5th-6th Sept 2018 Dublin, Ireland

Abiogenesis vs microRNA biogenesis (3)

 

My comment to

Thank you for helping to show what has been missing from neo-Darwinian theories and other claims that were based on de Vries 1902 definition of mutation. Theorists may now want to learn more about the energy-dependent molecular mechanisms of recombination.

Most of them will not like the findings you have provided. The peer-review process is especially deadly to those who challenge the current dogma. But since you have made the quantum leap see also:

Mechanisms of Recombination conference  Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Natural selection for codon optimality link quantized energy-dependent RNA-mediated DNA repair from biophysically constrained viral latency to sympatric speciation and all biodiversity.

When people who you thought were your peers reject your findings, you need only wait until after “Schrödinger at 75 – The Future of Biology” – September 2018 to resubmit and publish in a top-tier journal (if you have not already done so).

Until then, see also: Systematic analysis of complex genetic interactions

Reported as: How Many Genes Do Cells Need? Maybe Almost All of Them
Theorists failed to note that the creation of genes in yeasts is quantized energy-dependent and biophysically constrained by the physiology of reproduction. Most of their ridiculous claims try to link abiogenesis to genome evolution.
See for example:  Genome evolution across 1,011 Saccharomyces cerevisiae isolates
The origin of the yeast species in China has been linked to all biophysically constrained sympatric speciation via the section on molecular epigenetics from this 1996 review of RNA-mediated cell type differentiation.
From Fertilization to Adult Sexual Behavior

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…

From the Discussion:

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

See also: Correction of β-thalassemia mutant by base editor in human embryos
See for comparison: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

…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.

Theorists must now face the facts about mitochondrial DNA that also attest to their ignorance. They will be forced to link the creation of anti-entropic virucidal energy to the creation of ATP synthase, the creation of ATP, and the creation of RNA, which links microRNA biogenesis from naturally occurring energy-dependent base editing and the origin of microbial yeasts in China to morphological and behavioral phenotypes in humans via biophysically constrained changes in the microRNA/messenger RNA balance.
After comparison to these “Levels of Biological Organization” (See slide # 6) and the examples from all species, anyone left touting ridiculous theories will be dismissed.

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Is meat protein unhealthy? (2)

See also: Microbiome-Grade DNA Extraction Kits

…the thermal and chemical methods effectively lyse the gram-negative organisms and boost their population in the final profile, amplifying the bias.

This suggests that all links from food energy-dependent de novo creation of the pheromone-controlled biophysically constrained bull sperm microRNAome have been misinterpreted in the context of virus-driven fescue toxicosis.

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Fescue toxicosis links the virus-driven creation of enzymes to the degradation of messenger RNA in bull sperm and to the transgenerational epigenetic inheritance of mutations, which all serious scientists have linked from damage to supercoiled DNA to all pathology in humans and other species.

Eating the meat from other animals that have not ecologically adapted to the virus-driven theft of quantized energy has been linked from the viruses in their genomes to human pathology via the degradation of messenger RNA in bacteria that become archaea and L-forms.

See also: Dobzhansky (1973)

…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 also: The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

No serious scientist has ever reported a link from the Virus-mediated archaeal hecatomb in the deep seafloor to the evolution of anything except pathology. All serious scientists have, for comparison, linked ecological variation to food energy-dependent  polycombic ecological adaptations via biophysically constrained viral latency in species from microbes to humans.

From Fertilization to Adult Sexual Behavior (1996)

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…

See also: Cytosis: A Cell Biology Board Game for ages 10+

 A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

Biology to a Physicist

Energy-dependent epigenetic translation to mRNA stability (2)

See first:

Energy-dependent epigenetic translation to mRNA stability

Universe’s ultraviolet background could provide clues about missing galaxies

Simulations show that there should be more small galaxies in the Universe, but UV radiation essentially stopped them from developing by depriving them of the gas they need to form stars.
UV light constrains the creation of galaxies and also biophysically constrains the creation of the mutations in cancer cells.
When will Stephen Hawking and other biologically uninformed theorists admit that their ridiculous theories can only be linked to other ridiculous neo-Darwinian theories? When will all theorists admit that they do not understand how biophysically constrained virus-driven energy theft must be linked from the Creation of the sun to all biodiversity on Earth via the physiology of energy-dependent reproduction? Here is a clue to that missing admission.
Stephen Hawking And 32 Top Physicists Just Signed a Heated Letter on The Universe’s Origin

Unfortunately there’s no neat resolution to this debate on the horizon, with both sides standing pretty firm. The one thing they both agree on is the fact that inflation theory isn’t perfect, and we should all keep an open mind about what really happened at the birth of our Universe as new data comes in.

