Selective reporting of inferences: examples of pseudoscience

By: James V. Kohl | Published on: March 19, 2016

(click to enlarge)

In the narrative of this presentation on RNA mediated molecular epigenetics and virus driven entropy, I mentioned that Cori Bargmann is scheduled to deliver a lecture entitled “Genes, neurons, circuits and behavior: an integrated approach in a compact brain.” An integrated approach will help others understand what is currently known about how ecological variation leads to ecological adaptation.

Works, like hers, with the nematode model organism will help others understand how ecological adaptation leads to biodiversity in the morphological phenotypes and behavioral phenotypes of all living genera. For example, P. pacificus is an ecologically adapted C. elegans. It is like a C. elegans with teeth that eats other nematodes.

Anyone who continues to report differences in the two nematodes context of selective inferences based on theories about mutations and evolution should promptly be dismissed from the ranks of serious scientists. People like that are biologically uninformed and they seem to know nothing about biophysically constrained RNA-mediated cell type differentiation. Many of them have built careers on funding from the evolution industry, which supports ridiculous misrepresentations of biologically-based cause and effect by placing them into the context of statistical analyses. The representations omit what is known about biologically-based facts, and report inferences as if the inferences wer based on something besides the definitions and assumptions of others who are biologically uninformed.

It’s not the p-values’ fault – reflections on the recent ASA statement (+relevant R resources)

Excerpt 1)

…the selective reporting of inferences problem is serious enough a problem in our current industrialized science even when no omission takes place.

Excerpt 2)

What, then, went wrong in the last decade or two? The change in the scale of the scientific work, brought about by high throughput experimentation methodologies, availability of large databases and ease of computation, a change that parallels the industrialization that production processes have already gone through. In Genomics, Proteomics, Brain Imaging and such, the number of potential discoveries scanned is enormous so the selection of the interesting ones for highlighting is a must.

My comment: The selection of interesting discoveries led serious scientists to link everything known about physics, chemistry, and the conserved molecular mechanism of RNA-mediated protein folding from hydrogen-atom transfer in DNA base pairs in solution to biologically-based ecological adaptation in species from microbes to humans. Ecological variation has been linked from nutrient-dependent microRNAs and microRNA flanking sequences to all biodiversity in all invertebrates and vertebrates via supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy.
See for comparison:

Krauss, Meyer, Lamoureux: What’s Behind it all? God, Science and the Universe

PROF. DR. LAWRENCE M. KRAUSS, is an internationally known theoretical physicist…
DR. STEPHEN C. MEYER …has expanded the scope of the case for intelligent design to the whole sweep of life’s history.
DR. DENIS O. LAMOUREUX… academic specialty focuses on the modern origins controversy.

My comment: The controversy that some people think exists is the focus of this inference: Young Earth Creationists killing Christian credibility? Perry Marshall, like many other biologically uninformed people who are not scientists, failed to grasp the systems complexity that has been detailed in my works, which include citations to the works of those who have established biologically-based cause and effect at every level of examination from angstroms to ecosystems. Perry Marshall’s ignorance led to this attack on Ken Ham’s creationist claims.
When all else fails to detail what theorists know about how mutations lead to evolution, young earth creationists are easy targets. Theorists, like Perry Marshall, attack what they think people like Ken Ham believe. They do not look at experimental evidence that proves how nucleic acids and cells were created in the context of biophysically constrained RNA-mediated protein folding chemistry. The biophysically constrained chemistry of protein folding links supercoiled DNA to protection from virus-driven entropy in all cell types of all individuals of all living genera that have organized genomes. (Note to theorists: All living genera have organized genomes.)
Excerpt (from Perry Marshall’s inferences):

When folks like Ham stand up and claim to speak for all Christians, we lose face in the debate.
The good news is, there’s another narrative that allows for God and evolution — religion and science — to coexist. One where all of modern science’s discoveries only support the mystery of God, not debunk it.

My comment: Perry Marshall does not tell us which discoveries he believes support the mystery of God. Does he believe fossil record discoveries that some researchers claim link what is known about dead organisms to genome organization in living genera? Does Perry Marshall have evidence of biologically-based cause and effect that can be placed into the context of his inferences and the simultaneous emergence of hens and eggs?
See, for example: Was ribosome the first self-replicator?
Excerpt:

…does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

My comment: The claim that ‘Hens and eggs emerged simultaneously’ can be compared to Perry Marshall’s inference that young earth creationists may be killing Christian credibility. See my comments to Perry Marshall’s site, but also see the support for Ken Ham’s scientific/Biblical perspective which begins with atomistic insight, not evolutionary theory:
For example:
1) The phylogenetic utility and functional constraint of microRNA flanking sequences

The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.

