RNA methylation (2)

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

Conditioning as an adjunct in the pharmacotherapy of lupus erythematosus

Several studies have provided evidence suggesting that “placebo effects” represent conditioning phenomena and that learning processes influence the response to placebo medication. This case report describes an adolescent with severe lupus erythematosus who received cyclophosphamide (CY) paired with taste (cod liver oil) and smell (rose perfume) as conditioned stimuli. The regimen was based on conditioning experiments with animals who had lupuslike autoimmune disease. After the initial pairings, the taste alone was offered between CY treatments. Over 12 months, the patient received six rather than 12 CY treatments, half the cumulative dose that might have been administered. The patient improved clinically, and 5 years later continues to do well.

My comment: Based on experiments with rodent they prevented the death of a young girl via the classical conditioning of her energy-dependent RNA-mediated innate immune system. Twenty-four years later, a correspondent mentioned the zebrafish model organism would be the focus of her master’s thesis, so I asked:
Will you be linking G protein-coupled receptor-mediated behaviors from chemotaxis and phototaxis in all invertebrates via the the innate immune system, and the GnRH neuronal system in all vertebrates?
See also: The Dlx5 and Foxg1 transcription factors, linked via miRNA-9 and -200, are required for the development of the olfactory and GnRH system (2015)
See also:  Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors (June 10, 2016)
See also: Defective crystals is the explanation that neo-Darwinian theorists must use to stay consistent with their ridiculous theories.

See for comparison: Scientists just confirmed there’s a second layer of information hidden in our DNA


“In recent years, biologists have even started to isolate the mechanical cues that determine the way DNA is folded, by ‘grabbing onto’ certain parts of the genetic code or changing the shape of the ‘spool’ the DNA is wrapped around.

So far, so good, but what do theoretical physicists have to do with all this?”

My comment: Theoretical physicists are like neo-Darwinian theorists. They do not want people to know that all cell type differentiation is energy-dependent and RNA-mediated. That fact is a theory killer. The theorists are still trying to link the emergence of life and evolution of biodiversity to beliefs about consciousness.
See:  The Evolutionary Origins of Hierarchy
Abstract excerpt:

Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet.

Reported as: Hierarchies exist in the brain because of lower connection costs, research shows
My comment: Theoretical physicists and neo-Darwinian theorists want you to believe that their personal beliefs make sense to serious scientists.
See, for example: Personal beliefs versus scientific innovation: getting past a flat Earth mentality

In a perfect world, peer review is supposed to determine if the study is solid, based on the quality of the research. It’s meant to be an unbiased evaluation of whether the findings should be reported via journal publication. This important step prevents sloppy research from reaching the public.
However, in the real world, scientists are human beings and are often biased. They let their own beliefs influence their peer reviews. For example, numerous reports indicate that scientists rate research more favorably if the findings agree with their prior beliefs. Worst of all, these prior beliefs often have nothing to do with science but are simply the scientists’ personal views.

My comment: Peer review has prevented others from learning that virus-driven energy theft is the source of all pathology and that nutrient energy-dependent RNA methylation links differences in healthy longevity across all living genera via supercoiled DNA, which protects organized genomes from virus-driven genomic entropy.
For example, this invited review was returned without review:  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Based on what I’ve learned about microRNAs since 2012, I wrote:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

Fortunately, Paul M. Lieberman just got this published despite attempts by “peers” to limit the dissemination of accurate representations of biologically-based cause and effect.
See: Epigenetics and Genetics of Viral Latency

…viral latency is responsible for life-long pathogenesis and mortality risk…

See also: Phage spread antibiotic resistance

Unlike bacteria, which are true living creatures, viruses, including phages, can be thought of more as complex molecular machinery.

My comment: Richard Lenski and David Sloan Wilson still do not realize what is causing the changes in the organisms in cultures that have been reported in the context of a long-term evolutionary experiment.
See: Evolutionary Biology’s Master Craftsman: An Interview with Richard Lenski

And yes, all 12 lines have become much better at using glucose.  They grow faster than the ancestor, they’re more efficient, and they outcompete the ancestor in the glucose medium where they evolved.  To an evolutionary biologist, these changes aren’t surprising.  But it’s a nice, clear, and simple demonstration of adaptation by natural selection in real time.

