Hybrids: making microbes and Democrats into monkey’s uncles?

By: James V. Kohl | Published on: February 16, 2016

Darwinists Underestimate Nature. Creationists Underestimate God.


Doug, here’s what we know: Two processes produce new species in real time –
1) Hybrids, where Species 1 crossed with Species 2 gives you Species 3. Example: Emmer wheats + goat grass = modern wheat.
This doubles the number of chromosomes. After this merger, “hybrid dysgenesis” kicks in. Extensive genome editing re-arranges and deletes parts of the new DNA.
Genome studies indicate that a hybridization event of this kind got us from invertebrates to vertebrates. Then a second one got us from vertebrates to jawed vertebrates. This is called “Ohno’s 2R hypothesis,” where the “2R” stands for “2 Rounds of doubling” of chromosomes.

My comment: Biologically uninformed pseudoscientists underestimate serious scientists. Here is what serious scientists, including many who are creationists, already know.
Ecological variation links atoms to ecosystems via biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry and the physiology of reproduction. The nutrient-dependent pheromone-controlled physiology of reproduction links the biodiversity of morphological and behavioral phenotypes from microbes to human biodiversity. I’m not sure why Perry Marshall claim that “Creationists Underestimate God.” For comparison, it is obvious that neo-Darwinists underestimate the ability of serious scientists to link what is known about physics, chemistry, and molecular biology to cause and effect. The molecular mechanisms that link biodiversity to humans were placed into the context of an invited review of nutritional epigenetics, which I submitted for publication in the journal “Nutrients.”
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
See also: Cancer: Evolution 2.0’s Blind Spot for information on the first report of findings published as Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs
The misrepresentations of facts I submitted in my invited review were changed from January 28, 2016 Team uses internet network theory to decipher the first epigenetic communication network to this representation, which was reported on February 12, 2016: Gene switch may repair DNA and prevent cancer

Our results imply that loss of TET enzymes and 5hmC depletion could contribute significantly to genome instability and inaccurate chromosome segregation, perhaps explaining the correlation of low 5hmC levels with cancer,” say the researchers.

For a historical perspective,  see the conclusion from the earlier report:

The next step is to establish whether the results can also be assigned to other cell types. “We knew that 5hmC was extremely abundant in embryonic stem cells, but now we also know that this is true for other cell types, such as neurons or certain tumours,” assert the authors of the paper.

And then they add:

Cancer cells have stem cell features; therefore it seems appropriate to investigate whether these results can also be transferred to cancer epigenomes, which would provide new outlooks on how they are regulated.

In my invited review, I wrote:

Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes (Adipietro, Mainland, & Matsunami, 2012; Blaschke et al., 2013; Jazin & Cahill, 2010; Lyons et al., 2013; Tan, Zong, & Xie, 2013).
Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).

My comment: In my opinion, they realized my invited review already detailed many of their claims about cell type differentiation. In my opinion, they could hardly avoid the fact that I linked nutritional epigenetics from metabolic networks to genetic networks in the context of ecological variation and ecological adaptation. I made no claims about natural selection, evolution, or ridiculous claims about beneficial mutations. Instead, I included facts about biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry linked to healthy longevity.
Viruses perturb protein folding chemistry, which is how they are linked to all pathology.
See also: Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity
Abstract excerpt:

Here, we show that transcription-dependent targeting results in a sharp increase of viral genomes in the host cell when the target is located in a late-expressed phage gene. In this targeting condition, mutations in the active sites of the type III-A RNases Csm3 and Csm6 lead to the accumulation of the target phage mRNA and abrogate immunity.

My comment: Abrogate appears to be a legal term that, in my opinion, can best be viewed in attempt to repeal or do away with a law, a right, a formal agreement or to evade responsibility duties associated with a formal agreement. I think it is unusual to see such a term used in the context of virus-perturbed protein folding chemistry and pathology, which in my model links viruses in bacteria to all pathology in humans via the nutrient-dependent innate immune system.
Reported on February 4, 2016 as A newly discovered form of immunity helps explain how bacteria fight off viruses

A viral infection can kill a bacterial cell—or in some cases, the viral genetic material can provide benefits, such as protection against other viruses. Harmful viruses immediately begin replicating, but beneficial ones implant themselves into the bacterial genome,” says Luciano Marraffini, assistant professor and head of the Laboratory of Bacteriology. “By using a wait-and-see approach, and tolerating the initial phase of the infection, the bacteria are able to make an intelligent choice.