What new data might come in for comparison to this claim, which is based only on ridiculous theories?
Physicists make the case that our brains’ learning is controlled by entropy

…consciousness could simply be a side effect of entropy, and our brains organising themselves in the most efficient manner.

No new data supports that claim.
For comparison, see this data: Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment
reported as: OLYMPUS experiment sheds light on structure of protons

…two photons are indeed exchanged during electron-proton interactions.

However, unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

See also:  UPR Transducer BBF2H7 Allows Export of Type II Collagen in a Cargo- and Developmental Stage-Specific Manner

The unfolded protein response (UPR) handles unfolded/misfolded proteins accumulated in the endoplasmic reticulum (ER). However, it is unclear how vertebrates correctly use the total of ten UPR transducers. We have found that ER stress occurs physiologically during early embryonic development in medaka fish…

ER stress links the virus-driven degradation of messenger RNA to all pathology in all living genera. Negative supercoiling in DNA links the degradation of messenger RNA from mutations via the accumulation of unfolded/misfolded proteins. For comparison, the nutrient energy-dependent pheromone-controlled physiology of reproduction in bacteria links the growth of trees in the forest to cell type differentiation in birds that have different diets.

Untangling the knots in cell stress

“We found that at first the production of short chain collagen causes a certain transducer to be activated for quality control.” Collagen is the most abundant protein in vertebrates, providing external support for cells.

In the next stage of development, cells received a signal from main actor proteins and started to produce longer-chain collagen. In response to this new ER stress, a new UPR transducer was activated to produce components to export the larger collagen out of the ER. Without this, larger collagen would be unable to leave the cells and do its job.

“This showed us that different UPR transducers are activated to cope with different ER stresses caused by different proteins,” says Ishikawa.

ER stresses are not caused by proteins. Unfolded/misfolded proteins accumulate outside the context of energy as information and biophysically constrained supercoiling of functional DNA. See: Structural diversity of supercoiled DNA
The supercoiled DNA of soil bacteria links the energy-dependent growth of trees to the diet of the birds and the bees.
See: Genome divergence and diversification within a geographic mosaic of coevolution

Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

Coevolution was reported as energy-dependent biophysically constrained ecological adaptation in: The seeds of speciation

The details of the crossbill-lodgepole mosaic have been studied extensively, but it’s not been clear whether South Hills crossbills are genetically isolated by coevolution with pine in that one tile of the mosaic. If they are, the birds’ [nutrient-dependent] adaptation to the tree’s defenses might be setting the South Hills crossbills on the road to the origin of a new species.

For comparison to claims about new species of birds being created by evolution across 6000 years, see also: Talking Trees—Secrets of Plant Communication

When one tree is sick, nearby trees may share nutrients through their roots to help it get well again. If a lodgepole pine sapling springs up in the shade of a thick forest, older trees somehow sense that it doesn’t get enough sunlight to make food for itself, so they may share their bounty. They even change their root structure to open space for saplings.

The complexity of systems biology among all energy-dependent ecosystems is difficult for serious scientists to place back into the context of coevolution and impossible to place back into the context of Mutation-Driven Evolution (p 196)

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

See also: Hypothalamic microRNAs flip the switch for fertility

Figure 1) MicroRNA-gene network controlling GnRH transcription: the timely switch in GnRH expression from repression to induction leads to puberty onset

MicroRNAs are the link to GnRH transcription from what we referred to as pre-mRNAs in our section on molecular epigenetics from this 1996 review: From Fertilization to Adult Sexual Behavior

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.

If microRNAs are not the link from energy-dependent epigenetic translation to mRNA stability, theorists will need to find experimental evidence of how the sun’s anti-entropic virucidal energy as information is linked from top-down causation to hormones and behavior, and present that evidence to serious scientists for consideration.

