Systems biology vs pseudoscientific nonsense

By: James V. Kohl | Published on: April 24, 2019

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A de novo transcriptome assembler was substituted for the light-activated assembly of the microRNA-RNA-peptide nanocomplex.
See: Systems biology based meth-miRNA–mRNA regulatory network identifies metabolic imbalance and hyperactive cell cycle signaling involved in hepatocellular carcinoma onset and progression (4/8/19)
The regulatory methylation-miRNA–mRNA (meth-miRNA–mRNA) network fails to link the creation of sunlight from the creation of the enzyme ATPase, which is required to link the creation of ATP to the creation of RNA and the RNA-mediated fixation of amino acid substitutions in peptides that link the physiology of reproduction to all biodiversity via feedback loops.
For a brief two-article review of what is known about the feedback loops, see: Unraveling the Enzymology of Oxidative Phosphorylation: the Work of Efraim Racker

…Racker incorporated bacteriorhodopsin, a protein that functioned as a light-driven proton pump, and the F1Fo-ATPase into liposomes (6). They showed that the protons pumped out by the illuminated bacteriorhodopsin flowed back through the F1Fo-ATPase and generated ATP from ADP and inorganic phosphate…

The extension from the creation of light energy as information to all biodiversity on Earth was published as: Feedback loops link odor and pheromone signaling with reproduction. One of the co-authors is the 2004 Nobel Laureate in Physiology or Medicine, Linda Buck.
For ages 10+, see how the creation of light energy as information is linked from the creation of subatomic particles to biophysically contrained viral latency and healthy longevity via autophagy in: Subatomic: An Atom-Building Board Game, and in Cytosis: A Cell Biology Board Game
For comparison, a 2018 Nobel Laureate in Chemistry, Frances H. Arnold, still seems to believe that proteins automagically evolve. See below: “evolution is nature’s way”
“What I do is copy nature’s design process.” (10/3/18 – video)

For 2018 Nobel Chemistry Prize Laureate Frances H. Arnold, evolution is nature’s way of overcoming new challenges. In a world filled with challenges, Arnold’s discovery has helped us emulate this problem-solving process in the lab.

The claim that “evolution is nature’s way of overcoming new challenges” flies in the faces of all intelligent Nobel Laureates who have linked the creation of sunlight from microRNA biogenesis and the growth of plants as food to the physiology of reproduction and all biodiversity via feedback loops that start with the creation of the light-driven proton pump and the enzyme ATPase.
For example, this 2016 Nobel Laureate in Chemistry coauthored Dynamic control of chirality and self-assembly of double-stranded helicates with light (2016)
He linked the future of chemistry to the future of biology without any philosophical nonsense via Biblical Prophesy in: The Future of Chemistry – Schrödinger at 75: The Future of Biology (11/20/18)

Disabled were walking again, the blind were seeing again, and the death rose from the grave. 2013 was the year in which prophesy from the bible became reality. — De Correspondent (dec 2013)

For comparison, the conflict of interest expressed by Frances H. Arnold and others occur in the context of their support for GMOs.
See: Nobel laureates dismiss fears about genetically modified foods: Winners of chemistry prize say excessive concerns could limit scientific progress

Arnold argued that genetically modified crops could make food production more environmentally sustainable and help feed the world’s growing population.

See for comparison: Biocontainment of genetically modified organisms by synthetic protein design (2/5/15) link opens pdf

DNA transfer within an ecosystem enables a GMO to escape biocontainment.

That fact predicted this report: CRISPR base editors can induce wide-ranging off-target RNA edits (4/17/19)
That report led “The Scientist” to report the facts more succinctly as: Base Editors Cause Off-Target Mutations in RNA (4/18/19)

“Most investigation of off-target base editing has focused on DNA, but we have found that this technology can induce large numbers of RNA alterations as well…”

Watch as the investigations of the CRISPR Cas9 threat are examined in Off-target Effects in CRISPR-Cas9 Genome Editing: Securing Specificity (5/7/19)
Please note, however, that one of the two people who are presenting during this free webinar is the co-author of From catalytic asymmetric synthesis to the transcriptional regulation of genes: in vivo and in vitro evolution of proteins. (2000)
DJ Segal is stuck with a ridiculous theory about the evolution of proteins.
So is Eugene Koonin. See: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

The claim that anything that varies between taxa has evolved in the context of amino acid composition in proteins exemplifies human idiocy.
For contrast, see: RNA-catalysed synthesis of complementary-strand RNA (1989)

The Tetrahymena ribozyme can splice together multiple oligonucleotides aligned on a template strand to yield a fully complementary product strand. This reaction demonstrates the feasibility of RNA-catalysed RNA replications.

That feasibility led to this patent application: RNA-Guided Human Genome Engineering (2015)

5. 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).

The somewhat concealed claim that human endogenous retroviruses can be targeted with engineered Cas+gRNA systems attests to the well-established fact that light-activated microRNA biogenesis links natural selection for energy-dependent codon optimality to DNA repair and the physiology of reproduction in all living genera. That fact eliminates the claims of neo-Darwinian theorists and Big Bang cosmologists from any further consideration whatsoever.
See for instance: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016)

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

The energy-dependent optimization of EDAR V370A is the link to human disease prevention in populations from the Old World to the New World.
See: Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago.

There is no scientific support for the claim about positive selection likely to have occurred circa 20,000 y ago. The support for the idea of positive selection for food and heterosexual mates is overwhelming in the context of biophysically constrained viral latency in all living genera.
But see: How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers (2019)

…there are not yet any strong reasons to think that ‘emergent’ properties of the whole microbiome play a causal role.

The microbiome has no ’emergent’ properties.
See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression 12/2/14
See also: Search Results for “”the eternal significance of microRNAs””
Alternatively, ask a philosopher what should be included in your medical care.