2) Structural diversity of supercoiled DNA

Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

3) Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
Reported as: Reprogramming Cancer Cells Back to Normal Cells

…adhesion proteins — the glue that keeps cells together — interact with the microprocessor, a key player in the production of molecules called microRNAs (miRNAs). The miRNAs orchestrate whole cellular programs by simultaneously regulating expression of a group of genes. The investigators found that when normal cells come in contact with each other, a specific subset of miRNAs suppresses genes that promote cell growth. However, when adhesion is disrupted in cancer cells, these miRNAs are misregulated and cells grow out of control. The investigators showed, in laboratory experiments, that restoring the normal miRNA levels in cancer cells can reverse that aberrant cell growth.

My comment: More than 48,000 published works that link atomistic insight to supercoiled DNA are indexed here: “microRNA.” Taken together there is no doubt that nutrient-dependent microRNAs biophysically constrain protein folding in the context of the physiology of reproduction that links supercoiled DNA to protection from virus-driven genomic entropy and all biomass and all biodiversity in all living genera. The published works also are beginning to show that virus-driven energy theft links mutations to all pathology (see below).
See for comparison:

Human adaptation and population differentiation in the light of ancient genomes
Excerpt:

…our results provide clear evidence that local adaptation contributed to these allele frequency changes in European populations, as strongly differentiated alleles in Europeans are enriched in likely functional variants: genic, previously constrained and putatively regulatory.

Reported as: Stone Age hunters contributed adaptive variants to present-day Europeans
Excerpt:

…the team speculates that these variants may be beneficial in populations living at high latitudes with limited exposure to UV light. However, Key is cautious, commenting that: ‘We have to note that our functional understanding of human genetic variants is still limited.’

My comment: Neo-Darwinian theorists consistently fail to grasp any of the experimentally established facts that link ecological variation to nutrient-dependent ecological variations via top-down causation. Key phrases such as “variants may be beneficial” in the context of “local adaptation” manifested in “allele frequency changes”are not linked from top-down causation to biodiversity. Top-down causation links the speed of light on contact with water from UV light to energy-dependent hydrogen-atom transfer in DNA base pairs in solution.
See also: Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels
Excerpt:

Using Mendelian randomization, we found that there is evidence for lincRNAs having distal effects on the expression levels of protein-coding genes in a dosage-dependent way across the genome in similar proportions to distal effects of mRNA.

My comment: They link what organisms eat from metabolic networks to genetic networks and obesity, but attribute the obesity to genetic predispositions linked from expression quantitative trait loci (eQTLs) to obesity-linked pathology in the context of Mendelian randomization. In this regard, Mendelian randomization can be thought of as a “natural” randomized controlled trial. From a statistical perspective, it is an application of the technique of instrumental variables (Thomas & Conti 2004, Didelez & Sheehan 2007), with genotype acting as an instrument for the exposure of interest.
In other words, Mendelian randomization allows them to report selective inferences in the context of biologoically-based caues and effect without mentioning the fact that nutrient-dependent microRNAs have been linked to biophysically-constrained RNA-mediated cell type differentiation via what is known to serious scientists about protein folding in all living genera.
When people like Perry Marshall stop attacking others, and start learning what serious scientists know about UV light and energy-dependent cell type differentiation, they may also learn that young earth creationists were among the first to recognize how viruses would be linked to all pathology.
See: Viral Genome Junk Is Bunk
Excerpt:

…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

Works cited by the young earth creationists include:
Holmes E. C. 2003. Molecular Clocks and the Puzzle of RNA Virus Origins. Journal of Virology. 77 (7): 3893–3897.
Chuong, E. B. et al. 2013. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nature Genetics. 45 (3): 325-329.
See also: Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Conclusion:

Regardless of how these sequences originated, our study illuminates how selfish genetic elements have contributed raw material that has been repurposed for cellular innovation.

