Ecological genomics: teleophobes respond (too late)

By: James V. Kohl | Published on: January 11, 2016

(click to enlarge)

Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing

Conclusion:

Twenty years ago, an essay about sequencing genomes and remotely tracking animals across the globe in real time would have been the subject of science fiction. In 2015, there are over 50,000 animals being tracked [12], and single research groups now sequence dozens, up to hundreds, of individual genomes [17,82]. By embracing new technology and integrating these data streams into an ecological genomic framework (Fig 1), we are now poised to inform, challenge, and develop biological theory.

My comment: Twenty years ago, The Scent of Eros: Mysteries of Odor in Human Sexuality, developed the theme that Lewis Thomas (p. 732) used to challenge biological theory when he wrote:

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries.

Review by Mark Sergeant
Reviewed by Ralph Underwager, Institute for Psychological Therapies.
Reviewed by Jan Peregrine
Note: At the Continuum editor’s insistence, co-author (the late) Robert T. Francoeur, included a few attestations to ridiculous theories about random mutations and/or mutations and evolution. These attestations were made to placate the teleophobes, which was required to publish a book that clearly portrayed how ecological variation was linked to ecological adaptation by the pheromone-controlled physiology of reproduction. Symbiotic Planet: A New Look at Evolution had not yet been published and few people knew that

[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.

See for comparison:

Linking gene expression and DNA methylation in single cells

Excerpt:

Recent single-cell protocols also allow researchers to explore chemical modification of DNA (‘epigenetics’), for example DNA methylation, which is a driving force behind changes to gene expression.

My comment: Odor is driving force behind changes to gene expression. Since 1995, the driving force of odor has been placed into the context of experience-dependent nutrient-dependent RNA-directed DNA methylation.
See: Feedback loops link odor and pheromone signaling with reproduction
See also: From Fertilization to Adult Sexual Behavior
Excerpt:

Molecular epigenetics. It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes (Razin and Shemer, 1995; Reik, 1989; Surani, 1991; Zuccotti and Monk, 1995).

My comment: Anyone who starts with DNA methylation as their “driving force” excludes what is known about odors and hydrogen-atom transfer in DNA base pairs. The experience-dependent de novo creation of olfactory receptor genes links everything currently known about nutrient-dependent non-genetic modifications of specific genes.
See: An Epigenetic Trap Stabilizes Singular Olfactory Receptor Expression
My comment: The epigenetic trap stabilizes hydrogen-atom transfer in DNA base pairs.
See also: How keeping active pays off in the olfactory system
In an attempt to discuss this, I wrote:

jvkohl • 3 years ago

Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?
Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338. DOI: 10.3402/snp.v2i0.17338.

Stavros Lomvardas echoed my claim but refused to discuss it further.

The article elucidates how the environment can broadly influence gene expression through an epigenetic effect chromatin – the way DNA is package and organized. This allows the environment to influence sensory function, to tune the olfactory sense to better suit the surrounding environment, because these environmentally regulated chromatin changes are coupled to cell longevity. This results in a change in the distribution of cells in the tissue that have made particular stochastic choices, where the stochastic choice is which olfactory receptor to express, without affecting the mechanism of stochastic gene expression.

My comment: Most people who exclude nutrient energy-dependent non-genetic modifications in DNA base pairs appear to be teleophobes who want others to believe in the pseudoscientific nonsense of neo-Darwinian theories. Their theories start with mutations, not with experience-dependent epigenetic traps that link stochastic choice to gene expression and feedback loops that link odor and pheromone signaling with reproduction.
In the context of those epigenetic traps and feedback loops, nutrient-dependent microRNAs typically repair the mutations. That is why teleophobes do not start with ecological variation and nutrient-dependent RNA-directed DNA methylation and DNA repair. They known that the microRNA/messenger RNA balance is linked from RNA-mediated events to teleophobic theory killers.
In the past 20 years more than 46,000 indexed publications from the NIH PubMed database, link microRNAs to biophysically constrained RNA-mediated cell type differentiation in the 50,000 animals being tracked. In 2016, serious scientists expect to see the tipping point reached. There will be more publications that explain how cell type differentiation occurs than publications that track the observations of researchers who Dobzhansky (1964) referred to as bird watchers and butterfly collectors. Teleophobic theories will finally be dismissed with extreme prejudice against those who invented or touted them.
See: Biology, molecular and organismic (p. 443)
Excerpt:

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!