My comment: I do not think that bacteria make choices. In my model, hydrogen-atom transfer in DNA base pairs in solution links UV light from ecological variation to ecological adaptation via the ability of nutrients to repair DNA damage and the physiology of reproduction.  Had I not already put all pseudoscientists on notice that I would not put up with any more of their nonsense about beneficial mutations, I don’t think the legal term, abrogate, would have entered into the picture of RNA-mediated events that I portrayed.
I think that Marraffini’s group has repeatedly provided expert supporting documentation for my model and all accurate representations published on this blog site. Someone from Marraffini’s group might make a good expert witness who could offer damning testimony against the neo-Darwinists who left out the role of viruses in the “Modern Synthesis,” which reportedly was invented based on de Vries definition of mutation and assumptions about how long it would take accumulated mutations to lead to the evolution of one species from another.
See: 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
See also: [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. — Lynn Margulis
Perry Marshall and others may think they can abrogate responsibility for ignoring models that link atoms to ecosystems via what is currently known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution. Until now, that’s what they have done. For twenty years, I have done my best to help ensure that no pseudoscientist is left with any of the ridiculous claims from their past. Until litigation is initiated by those who are Combating Evolution to Fight Disease, I recommend that others visit the Scopes Museum in Dayton, Tennessee to get a better perspective on what the nonsense about teaching evolution in schools was all about — and why pseudoscientists seem to want the nonsense to continue.
This book is on display: A Civic Biology: Presented in Problems (New York, 1914)
It was opened to pages 195 and 196 last time I visited, which is when I took the picture (above).

Evolution of Man. – Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants. If we follow the early history of man upon the earth, we find that at first he must have been little better than one of the lower animals. He was a nomad, wandering from place to place, feeding upon whatever living things he could kill with his hands. Gradually he must have learned to use weapons, and thus kill his prey, first using rough stone implements for this purpose. As man became more civilized, implements of bronze and of iron were used. About this time the subjugation and domestication of animals began to take place. Man then began to cultivate the fields, and to have a fixed place of abode other than a cave. The beginnings of civilization were long ago, but even to-day the earth is not entirely civilized.
The Races of Man. – At the present time there exist upon the earth five races or varieties of man, each very different from the other in instincts, social customs, and, to an extent, in structure. These are the Ethiopian or negro type, originating in Africa; the Malay or brown race, from the islands of the Pacific; the American Indian; the Mongolian or yellow race, including the natives of China, Japan, and the Eskimos; and finally, the highest race type of all, the Caucasians, represented by the civilized white inhabitants of Europe and America.

My comment: After visiting the Scopes Museum, you may be more interested in visiting the Creation Museum.
The statement in this picture seems to be a theme throughout the Creation Museum, and the theme appears to link ecological variation to ecological adaptation over-the-weekend via two nutrient-dependent amino acid substitutions, which were reported as if they were mutations in: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Resurrection… is the concept of a living being coming back to life after death. It is a religious concept… 
I reiterate: Abrogate appears to be a legal term…
In my opinion, the use of terms such as abrogate and resurrection by researchers (and Perry Marshall’s opinions about hybrids) will lead to another trial that could pick up from where the Scopes trial left off. However, at the next trial, serious scientists could testify to facts that link the microRNA/messenger RNA balance to energy-dependent healthy longevity or to virus-perturbed protein folding and mutation-driven pathology. The next trial could be based on what is known about energy, microRNAs, energy theft, and ecology.
See for example: Phytochemicals modulate carcinogenic signaling pathways in breast and hormone-related cancers
Also, see: Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

My comment: I think that it might benefit all evolutionary theorists if the next trial was held very soon. Each week it becomes more difficult for them to deny Dobzhansky’s claims from 1964 and from 1973.

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! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.
Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.”


…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.

And, each week during the past two months I have become increasingly annoyed by Perry Marshall’s claims. I’m beginning to think he was hired to advertise the claims of of evolutionary theorists who believe that hybrids created in the lab exemplify creation.

Hybrids of Drosophila pseudoobscutra and D. persirnilis are easily obtainable in the laboratory, but they are absent in localities where both species occur side by side (14).

See also:

The lowest common denominator is nutrient-dependent RNA-mediated DNA repair. In the context of the physiology of reproduction, it links atoms to ecosystems via the innate immune system. Fixed amino acid substitutions stabilize all organized genomes.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. https://dx.doi.org/10.6084/m9.figshare.994281
Now see: “Team uses internet network theory to decipher the first epigenetic communication network” January 28, 2016 https://phys.org/news/2016-01-team-internet-network-theory-decipher.html
They are reporting what I detailed in an invited review of nutritional epigenetics. But they place it into the context of nutrient-dependent epigenomic co-localization and co-evolution. They don’t seem to realize the communication hub in the chromatin network of embryonic stem cells does not automagically evolve.