Reported as: Viral ‘fossils’ in our DNA may help us fight infection
See my comment:

Re: “The work suggests that these viral fossils probably played a key role in the evolution of our species…”
The work shows that Greg Bear accurately portrayed virus-driven energy theft when he linked it to the creation of new species. In 1999 and 2003, he linked what is now known about the anti-entropic effects of sunlight and hydrogen-energy transfer in DNA base pairs in solution to the creation of a new human subspecies.
What’s currently known outside the context of science fiction also links Einstein’s math and physics to molecular mechanisms of adaptation via Schrodinger’s claims about sunlight when paired with Dobzhansky’s claims about amino acid substitutions in the context of transgenerational epigenetic inheritance.
For example, the Zika virus clearly links primate craniofacial morphology and brain development. DNA damage linked to variations can be compared in the context of the fossil record and what is known about how cell type differentiation occurs. Nutrient energy-dependent RNA-mediated DNA repair and amino acid substitutions are linked to species-wide ecological adaptations.
The energy-dependent adaptations link ecological variation to morphological and behavioral phenotypes in species from microbes to humans. Virus-driven energy theft links a single amino acid substitution to increased virulence when nutrient-stress and/or social stress cause changes in pH that favor viral replication instead of nutrient-dependent immune system-support of controlled cell type differentiation.
Simply put, Dobzhansky’s claims can be placed into the context of what is known about all virus-driven pathology. He wrote: “…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 ( p. 127)” — See: Nothing in Biology Makes Any Sense Except in the Light of Evolution
The “light” is sunlight and it is linked to hydrogen-atom transfer in DNA base pairs in solution to fixation of amino acid substitutions and supercoiled DNA by everything currently known to physicists, chemists, and molecular biologists about biophysically constrained chemistry and the nutrient-dependent biological basis of the physiology of reproduction in all living genera.
Viruses increase their virulence via energy theft linked to a single amino acid substitution. All nutrient-dependent life must ecologically adapt by at least one nutrient-dependent amino acid substitution, which must be linked to supercoiled DNA via the physiology of reproduction in all living genera.
What some people call “viral fossils” are clear indicators of how the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding prevents virus-driven entropy of organized genomes in the context of the physiology of reproduction.

Summary: Claims that include statements like this: “Regardless of how these sequences originated…” invariably lead to claims that link pseudoscientific nonsense to the evolution of what serious scientist understand about the origin of the innate immune system. It is called the innate immune system for a reason. It it did not exist to protect the organized genomes of all living genera from virus-driven entropy, there would be no claims about “…how selfish genetic elements have contributed raw material that has been repurposed for cellular innovation.”
Viruses may be used to frame arguments that include claims about “selfish genetic elements.” But virus-driven energy theft cannot contribute any raw material that can be repurposed for cellular innovation. Cellular innovation is nutrient-dependent, and only the innate immune system can enable repurposing via nutrient energy-dependent feedback loops that link supercoiled DNA to the innate immune system’s protection from virus-driven entropy in the organized genomes of all living genera.
See for examples from the past few days.
2016 Mar 15 Downregulation of the stress-induced ligand ULBP1 following SV40 infection confers viral evasion from NK cell cytotoxicity.
2016 Mar 16 Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
2016 Mar 16 MicroRNA-1229 overexpression promotes cell proliferation and tumorigenicity and activates Wnt/β-catenin signaling in breast cancer

2016 Mar 15 Phenotypic switching of vascular smooth muscle cells in the ‘normal region’ of aorta from atherosclerosis patients is regulated by miR-145
2016 Mar 15 A preliminary microarray assay of the miRNA expression signatures in buccal mucosa of oral submucous fibrosis patients
2016 Mar 14 Role of cancer stem cells in racial disparity in colorectal cancer
Excerpt:

Our findings suggest that an increase in CSCs, specifically the CD44⁺ CD166^– phenotype in the colon could be a predisposing factor for the increased incidence of CRC among AAs. MicroRNA 1207-5p appears to play a crucial role in regulating stemness in colonic epithelial cells in AAs.

My comment: Each of the articles linked above links stress perturbed changes in pH from virus-driven energy theft to mutations and pathology. Serious scientist have arrived at conclusions that link everything known about RNA-mediated cell type differentiation to the nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Energy-dependent changes in base pairs link atoms to ecosystems in the context of supercoiled DNA and the physiology of reproduction.
Links from atoms to funcitonal ecosystems do not include mutations and evolution except in the context of virus-driven energy theft, genomic instability, and pathology. That fact will lead to the public humiliation of any neo-Darwinian theorist who continues to tout their pseudoscientific nonsense about beneficial mutations. The careers of the pseudoscientists already have begun to end. Do not let them take your career with them or kill anyone else with their theories as they make a hasty exit. At the same time, watch them change the terms they have used to link mutations to evolution.
Learn the difference between a nutrient-dependent RNA-mediated amino acid substitution and a mutation and you won’t get caught making ridiculous claims about weekend evolution of the bacterial flagellum.
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).