See also: A Fear of Pheromones and The Great Pheromone Myth
Excerpt:

…it is erroneous to infer that a plurality of mammalian behaviors and endocrine responses is uniquely determined in an invariant way by single or small sets of chemical stimuli and to apply a generic and misleading name to the presumptive agents in support of such an inference.

My comment: No serious scientist is afraid of the facts about human pheromones. No serious scientist has ever inferred that atoms and ecosystems could be linked to mammalian behaviors and endocrine responses in an invariant way by anything else. For comparison, most teleophobes have continued to make claims like this:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

My comment: Mutations are linked from perturbed protein folding to pathology. Claims by teleophobes fail to address everything known to serious scientists about physics, chemistry, and the conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding chemistry and cell type differentiation in all individuals of all species of all living genera. The teleophobes link mutations to the enormous amount of biodiversity in this world.
See also: Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution
Excerpt:

Why then did the number of OR genes change so dramatically in mammals but not in Drosophila? One possible explanation is the difference in the mechanism of gene expression system between mammals and Drosophila.

My comment: There is no difference in how the molecular mechanisms of gene expression link atoms to ecosystems in species from microbes to humans. The epigenetic landscape must be linked to the physical landscape of supercoiled DNA by nutrient-dependent changes in the microRNA/messenger RNA balance. The changes link the physiology of reproduction to the stability of organized genomes in all living genera.
For example, see: Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors
Excerpt:

Evolution appears to favor efficient circuits and signaling elements that can accomplish many different tasks (13, 14). The diverse social behaviors that are enabled by the functional flexibility of the secrete-and-sense circuits (Fig. 5C) may explain the frequent occurrence of this class of circuits in nature.

My comment: Evolution favors nothing. The key phrase is that it appears to favor efficient circuits and signaling elements. That suggests evolution favors itself and that favoritism enabled weekend evolution of the bacterial flagellum.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt:

Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

My comment: These researchers seem to think mutations cause nutrient-dependent RNA-mediated DNA methylation, which they linked to the two amino acid substitutions. Apparently, they have not learned anything about the biophysically constrained chemistry of RNA-mediated protein folding. Thermodynamic cycles of protein biosynthesis and degradation are perturbed by mutations and linked by RNA-mediated amino acid substitutions to cell type differentiation and healthy longevity.
See also: Intelligent Microbe Secretory Weapons
Conclusion:

It is absurd to think that this occurs randomly. Doesn’t the microbe need to have some way of knowing what needs to be built and what its uniquely produced effector molecules will do in the distant host cell.
How can anyone not think that these microbes exhibit extremely intelligent behavior?

Excerpt:

…when we eat food nucleic acids can get into our cells. Also, there is a theory that our cells in the body keep sending out nucleic acids and one theory has it that it seems to correct the mistakes that other cells have suffered from mutations. . .

My comment: All serious scientists know that RNA-mediated DNA repair of mutations is required to prevent virus-driven genomic entropy. Nutrient-dependent RNA-mediated DNA repair is linked to the pheromone-controlled physiology of reproduction by supercoiled DNA.
See: Structural diversity of supercoiled DNA
Conclusion:

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Reported as: How Strange Twists in DNA Orchestrate Life
Excerpt:

Simply twisting DNA can expose internal bases to the outside, without the aid of any proteins. Additional work by David Levens, a biologist at the National Cancer Institute, has shown that transcription itself contorts DNA in living human cells, tightening some parts of the coil and loosening it in others. That stress triggers changes in shape, most notably opening up the helix to be read.