Alternative splicing of pre-mRNA

80 years of causal analysis (1936 – 2016)

Roles of Mutation and Selection in Speciation: From Hugo de Vries [1902 definition of mutation] to the Modern Genomic Era
Excerpt:

…mutation is crucial in speciation because reproductive barriers cannot be generated without mutations.

My comment: Chromosomal rearrangements link autophagy from energy-dependent changes in RNA-mediated amino acid substitutions and supercoiled DNA to all biodiversity via speciation.

Some Principles of Causal Analysis in Genetics (1936)

Extract:

…high frequency radiation and particles of high velocity are very important components of the environment, causing heritable changes by a process called mutation. Even if we could conduct our experiments behind 30 metres of lead the fact that mutation has a temperature coefficient is enough to show that it depends in part on energy fluctuations which are uncontrollable.

My comment: In 1902, De Vries defined the uncontrollable energy fluctuations in the context of his definition of “mutation.” Others have since linked Darwin’s “conditions of life” from  energy fluctuations to natural selection for energy-dependent codon optimality and healthy longevity via biophysically constrained polycombic ecological adaptation.
See for example: miR-125a-5p regulates differential activation of macrophages and inflammation

My comment: Nutrient energy-dependent changes in the microRNA/messenger RNA balance link autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

See for ~54,000 examples: microrna and autophagy

See for comparison: A new function for oncoproteins of DNA tumor viruses

Excerpt: 

…the same five amino acid sequence that binds cGAS also binds cellular proteins (such as Rb), disrupting their function and leading to uncontrolled cell growth!

Re: Could both functions have been simultaneously selected for?
My comment: No. Both functions could not have been simultaneously selected for!
Nothing known to serious scientists about top-down causation suggests that the RNA-mediated amino acid sequences in proteins can be simultaneously selected to link natural selection for energy-dependent codon optimality to healthy longevity and to simultaneously link virus-driven energy theft to all pathology. In the context of everything known to serious scientists about all living genera, cell type differentiation is energy-dependent and it must be biophysically constrained.
For a review of the biophysical constraints that link all invertebrates to all vertebrates, see: 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.

My comment: In 1996, we reviewed the established facts about energy-dependent biophysically constrained polycombic ecological adaptation based on what was known about the small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb.  The facts about energy-dependent polycombic ecological adaptation have not changed. Only the pseudoscientific nonsense of neo-Darwinian theories has been forced to include the changes portrayed in the context of virus-driven hecatombic evolution.
See for comparison:  Virus-mediated archaeal hecatomb in the deep seafloor

We estimated that viral infections were responsible for the abatement of 1.0 to 2.2% day−1 (on average 1.6% day−1) of the bacterial abundance and 2.3 to 4.3% day−1 (on average 3.2% day−1) of the archaeal abundance in deep-sea sediments (Fig. 6).

My comment: The claim that viruses kill ~1.6% of bacteria each day and ~3.2 % of archaea in deep-sea sediments is buried in technical jargon. It was previously resurrected in the report of the weekend resurrection of the bacterial flagellum.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The nutrient energy-dependent pheromone-controlled weekend resurrection of the bacterial flagellum eliminates the confusing rhetoric that theorists use to explain how differences in cell death from archaea to bacteria might be attributed to evolution. The differences are obviously linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptation in all living genera. For comparison to hecatombic evolution, healthy longevity exemplifies polycombic ecological adaptation.
The cause of death in all cell types is linked to virus-driven energy theft and nutrient energy-dependent healthy longevity is linked from cell type differentiation to all biodiversity. Simply put, virus-driven energy theft is linked from hecatombic evolution to all pathology.
The claim that mutation-driven hecatombic pathology and polycombic ecological adaptation could be simultaneously selected is a claim that only a biologically uninformed theorist would make, or accept.
See for comparison: Neurons adjust their proteins during homeostatic scaling
Excerpt:

Changes in the synthesis of cellular proteins lie at the heart of all adaptations that cells undergo.

My comment: That fact was reported in the context of this publication. Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses
Excerpt:

In addition, although it has not been explicitly addressed here, it is obvious that the regulated degradation of proteins must also play a role in sculpting the proteome during homeostatic scaling. Indeed, we observed many proteins in the ubiquitin proteasome pathway that were regulated by scaling (Figure 3C; Table S3).

