Intelligent viruses and cancers?

The Very Intelligent Ebola Virus Takes Front and Center

Excerpt 1) “Ebola doesn’t enter the nucleus. It uses the cell’s machinery of ribosomes and transfer RNA to make proteins from the viral messengerRNA.”
Excerpt 2) “Normally, mechanisms inside the nucleus have complex relations with messenger RNA and the alternative RNA editing process (see RNA alternative editing post). Specific protein complexes help splice the messengerRNA before it is sent from the nucleus to the ribosomes in the cytoplasm to make proteins.”
My comment: Dr. Lieff may be the only one capable of detailing the problem presented by the Ebola viruses in terms of cell type differentiation that other scientists from different disciplines can understand. But first, others must want to understand the complexity that is involved. That requires them to stop thinking that the problem can be attributed to mutations and start thinking in terms of how ecological adaptations occur via nutrient-dependent amino acid substitutions that stabilize the organized DNA in the genomes of non-viral cell types.
See also: Intelligent RNAs in the Brain

Excerpt 1) ‘Viruses and jumping genes changed this dogma into a bidirectional flow of code in and out of the DNA. Alternative splicing added an additional major step with very complex editing of the pre-messenger RNA. In humans as many as 500 different messenger RNAs, and therefore 500 different proteins, can be made from one pre-messenger RNA.”

My comment: No one else seems to recognize the link from pre-messenger RNAs (pre-mRNAs) to the alternative splicings that lead to the production of different messenger RNAs (mRNAs). Alternatively, if they do recognize the link from pre-mRNAs to different mRNAs and cell type differentiation, they may not recognize the fact that the conserved molecular mechanisms of alternative splicings appear to link ecological variation to RNA-mediated amino acid substitutions that determine the virulence of viruses and their ability to manipulate the cell types of different species.
Cross species examples have already been seen in the light of what has happened with other viruses that infected other mammals, but now infect humans. If the molecular mechanisms of cell type differentiation are conserved across species, the amino acid substitutions that determine seasonal variations in the ability to infect humans also reflect that fact that viruses adapt via their ability to use materials found in different cell types of different species to produce new amino acids that allow the viruses to proliferate via subtle changes in their cell types.
See for example: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (with my comment) reported as:Research reveals details of how flu evolves to escape immunity
Excerpt:“…seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution.
My comment: The ability of viruses to change via a single amino acid substitution enables them to escape the immunity of vaccines. This drives the seasonal need to develop new vaccines. Can we expect the same ability to drive changes in the Ebola viruses, which link them to their ability to escape the natural immunity already established in some but clearly not all other animals, including some humans?

See also:

1) The Wall Street Journal (11/3, A8, Marcus, Subscription Publication) reports that researchers have begun to look at the children of individuals who have the rare and fatal genetic disease Niemann-Pick Type C, a disease whose gene may offer protection against the Ebola virus. Institutions whose researchers are investigating such a connection include Albert Einstein College of Medicine, the US Army Medical Research Institute of Infectious Diseases, the Netherlands Cancer Institute and Harvard Medical School.

My comment: Does the gene offer protection or is an amino acid substitution in the DNA of the organized genome the protector against the Ebola virus?

2) Virologists Investigate Ebola’s Connection To Bats. NPR (10/31, Greenfieldboyce) reported in its “Shots” blog and on its “Morning Edition” program on virologists who are focusing on studying Ebola. While “scientists believe the virus circulates in fruit bats…no one knows the details of how bats pass it to humans or other species,” including gorillas, chimpanzees, and antelope, species which have been known to have the virus in the past. A second concern for researchers is the drastic variation in sickness levels among infected humans. Researchers are examining why “some people get very sick, others seem to get less sick, and others may not get sick at all.”

My comment: See my blog post: Are evolutionary theorists ‘nob ends’? “…some researchers seem to think the Ebola viruses mutate and automagically change the biophysically-constrained properties of their chemical bonds. Supposedly, that’s how mutations in viruses enable changes in virulence, which actually arise via amino acid substitutions and changes in hydrogen bonds that link atoms to ecosystems.” Without the link from atoms to ecosystems, even serious scientists are left with only their speculation about how viruses are transmitted across species and why some individuals are more susceptible than others to diseases.