My comment: The teleophobic claim about Strange Twists in DNA Orchestrate Life fails to address anything known to serious scientists about the questions posed by Schrodinger in What is Life? The teleophobes also fail to address Schrodinger’s answer.
Excerpt 1)

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)

My comment: All serious scientists understand why Schrodinger’s anti-entropic force is required.
Excerpt 2)

But about forty years ago the Dutchman de Vries discovered that in the offspring even of thoroughly pure-bred stocks, a very small number of individuals, say two or three in tens of thousands, turn up with small but ‘jump-like’ changes, the expression ‘jump-like’ not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries’s mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule. But quantum theory was but two years old when de Vries first published his discovery, in 1902. Small wonder that it took another generation to discover the intimate connection! (page 33-34)

My comment: Since 1944, teleophobes have still not realized that the quantum jumps in DNA base pairs are nutrient-dependent. Nutrient energy-dependent changes in hydrogen atom transfers in DNA base pairs are not mutations. The discontinuity is nutrient-dependent and controlled by the physiology of reproduction. That is why, even to a teleophobe, the “strange twists” in DNA that orchestrate life can now be explained only in the context of Ecological Genomics. A model of biologically-based cause and effect that links atoms to ecosystems is required.
The model must include the conserved molecular mechanisms of nutrient-dependent pheromone-controlled RNA-mediated events that link chromosomal rearrrangements to all biodiversity in all individuals of all living genera.
See also: Evolution’s Science Status
Excerpt:

The problem stems from the absence of empirical evidence to scientifically supported these new concepts. Dawid argued that the essence and definition of science should be revised to allowing for three kinds of “non-empirical” evidences.

My comment: Non-empirical evidences are theories. Teleophobes are theorists, not serious scientists.

Excerpt:

Everything here is directed at being a pan-cancer test, something that is a universal test,” says Jay Flatley, who has been Illumina’s chief executive for sixteen years and has improved the power of DNA sequencing at a rate that exceeds improvements in microchips over the same period of time.

Conclusion:

The cancer world is changing, Nelsen says. “I think these things will converge pretty rapidly. If I was a big pharma with a minimally effective, medium toxicity chemotherapy drug I would be nervous. I think it’s going to be really a fascinating time.”

My comment: Nothing about the claims of teleophobes attests to the the power of DNA sequencing, or to the fact that hydrogen-atom transfers in DNA base pairs are the link between nutrient-dependent health and mutation-driven pathology. Claims like this one should make c nervous.

“It was really surprising,” Dr. Bernstein said. “Why would a metabolism gene cause cancer?”

For comparison, see: The convergent cancer evolution toward a single cellular destination

Excerpt:

Complex multicellular organisms, including humans, must possess sophisticated genetic constraints that suppress the fitness of individual cells in order to ensure the fitness of the whole organism 2. However, accidental events such as somatic mutations or viral infections can wipe out such constraints and reactivate the cell’s otherwise dormant capacity of seeking for its own fitness, often resulting in cancer 3-5.

Reported as: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer

My comment: The dominant evolutionary theme did not include the role of viruses.

If it had, we would already have effective treatments for cancer and the focus would have been on prevention long before now. Neo-Darwinists are teleophobes who have stalled the “Precision Medicine Intiative” and will continue to do that for as long as serious scientists allow it.

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… –Eugene Koonin (2015)

See for comparison: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Conclusion:

Taken together, our data untangle the complicated roles of E-cadherin and p120 in the context of distinct junctional complexes, spatially separating their functions and providing an explanation for their conflicting behaviour in cell growth. In addition, they identify PLEKHA7 as a specific marker of ZA that mediates suppression of growth-related signalling. Finally, they reveal an interaction of the ZA with the microprocessor complex, and uncover a mechanism whereby the ZA regulates a set of miRNAs to suppress cellular transformation and maintain the epithelial phenotype.

Excerpt:

“LEDs are great things, and people should be buying them,” Soljačić says. “But understanding these basic properties” about the way light, heat, and matter interact and how the light’s energy can be more efficiently harnessed “is very important to a wide variety of things.”

My comment: Indeed, the anti-entropic epigenetic effects of virucidal UV light appear to link hydrogen-atom transfer in DNA base pairs to the answer to Schrodinger’s question: “What is Life?” Nutrient-dependent life and the physiology of reproduction are epigenetically-effected ways that supercoiled DNA traps energy to ensure organized genomes are protected from virus-driven entropy.