My comment: Nascent proteome remodeling links nutrient energy-dependent autophagy from natural selection for codon optimality to changes in protein biosynthesis and degradation. The changers link RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera in the context of the physiology of reproduction.  Pseudoscientists, atheists, and most science journalists do not seem to understand that fact.
For comparison, serious scientists do not need more proof that autophagy did not simply emerge to link energy as information to all biodiversity via the conserved molecular mechanisms of cell type differentiation that link angstroms to ecosystems in species from microbes to humans. Serious scientists do not need more proof that all neo-Darwinian pseudoscientific nonsense is nothing more than one theory added to another after de Vries defined “mutation” in 1902.
Do you know any serious scientists who has used any definition in the context of reporting their results of testing in the medical laboratory? For example, have you ever used a definition to link the results of a blood gas analysis from hydrogen-atom transfer in DNA base pairs in solution to the patient’s outcome?

See also (video): Feynman explains the difference between science and the pseudoscientific nonsense of neo-Darwinian theory with added feedback on the claims of expert theoretical physicists who have failed to link energy-dependent changes from angstroms to ecosystems in all living genera.
http://dai.ly/x24hxji
My comment: Experimental evidence of biologically based cause and effect links physics and chemistry to the conserved molecular mechanisms of cell type differentiation that we detailed in our 1996 Hormones and Behavior review.
See for comparison: Different rates of mRNA degradation can be explained by the existence of different regulatory mechanisms.


My comment: Researchers like him should stop ignoring the facts. Energy-dependent autophagy mediates the mRNA turnover rate and links nutrient energy-dependent RNA-mediated amino acid substitutions to healthy longevity via the physiology of reproduction and transgenerational epigenetic inheritance of morphological and behavioral phenotypes. Virus-driven energy theft links mRNA degradation to all pathology.
See also: This virus may have stolen deadly DNA from black widow spiders (10/12, Feltman) reports researchers have discovered that the WO virus, which infects bacteria, contains “snippets” of DNA from several animals including black widow spiders, according to a study published in Nature Communications. The virus infects the Wolbachia bacteria, which primarily affects arthropods including insects and spiders. Researchers found that the WO virus “contains part of the gene for latrotoxin, the chemical that gives the black widow spider venom its punch.”

The Virus With Spider DNA (10/12, Yong) reports the researchers suspect that the virus obtained the genetic material directly from the spiders infected by Wolbachia, or the bacteria may have obtained it from the spiders before passing it on to the virus.

        Additional coverage is provided by: How the Heck Did Black Widow Spider DNA Get Inside a Virus? (10/11, Choi) and Virus stole poison genes from black widow spider (10/12, Rincon).
My comment: Virus-driven energy theft occurs in only one direction. It links cell type death from archaea to Zika virus damage in human infants via transgenerational epigenetic inheritance of pathology. The idea that a virus that infects bacteria could have come from the DNA of animals is one that misrepresents everything currently known to serious scientists about autophagy.
Ideas like that are the source of pathology that alters the behavior of family members who believe that any idea is as good as a model of biologically-based cause and effect.

Biologically uniformed family members have unfriended me on Facebook because they do not want anyone to become informed.