3) Reuters (11/2, Hirschler) also reported bats to be the prime suspect for spreading Ebola to humans, although bats themselves do not get sick with the virus. Additionally, bats are known to carry several other viruses which can include rabies and severe acute respiratory syndrome (SARS). Researchers are investigating bats’ ability to carry such disease without becoming sick and learn the mechanisms by which they do so.

My comment: The most likely reason that frugivorous (fruit) bats carry — but do not succumb to such viruses, is that levels of ingested vitamin C stabilize their organized genomes via nutrient-dependent amino acid substitutions associated with the complexity of  DNA repair mechanisms. The most likely mode of transmission to humans during their preparations to eat the bats (categorized as bush-meat). Food preparation is the suspected mode of transmission that supposedly enabled the change from SIV in other primates to HIV in humans. However, even if no one ever killed, cooked, and ate a bat, transmission might still occur as was represented in the recent science fiction movie “Contagion.”
Excerpt: “The fictional virus reaches humans through a series of animal encounters: a bat eats some fruit then drops it in a pig pen, the pig eats it, then is butchered and handled by a chef who comes in contact with Gwenyth Paltrow.”
My comment: I am reminded of how Greg Bear linked human endogenous retroviruses to the evolution of human biodiversity in his science-fiction novels, ‘Darwin’s Radio’ and ‘Darwin’s Children’. However, the changes caused by the viruses were beneficial, not deadly.
4) US Hospitals Prepare For Ebola. The Wall Street Journal (10/31, Armour, Subscription Publication) explored the debate about treatment for Ebola patients in US hospitals. An ethical dilemma exists because physicians may want to pursue aggressive treatments for Ebola patients, though some of those treatments increase the risk of exposure of the disease to hospital staff. Stephen Cantrill, the American College of Emergency Physicians’ Ebola panel chairman, explained that the issue of defining “futile care […] with modern Western medicine […] is going to be very tough.” The Journal reported on several hospitals who said they may not provide CPR to an Ebola patient.
My comment: What if the most effective preventative treatment was supplementation with vitamin C. It could facilitate DNA repair to prevent the damage in infected humans from the cytokine storms associated with the ability of the virus to adapt to different mammalian hosts — perhaps via a single amino acid substitution? Alternatively, what if the thermodynamic cycles of protein folding in the viruses could not occur at body temperatures above 104 degrees? Could a steaming hot bath or sauna cure before the virus killed?
Will someone like Jon Lieff or Brian Cox comment, or will we all be killed by the pseudoscientific nonsense about evolution touted by people like Neil deGrasse Tyson in the series Cosmos? See his comments on Episode#2 . Note the difference between serious scientists and creative pseudoscientists, like Tyson, reported here: “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. 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…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.”
May God help us all if the pseudoscientists do not quit touting their nonsense about “emergent truths” while trying to teach others to believe in the magic of Mutation-Driven Evolution as if “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.”
For comparison, see Nutrient-dependent/pheromone-controlled adaptive evolution: a model, with its examples of how ecological variation leads to ecological adaptations. The conserved molecular mechanisms of RNA-mediated cell type differentiation via amino acid substitutions in species from microbes to man seem to be consistent with what Jon Lieff suggests is a very intelligent virus.
Its level of intelligence can be compared to the intelligence of evolutionary theorists who think that viruses mutate and evolve or that bacteria evolved into humans. Why don’t they know that viruses ecologically adapt to ecological variation that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of every living species on this planet? Do they not understand how the physics, chemistry, and conserved molecular mechanisms are manifested in species from microbes to man? It’s beginning to look like some people are not intelligent enough to think about anything except what they were taught to believe in.
See also: A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats
Excerpt: “We found shifts associated with frugivory across the entire OR subgenome. Particular shifts in diversity within functional genes and pseudogenes, rather than the simple pseudogenization of a large number of ORs, suggests adaptive changes linked to ecological specialization in the highly derived frugivorous phyllostomids.
My comment: Ecological specialization links the nutrient-dependent pheromone-controlled physiology of reproduction to the highly successful radiation of bats via the experience-dependent de novo creation of olfactory receptor genes. De novo creation of genes has been touted as if it were the holy grail of evolutionary biology. However, it appears to be the holy grail of creationists like Dobzhansky since it is linked from RNA-mediated events to the amino acid substitutions that differentiate cell types in species from microbes to man. Dobzhansky he noted what occurred among primates: “…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.” see: Nothing in Biology Makes Any Sense Except in the Light of Evolution
It appears that nothing about evolution makes sense, unless it is placed back into the context of the light of creation via the de novo creation of olfactory receptor genes. Experience-dependent de novo creation of receptors can be linked from light-induced amino acid substitutions to nutrient-induced receptor-mediated RNA-mediated amino acid substitutions in animals via quaternary and ternary switches. The complexity of these switches is linked directly to cell type differentiation in health and disease via the conserved molecular mechanisms manifested in the morphological and behavioral phenotypes of species from microbes to man.