Re: “Laplace demonstrated that perturbations were not cumulative…”
I’m interested in attempts to apply mathematical models to biologically-based cause and effect. For example, the misrepresentations include this one: Human brain networks function in connectome-specific harmonic waves https://dx.doi.org/10.1038/ncomms10340
Excerpt: We found that structured oscillatory patterns naturally self-organize on the human connectome for a wide-range of diffusion parameters in the model (Fig. 4a–d; Supplementary Figs 8 and 9; Supplementary Movies 1–4).
Theorists willingly extend “…a universal mathematical framework, eigendecomposition of the Laplacian, to the anatomical structure of the human connectome…” without the energy-dependent organization of cells and RNA-mediated cell type differentiation.
That’s why theorists are the subjects of parodies like this one. It links atoms to ecosystems by what is known to serious scientists about energy-dependent changes in base pairs.

Plants with biosensors may light the way https://news.harvard.edu/gazette/story/2016/02/plants-with-biosensors-may-light-the-way/
The technology they introduce shows how “…ordinary organisms can be transformed into extraordinary living cellular devices that can sense specific signals and produce appropriate responses…”
All living genera must sense, signal, and respond appropriately. The sensing, signaling and responding begin involve RNA-mediated amino acid substitutions. That fact was the subject of my reviews in 2012 and 2013.
https://www.ncbi.nlm.nih.gov/pubmed/24693349 2012 Excerpt: “Philosophically and metaphorically, these neural networks extend to mammalian brains. The concept that is extended is the epigenetic tweaking of immense gene networks in ‘superorganisms’ (Lockett, Kucharski, & Maleszka, 2012) that ‘solve problems through the exchange and the selective cancellation and modification of signals (Bear, 2004, p. 330)’. It is now clearer how an environmental drive probably evolved from that of food ingestion in unicellular organisms to that of socialization in insects.”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960065/ 2013 Excerpt: “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. (Max Planck, 1858–1947)”

Like many others, you seem to be confused about what can happen in the lab compared to what does not happen outside the lab.
For example: Re: “1) Hybrids, where Species 1 crossed with Species 2 gives you Species 3. ”

For comparison: Species of Drosophila https://www.sciencemag.org/content/177/4050/664.short

Excerpt: “Hybrids of Drosophila pseudoobscutra and D. persirnilis are easily obtainable in the laboratory, but they are absent in localities where both species occur side by side (14).”

Conclusion: I’ve become less tolerant of Perry Marshall’s ignorance, and this claim: Creationists Underestimate God.

In my opinion, he underestimated at least one creationist. He also offered a Technology Prize for Origin of Information, but has not yet made any Non-Disclosure Agreement available to me, or any submission form. The revision of claims made by theorists seem to me to be the clearest indicator of the threat that the origin of information poses to theorists who have built their theories on the automagical appearance of the code and the concurrent appearance of the nutrient-dependent innate immune system that appears to protect all organized genomes from virus-driven entropy.

See also: Make them talk about evolution: Why won’t a single Republican presidential candidate admit that Darwin’s right

Excerpt 1)

Scopes Monkey Trial Redux

In brief, a fundamentalist majority of the Dover (population 1,999) School Board threatened to block the adoption of a biology textbook that one board member described as “laced with Darwinism”––unless the district purchased a companion set of Christian biology texts (Of Pandas and People). The board majority also required teachers to read an evolution disclaimer to all students enrolled in ninth-grade biology.

Excerpt 2)

Speaking to a group of Seventh Day Adventists in 2011, Carson attributed evolution to the Adversary (Satan). “I personally believe that this theory that Darwin came up with was something that was encouraged by the Adversary, and it has become what is scientifically, politically correct.”

My comment: What if Perry Marshall had been hired to write Evolution 2.0 as part of a campaign strategy for the Democrats? What if he knows young earth creationists have already claimed that viruses are the cause of all pathology?
See: Viral Genome Junk Is Bunk
Excerpt: So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6
See also: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
Authors’ comment: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
My comment: What if the Republican candidates force the Democratic candidates to talk about evolution of the bacterial flagellum in 4 days in the context of what is known about cell type differentiation in all living genera?


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