Jeanette C Seeman Wow, I’m sorry to hear that. The subject seems complex and a little grace could go a long way. They could have unfollowed you instead of unfriending you. Hope they will see you in person. Wishing you the best.
James Kohl
James Kohl Thanks for putting their actions into perspective, Jeanette C Seeman.
I’ve learned that expertise on any given topic may cause embarrassment in non-experts who think experts are insulting their intelligence or criticizing their beliefs. This is true at all levels. 2004 Templeton Prize winner, George FR Ellis, who is or was an active Quaker, unfriended me when I commented on the book he published in June. He left out the information on my model, even after he claimed I was correct.
He has had an ongoing disagreement with Roger Penrose about the fact that the source of all information links the creation of the sun to energy-dependent healthy longevity. Ellis and Penrose have co-authored with Stephen Hawking. I linked energy as information to the Resurrection of Christ via everything currently known to all serious scientists about biologically-based cause and effect. George FR Ellis refuses to address that fact in any context.
This is what he is avoiding. In 1991, Roger Penrose wrote: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”
Last month, this assault on the beliefs of all who tout nonsense about the emergence of everything from nothing and neo-Darwinian theories about millions of years of evolution should have cinched the election of Donald Trump for President. http://dx.doi.org/10.1038/nnano.2016.164
Trump, for example, is supported by young earth creationists such as Mike Pence and Dr. Ben Carson. Now, we have examples of ignorance from a well-respected cosmologist/astrophysicist (Ellis), for comparison to a mathematical physicist, mathematician and philosopher of science (Penrose), and Mike Pence and Dr. Ben Carson.
If Hillary wins, we will have another example of what the term “reprobate mind” actually means. It means people would rather believe anything they are told as long as it cannot be placed into the context of physics, chemistry, biology and Biblical Genesis via what is known about molecular epigenetics, which is that “…we eat food in order to gain energy?” The energy biophysically constrains the viral apocalypse that the liberals predictably will cause.
This is science, not religion: https://www.ncbi.nlm.nih.gov/pubmed/24693353 Why do you think it was published in Socioaffective Neuroscience & Psychology? What has any pseudoscientist/atheist written for comparison?

Socioaffect Neurosci Psychol. 2013 Jun 14;3:20553. doi: 10.3402/snp.v3i0.20553. eCollection 2013. Review
ncbi.nlm.nih.gov|By Kohl JV
James Kohl
James Kohl See also: http://dx.doi.org/10.1038/nnano.2016.164

nature.com

See also my attempt to discuss the fact that: NONE of the papers establish that SOMETHING can come into existence from NOTHING.

//Do you reject any of those claims?”//

I simply do not see the evidence for the claim that Viruses cause ALL pathology.
– Bacteria can cause pathology.
– Toxins can cause pathology.
– Heavy metals can cause pathology.
– Fungi can cause pathology.
– Parasites can cause pathology.
I do not see the warrant to state that NONE of the above can cause pathology and so ONLY viruses can cause pathology.

What is known about energy-dependent autophagy is the evidence for the claim that viruses cause all pathology. The 2016 Nobel Laureate in Physiology or Medicine won the prize for experimental evidence that autophagy was the link to chromosomal rearrangements and all biodiversity, which was addressed by the 1933 Prize winner, and 2004 Prize Winners. You are claiming to not see the evidence that I put into this context:
 
“Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
 
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
 
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.”
 
Read more at: http://phys.org/news/2014-01-americans-dont-evolution.html#jCp
See also:

Conclusion: Everything known to serious scientists about physics, chemistry, molecular epigenetics, chemical ecology, and adaptation is included in Biblical Genesis. Only biologically uninformed atheists and Demoncrats continue to challenge the only accurate representation of biologically-based cause and effect that starts with ‘you are what you eat’ and claims that ‘if you eat this you will surely die.’

Tweets

Future of environmental research in the age of epigenomics and exposomics
Excerpt:

Epigenetic mechanisms, particularly DNA methylation and miRNA expression, attract increasing attention as potential links between the genetic and environmental determinants of health and disease. Unlike genetics, epigenetic mechanisms could be reversible and an understanding of their role may lead to better protection of susceptible populations and improved public health.

See also my attempt to discuss: How new traits “emerge” in evolution
Peter Berean wrote:

I am an ex-atheist, a Philosophical Theist and a Mere-Christian.

James Kohl

I have asked that you offer experimental evidence of biologically-based cause and effect. You provide nothing but rhetoric and fail to address any of the evidence I have provided. I have asked you which part of the Holy Bible you believe in, and your only answer seems to be that you are a Christian.