See for comparison:

I reiterate, see also: Young Earth Creationists killing Christian credibility?

Perry Marshall says:

March 19, 2016 at 10:04 am

James, you are one step away from being banned because of your disingenuous comments, your accusations, and your unnecessary combativeness. I am getting tired of it. People accuse you of being a troll for a reason.
This is your final warning.
My comment: Obviously, I can say nothing more about Perry Marshall’s attacks on the credibility of young earth creationists — on his blog site. And there is no reason to reassert my claim that all serious scientists are Combating Evolution to Fight Disease.
My comments to the Science Magazine site:
1) “An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” https://www.sciencemag.org/content/332/6034/1161.short
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans https://www.cell.com/cell/abstract/S0092-8674(14)00806-X The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes https://linkinghub.elsevier.com/retrieve/pii/S0092867412015000
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events. Submitted on Sat, 09/13/2014 – 08:58
2) Re: “Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations.”Now see: A mechanistic link between gene regulation and genome architecture in mammalian development https://www.sciencedirect.com/science/article/pii/S0959437X14000495 for the refutation of neo-Darwinian pseudoscientific nonsense.Experimental evidence of biologically-based cause and effect does not support ideas about mutations, natural selection, and the evolution of biodiversity.Experimental evidence of biologically-based cause and effect supports the fact that ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms. Submitted on Tue, 07/15/2014 – 22:13
3) Re:”…the driver of evolution is not mutations or variation but selection, be it natural, artificial, kin or sexual selection. Mutation is but one of the factors that contribute to variation.”I thought Robert Frye knew better than that, because he attended a 1993 symposium I organized and my 2007 Reiss Plenary session of The Mind’s Eyes: Modeling the Development of Diverse Sexual Preferences.Perhaps this is a different Robert Frye or one who thinks that sexual orientation arises via mutations and natural selection in human males but via nutrient-dependent pheromone-controlled cell type differentiation in yeasts as we reported in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior “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…”Robert: What about Anne’s rams. Are they among the selected mutants that you think may have evolved their exclusive homosexual orientation? Submitted on Sun, 09/07/2014 – 20:51
4) Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection. There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”Deep understanding of the ‘conditions of life’ does not come from theory. Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression. Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction. It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution. Submitted on Fri, 03/07/2014 – 12:07
Addendum: With his book, and on the FB page and blog site that he controls, Perry Marshall, has joined the ranks of many others who are fighting to keep evolution and disease. The evolution industry has been successfully built from the pseudoscientific nonsense of theory, and Perry Marshall is riding the wave of success with Evolution 2.0.

See also:

James V. Kohl says:

Your comment is awaiting moderation.

March 19, 2016 at 11:10 am

I apologize, Perry. I thought you were attacking my beliefs. Typically, I am not combative, but I am not defenseless, either.
What aspect of my model are you willing to discuss?
For example, I presented this poster at the Labroots Neuroscience 2016 Virtual event last week:
From hydrogen atom transfer in DNA base pairs to ecosystems
https://www.youtube.com/watch?v=5CN2a0Z1fQI

For comparison to my model:
Here is a recent representation of the never-ending focus on visual input, which ignores the fact that chemotaxis must precede phototaxis during the integration of sensory input in the developing brain: Building A Brain: Mysteries of the Brain.
When someone like Perry Marshall, attacks Ken Ham, or anyone else for their beliefs, ask yourself what beliefs they are trying to sell you with their marketing campaign. Perry Marshall, for example, seems to be trying to sell you his belief that hybrids created in the lab are examples of God’s creation of different species.
Dobzhansky (1972)
Conclusion:

As a category of classification, species was and is being applied to all organisms, and this has led to futile search for universal biological properties of all species. What is actually found is a remarkable variety of different kinds of species. Even confining our attention to sexually reproducing and outbreeding forms, we find more or less monolithic “good” species, superspecies, and semispecies. Finally, it begins to look as if reproductive isolation may sometimes follow and at other times precede the adaptive divergence of gene pools of populations.

My comment: In either case, the physiology of reproduction is nutrient-dependent and must link what is known about the innate immune system from feedback loops to biodiversity via supercoiled DNA, which protects all organized genomes in all living genera from virus-driven entropy.