (2016) Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics

CNS-flanking genes were often found in evolutionarily conserved genomic neighborhoods. ChIP-Seq signal and gene expression patterns also suggested that CNSs regulate nearby genes. Interestingly, genes with more CNSs have more evolutionarily conserved expression than those with fewer CNSs. These computationally obtained results suggest that the genomic locations of CNSs are important for their regulatory functions. In fact, various kinds of evolutionary constraints may be acting to maintain the genomic locations of CNSs and protein-coding genes in mammals to ensure proper regulation.

Conserved non-coding sequences, which are typically reported as microRNA flanking sequences, are reported as CNS-flanking genes. Two decades after we reported how alternative splicings of pre-mRNA were linked from RNA-mediated cell type differentiation to biodiversity via sexual differentiation of cell type in species from yeasts to mammals, the experimental evidence forced Masatoshi Nei’s 1985 co-author to admit that the statistical evidence matches the facts. At first glance, it mght appear that Saitou and Nei never heard about virus-driven energy theft in the context of neo-Darwinian evolution. But wait, instead, they chose to ignore what they knew.
See: Naruya Saitou and Masatoshi Nei (1986) Polymorphism and evolution of influenza A virus genes
See also: Naruya Saitou and Masatoshi Nei (1986) The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence

When these five different tree-making methods, as well as Fitch and Margoliash’s method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are “gene trees,” and to obtain the correct “species tree,” sequence data for several independent loci must be used.

Simply put, they admitted that the nonsense about minimal mutational difference could not be used for comparison to the data from sequencing which now links natural selection for energy-dependent codon optimality to all biodiversity.
See also: Switching off the brain: Study implements an optogenetic tool that inhibits neural activity

In optogenetics, neurons are genetically modified to express light-sensitive ion channels (proteins that conduct electricity), such that light exposure may be used to activate or inhibit electrical activity.

The fact that femotosecond blasts of virucidal UV light have been linked from quorum-sensing in bacteria to repair of virus-driven DNA damage in species from archaea to humans, suggests the understanding of optogenetics has moved far beyond what was specific to neuronal activation.

See for example: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

By varying the time between two pulses of light, serious scientists saw how the structure of the protein morphed over time. They did not extend the time to millions of years and suggest that protein evolution had occurred during that time because they are serious scientists, not pseudoscientists.

See: Dobzhansky 1973 and precision medicine (4) in prep