Peter Berean James Kohl,
You asked be for scientific evidence for OEC (a old universe and/or an old-earth) and so I did so (see my comments above).
———————————————————————-
In Addition:
1) I subscribe to the view that Some Pathology can be caused by Bacteria. You do not appear to subscribe to that view?
2) I subscribe to the view that Some Pathology can be caused by some Biological Toxins that are Not Viruses. You do not appear to subscribe to that view?
3) I subscribe to the view that Some Pathology can be caused by some Inorganic Toxins such as some heavy metals. You do not appear to subscribe to that view?
4) I subscribe to the view that SOME Pathology can be caused by Viruses. You do not appear to subscribe to that view because of the word SOME?
5) All of the evidence you have provided shows that Viruses cause SOME pathology. However, NONE of the evidence you provided shows that Viruses cause ALL pathology.
6) I am arguing that the evidence is consistent with the view that there are MULTIPLE Causes for Pathology.
7) You appear to be arguing that there is ONLY ONE cause for Pathology (viruses).
Please correct me if I am wrong in understanding your positions regarding the numbered questions/points I bring up above.
Cordially.
James Kohl
James Kohl I asked for experimental evidence of biologically-based cause and effect and you twisted that request into one for scientific evidence. You may think you are devilishly clever, but no serious scientist would agree.
I do not care what you subscribe to and will not answer any more questions about my views. They have been detailed in a series of published works during the past 20 years and no one has refuted the model we presented in the molecular epigenetics section of this review. From Fertilization to Adult Sexual Behavior 

Alternative splicing of pre-mRNA

Chromatin: The structure of DNA

Update on Inflammation and Degenerative Brain Disease

Excerpt:

While mapping connections of neurons has become the holy grail of current neuroscience, it is clear that communication of neurons with many other types cells is, also, vitally important to every aspect of brain function.

My comment:

Understanding dementia was placed into the context of understanding how virus-driven energy theft alters the de novo creation of olfactory receptor genes and causes the loss of function that is linked to all pathology via chromatin remodeling. The energy-dependent chromatin remodeling is linked from alternative RNA splicing to supercoiled DNA via the innate immune system and nutrient-dependent RNA-mediated amino acid substitutions.

An example of what is known about biologically-based cause and effect was placed into the context of two very different patent applications. One addresses prevention, the other is referred to as Church’s “billion dollar baby.”
For prevention see: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis (2011)
For contrast, this is the billion dollar baby: RNA-Guided Human Genome Engineering (2015)
My comment: Nutrient-dependent pheromone-controlled codon optimality links natural selection for food to RNA-mediated cell type differentiation via amino acid substitutions in all cell types of all individuals of all living genera. Transgenerational epigenetic inheritance is the link to energy-dependent ecological adaptations.
Continuing to place the facts about cell type differentiation into the context of cellular intelligence and evolution, which is what Jon Lieff has done for several years, is a misrepresentation of what is known about biologically-based cause and effect. The facts about cell type differentiation place the experience-dependent energy-dependent de novo creation of olfactory receptor genes first.
The creation of new genes is the holy grail of biology. Misrepresentation of virus-driven energy theft, which causes all inflammation and pathology, is the link to replacing the holy grail of biology with the holy grail of neuroscience: mapping connections among neurons. Even when all the connections are mapped, most serious scientists agree that consciousness will not be found among the connections, and that only epigenetic effects on the connections will be linked to degenerative brain disease via chromatin structure and epigenetically-effected supercoiled DNA.
See: From Fertilization to Adult Sexual Behavior
Excerpt (with my emphasis):

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.

My comment: In the context of  our section on molecular epigenetics and sex differences that must be linked to alternative splicings of otherwise identical genes via chromosomal rearrangements in sex chromosomes, we included that fact that energy-dependent chromatin remodeling was the link from the alternative splicings to cell type differentiation via chromatin structure. Should we have specifically mentioned that what organisms eat determines the structure of chromatin?
What caused the 20 year-long delay between reporting what was known about role of epigenetically-effected chromatin in RNA-mediated cell type differentiation and what is being reported now in the context of mapping connections of neurons, which Jon Lieff refers to as the holy grail of current neuroscience? How did the holy grail of biology become the holy grail of neuroscience with the change from de novo gene creation to mapping the effects of new genes and the effects of gene losses in different cell types?
See:

Many researchers have reported the link from epigenetically-effected chromatin remodeling to gene regulation. Most have reported the link outside the context of energy-dependent chemical ecology and changes that must link angstroms to ecosystems in all living genera. The alternative is to dismiss everything known to physicists, chemists, and molecular biologists who have already done that.
See for example: Structural diversity of supercoiled DNA  Can you dismiss supercoiled DNA?
See also: Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection Can you dismiss what is known about the innate immune system and codon optimality?
See also: Direct interrogation of the role of H3K9 in metazoan heterochromatin function Can you dismiss the role of H3K9?
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Excerpt: 

Scientists discovered that the major developmental function of heterochromatin — a form of tight DNA packaging found in chromosomes — is likely the suppression of virus-like DNA elements known as transposons or ‘jumping genes,’ which can otherwise copy and paste themselves throughout the genome, potentially destroying important genes, and causing cancers and other diseases.