Time for a sermon or common sense?

The thing that hath been, it is that which shall be; and that which is done is that which shall be done: and there is no new thing under the sun. — Ecclesiastes 1:9
In the light of the sun, we can now revisit what JBS Haldane wrote in 1963 about “The four stages of acceptance:
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.” — Review of The Truth About Death, in: Journal of Genetics 1963, Vol. 58, (p.464)”
I learned of this approach to acceptance many years ago, and found a source for it. The source attests to the fact that acceptance of biological facts has always lagged behind the acceptance of the theory of evolution, which JBS Haldane helped to invent and define in terms of population genetics. See for examples: Science, Pseudoscience, and The Three Stages of Truth — cited in The Truth in Small Doses: Why We’re Losing the War on Cancer-and How to Win It.
See also:
Arguments against new ideas generally pass through three distinct stages, from `It’s not true’, to `Well, it may be true, but it’s not important’, to `It’s true and it’s important, but it’s not new — we knew it all along. (p. 1) — John D. Barrow. The Artful Universe. Oxford University Press, 1995.
We now can put what has been known all along about the link between light-induced amino acid substitutions into the context of “…no new thing under the sun” — Ecclesiastes 1:9, and what Dobzhansky (1964) wrote, presumably about people like JBS Haldane:
“…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!”
In the same article, Dobzhansky noted — 50 years ago — that “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.”
In 1973, he then placed that fact into this context “…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” into the context of Nothing in Biology Makes Any Sense Except in the Light of Evolution. He also linked his creationist beliefs to evolution via mutations and amino acid substitutions.
1) “It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist.”
2) “Most mutations involve substitutions of single nucleotides somewhere in the DNA chain coding for a given protein. Therefore, one can calculate the minimum numbers of single mutations needed to change the cytochrome C of one organism into that of another.”
Calculations were used that made it appear that mutations accumulated over eons and led to the evolution of biodiversity.
We now know that single nucleotide substitutions link amino acid substitutions to cell type differentiation via nutrient-dependent RNA-mediated events, which occur quickly and do not occur due to mutations. Simply put, it has become clearer that mutations do not change the cytochrome C or any other aspect of metabolism in one organism into that of another species.
Mutations cause perturbed protein folding that cannot lead to from one species to the evolution of another species. Mutations lead to pathology. The sooner theories about the evolution of biodiversity are removed from the facts about cell type differentiation, the sooner progress will be made towards understanding and treating cancer and the ecological adaptations manifested in the Ebola viruses and other viruses.
But wait, how did I get from the Ebola viruses to cancer and back? I did it with the explanatory power of  nutrient-dependent pheromone-controlled cell type differentiation. How would an evolutionary theorist do that? See also: From HIV to cancer, IL-37 regulates immune system for additional information that appears to link cell type differentiation in viruses to uncontrolled cell type proliferation in cancers via conserved molecular mechanisms.
What I’ve recently seen is attempts to link ‘protein isoforms’ and alternative splicings of pre-mRNA as if both were representations of biologically-based cause and effect. See this Wikipedia entry with my emphasis:
Excerpt: “A protein isoform is any of several different forms of the same protein. Different forms of a protein may be produced from very closely related gene duplicates—as ‘same protein’ or ‘a protein’ makes no sense for highly diverged paralogs that arose from a single ancestral gene that duplicated billions of years ago and subsequently diverged greatly in sequence, structure and functionality—or may arise from the same gene by alternative splicing. In older literature one can also encounter the use of the term isoform to describe alleles of the same gene, but currently the terms refers mostly to paralogous and alternatively spliced proteins, not alleles.”
Apparently, the theorists think they can get away with more misrepresentations of how nutrient-dependent cell type differentiation occurs within a few generations as recently shown in lizards. If they can continue to convince others that RNA-directed DNA methylation and RNA-mediated events that link cell type differentiation to a single ancestral gene and evolutionary events across billions of years, most of us may be dead by the time the rest of us realize we were tricked into believing in a ridiculous theory instead of biologically-based facts.

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