Selective reporting of inferences: examples of pseudoscience
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.
…the selective reporting of inferences problem is serious enough a problem in our current industrialized science even when no omission takes place.
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:
- 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?
…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:
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.
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.
…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
…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
…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
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
…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
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:
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
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
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?
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.
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.