My comment: Lenski is evolutionary biology’s poster child of ignorance. He equates the nutrient-dependent pheromone-controlled ecological adaptations with mutation-driven evolution via natural selection. David Sloan Wilson is showing him off. It’s all that theorists can do. See also the advance praise for the book George Ellis published earlier this month.
How Can Physics Underlie the Mind? Top-Down Causation in the Human Context
A stark lacuna lies at the heart of science: half the causal narrative has been omitted! Ellis makes a cogent and compelling case that the causal architecture of the universe is subtler and richer than the austere reductionist picture dictates. In this impressively scholarly volume, the author assembles evidence and argument from across the great sweep of intellectual inquiry, from pure mathematics and computation to neuroscience and engineering, and weaves them into a formal, systematic framework for understanding physical reality as we observe it, and for taking seriously human agency and moral choice. This book will set the agenda for the next leap forward in humanity’s attempt to make sense of how the world actually works.
Paul Davies, Beyond Center, Arizona State University
Physics went through a major revolution in its conceptual foundations a century ago with the arrival of quantum mechanics and the theories of relativity. All this passed by biology with virtually no impact. Ellis’s book makes it very clear why a major conceptual change is required also in biology, through the incorporation of top-down causation. The sweep of the book is enormous as it details the evidence and the impact in each area of science. It forms a major landmark, and it does so at an exciting time, when the purely gene-centric views of biology are being seriously challenged. Denis Noble, CBE FRS, University of Oxford
The culmination of three decades of work, Ellis’s magnum opus makes the most comprehensive case yet for top-down causation in the natural world. Encyclopedic in scope, yet guided by a single sustained argument, this defense of “strong emergence” sets a high, perhaps unreachable bar for scientific reductionists. As Ellis rightly notes, our entire conception of ourselves and our world depends on the outcome of this debate.
Philip Clayton, author of Mind and Emergence
Reductionism has been an extremely successful strategy in science. But, as George Ellis demonstrates in this important and provocative book, reductionism can’t be the whole story. Instead, other modes of explanation, including those based on emergence and top-down causation, are vital for a fully orbed account of the natural world.
Ard Louis, Rudolph Peierls Centre for Theoretical Physics University of Oxford
An admirable, systematic approach to the issue of emergence from physics to sociology, of great originality, broad scope, and deep understanding. George Ellis argues with admirable charity of thought that much of the world we live in is governed not by the blind dance of atoms, but by high-level causes and purposes.
Giulio Tononi, University of Wisconsin-Madison
An essential antidote to the shallow forms of reductionism that dominate both popular and academic thinking about our world. A carefully crafted argument, steeped in the scholarly literature, yet accessible to the ordinary reader.
Alister E. McGrath, University of Oxford
My comment: There is no reason for anyone to keep Combating Evolution to Fight Disease when people like this are unwilling to admit to their own ignorance. Instead, they congratulate those who continue to share it.
See also: Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level

… there are many single hydrogen bonds, van der Waals contacts and water-mediated bonds in combinations other than those deemed favourable. Many of these bonds are used for stability, but some are clearly essential for specificity in particular complexes. We term this type of recognition ‘context-dependent’ and the specificity provided is not universal to all protein–DNA complexes. The complications of identifying and isolating such interactions from those that provide universal specificity make predictions of protein–DNA contacts very difficult without structural data. However, given prior knowledge of the complex structure, the preferences summarised in Table ​Table88 can be used to highlight the specific interactions and interpret the data in a predictive manner such as anticipating the effect of amino acid mutations.

See for comparison: Discovery of the interstellar chiral molecule propylene oxide (CH3CHCH2O)
Reported as: Scientists just got one step closer to answering one of biology’s greatest mysteries

All living things exclusively use the right-handed form of the sugar ribose (the backbone of DNA), for example, and grapes only synthesize the left-handed form of the molecule tartaric acid. All amino acids – which make up proteins – skew left.”

My comment: No they don’t!

Achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide biophysically constrains the energy-dependent protein folding chemistry of all vertebrates. Glycine is the only achiral amino acid and it links food odors and pheromones to the physiology of reproduction via the RNA-mediated events we detailed in the context of our 1996 Hormones and Behavior review of RNA-mediated molecular epigenetics.
Two decades later, the world is stuck with the incredible amount of ignorance touted by theorists and reported by biologically uninformed journalists.
Nothing good can come from this! And no one seems willing to discuss the facts about biophysically constrained RNA-mediated protein folding. Feltman thinks that chirality is a nice word that should be easier to define. If you can define it in the context of de Vries 1902 definition of “mutation” you can keep your ridiculous theories and assumptions about how one species evolves into another, or how the bacterial flagellum evolved over the weekend.

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