What will be the next think that pseudoscientists are forced to dismiss if they continue to try to support their ridiculous theories?
See also: Grand project to unify global efforts to understand the brain
Excerpt:

As brainy gatherings go, it takes some beating. Neuroscientists are meeting in New York today to agree on a global mission to understand the workings of the human brain and how to fix it when something goes wrong.
The lofty aim of the Coordinating Global Brain Projects meeting is to unify worldwide efforts to study the brain, in the same way that international collaborations have spurred on astronomy, physics and genetics.
“Neuroscience is coming of age, and it’s now ready for big science,” says Rafael Yuste at Columbia University in New York, who organised today’s meeting with Cori Bargmann at Rockefeller University, also in New York. “This is the first real meeting with all the players in the same room together,” says Yuste.

I mentioned the award that Cori Bargmann won in the narrative of this poster presentation, which was published to Youtube March 2, 2016.
See:  RNA mediated molecular epigenetics and virus driven entropy

In two weeks, Cori Bargmann will receive an award that links a single neuron to all works on the lifespan and behavior of the nematode, C. elegans. That neuron integrates information from multiple chemical cues including food, oxygen and pheromones. The integration of the cues controls the expression of social behavior in the context of changes in pH. She is scheduled to present: “Genes, neurons, circuits and behavior: an integrated approach in a compact brain.

Perhaps she realizes there is no further need for her integrated approach, since energy-dependent RNA-mediated pheromone-controlled cell type differentiation has been linked from species of microbes to humans. Others do not seem to be aware of that fact.
See the discussion on the Neuroscience FB group
For example: Misha Zilberter is the first author of Dietary energy substrates reverse early neuronal hyperactivity in a mouse model of Alzheimer’s disease (2013). His work can be compared in the context of my model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model and also this 2016 report on A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation
Excerpt:

Critical amino acids for the stability and/or folding of the mintbody were revealed.

Reported as: New Probe Detects Histone Modifications in Live Cells
Excerpt:

Using genetic analysis and X-ray crystallography, the new work has also identified amino acids that are critical to the solubility and conformational stability of the H4K20me1-mintbody. Aberrant folding of the antibody fragments in the cellular cytoplasm usually causes solubility problems, but a potential solution has been found. As such, the researchers have overcome challenges to the performance of antibody fragments in live cells due to solubility issues.

For insight on what might prevent discussion of facts about RNA-mediated amino acid substitutions and cell type differentiation in all living genera, see:

Thanks to Anna Di Cosmo for calling attention to this. (Although he uses foul language to make his point, it is a point that needs to be made.)
 
Unfortunately, using Bill Nye to represent scientists may cause serious scientists to laugh along with anyone among the lay audience who does not believe what people like Bill Nye claim about evolution.
 
Like serious scientists, they may be waiting for Nye to present experimental evidence that links energy-dependent changes from angstroms to ecosystems in all living genera. Only then are they likely to believe that hydrogen-atom transfer in DNA base pairs in solution is contributing to the loss of species via climate warning.
If changes in the pH of the ocean are not considered, what experimental evidence that links ecological variation to ecological adaptation will be considered by those who think the “Science Guy” is biologically uninformed? Why, from his perspective on evolution, aren’t species simply acquiring more beneficial mutations to evolve —  if that’s what theorists want you to believe in?

See also this discussion of As simple as random can be
See also this discussion of  Four things you should know about brain research
What can anyone expect to come from any Grand project to unify global efforts to understand the brain.  All past grand projects have failed to link what is known about biophysically constrained RNA-mediated protein folding chemistry to cell type differentiation in all living genera via what is known about chromatin, which links energy-dependent changes in the microRNA/messenger RNA balance to biophysically constrained cell type differentiation in all living genera, including those with the primitive brain of a nematode or the brain of a conscious human.
Most the grand projects seem designed to support the ridiculous theories of the project organizers.