Half truths support theories without facts

By: James V. Kohl | Published on: March 31, 2016

How to lie by telling the truth


People… trot out half-truths, in full expectation and knowledge that they will create a false impression. And then, when others act on the false impression, the “truth-telling liars” can sit back and pretend that they aren’t liars. They get the benefit of lying, without any damage to their precious self-image.

My comment: It is more difficult for others to determine who benefits from half truths when more than one individual or research group fails to link biologically-based cause and effect. When two groups use the same model organism, but no model, they are not likely to report the truth about biologically-based cause and effect, .

Craig Venter’s Synthetic Genome 3.0 Evokes Classic Experiments

Venter’s group seems to have run into a common problem with attempts to explain nutrient-dependent RNA-mediated cell type differentiation. They try to keep it constrained by evolution, which leads them to use terms like mutation instead of amino acid substitution. See their references for a link to work on viruses that should have led to recognition of the difference between the amino acid substitutions the cause changes in virulence and the mutations, which are biophysically constrained.
Dobzhansky (1973) used “amino acid” and “mutation” in the context of claims that we know can be supported only with experimental evidence that links atoms to ecosystems in all living genera via the physiology of reproduction. The nutrient-dependent physiology of reproduction is biophysically constrained by the innate immune system, which is the RNA-mediated link to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven entropy.
See also: A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans

Synthesis of dsRNA is required for replication of RNA viruses and transposons, and therefore dsRNA constitutes a ‘‘danger signal’’ in many organisms, including humans, where it activates the interferon response (Wang et al., 2002). As in worms, RNAi is important for anti-viral defense (Lu et al., 2005); it is possible that the mere ‘‘sensing’’ of dsRNA (for example, by pattern recognition mechanisms [Melo and Ruvkun, 2012]) is sufficient to activate the RNAi system, regardless of whether the dsRNA molecule is further processed to trigger an RNAi response or not.

My comment: Nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in the nematodes, C. elegans and P. pacificus clearly shows how the innate immune system links metabolic networks and genetic networks to supercoiled DNA that protects the organized genome of all living genera from virus-driven entropy.
See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
Reported as: The neurobiological consequence of predating or grazing

While C. elegans feeds exclusively on bacteria, P. pacificus is able to switch its behaviour to prey on other worms if bacterial food gets scarce.

See also: Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory

Classical olfactory imprinting drives approach behavior, such as homing to the natal stream for salmon (Nevitt et al., 1994), bonding between mammals and their young (Lorenz, 1935), kin recognition in zebrafish (Gerlach et al., 2008), and acceptance of imprinted foods (Wilson and Sullivan, 1994). Positive imprinting to odors experienced early in life also has been described in C. elegans, although little is known about its mechanisms beyond a requirement for the orphan G protein-coupled receptor SRA-11 in AIY neurons (Remy and Hobert, 2005).

My comment: The nutrient-dependent de novo creation of G protein-coupled receptors links classical olfactory imprinting to supercoiled DNA via everything known about RNA-mediated cell type differentiation, which is controlled by the physiology of reproduction. Examples link all invertebrates to all vertebrates via the conserved molecular mechanisms we detailed in our section on molecular epigenetics in the Hormones and Behavior review.  From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Rechavi’s group recognizes the fact that RNA-mediated events are important for anti-viral defense. Bargmann’s group ignores the fact that virus-driven energy theft links perturbed protein folding chemistry to mutations and gene loss.
But her group does not link what nematodes eat to nutrient-dependent biodiversity via the de novo creation of olfactory receptors, which are G protein-coupled receptors. Instead, Bargmann wins another award.  McGovern Institute awards prize to neurogeneticist Cori Bargmann

Building on her olfaction work, Bargmann has also studied the neural basis of social behavior, which in worms is strongly regulated by chemical cues. In one set of papers, for example, she identified a single neuron that integrates information from multiple chemical cues including food, oxygen and pheromones, to control the expression of social behavior.

My comment: Her award-winning works fail to link virus-driven energy theft from perturbed protein folding chemistry to mutations and gene loss.  Perhaps no one else but me will ever know that she could have linked the works from Rechavi’s group from what is known about how olfaction and the immune system enable the fine-tuning of metabolic networks and genetic networks, which is linked from the physiology of reproduction to supercoiled DNA.
She could have stopped the threat of the Zika virus and other viruses by acknowledging the fact that supercoiled DNA protects all organized genomes in all living genera from virus-driven entropy. Instead, her works will continue to be well-funded.
Others will be forced to increase their efforts and focus on Combating Evolution to Fight Disease.


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