Big Bang

Richard P. Feynman refuted theistic evolution

Summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses. Updated information is presented in the context of refutations by many others who might otherwise claim to believe in theistic evolution.
The miR-23a~27a~24-2 microRNA cluster buffers transcription and signaling pathways during hematopoiesis
This is an uncorrected proof.
They link food energy-dependent changes in the microRNA/messenger RNA balance from amino acid substitutions to cell type differentiation via the physiology of pheromone-controlled reproduction in species from microbes to humans in the context of this claim from Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution.

…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).

Cell type differentiation during hematopoiesis links the amino acid substitution that differentiates the alpha chains of hemoglobin to the differentiation of all other cell types in all other individuals of all vertebrate species via the conserved molecular mechanisms of energy-dependent pheromone-controlled cell type differentiation in all invertebrates.

See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This is my invited review of nutritional epigenetics that was returned without review by the guest editors of a special edition of the journal “Nutrients.”

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.

See for comparison: Surely You’re Joking, Mr. Feynman! (Adventures of a Curious Character)

Chapter 10: A Map of the Cat?

My summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses.

The delayed dissemination of accurate information about biophysically constrained biologically-based cause and effect has already contributed to the unnecessary suffering and premature deaths of thousands to millions of people since the time that Richard Feynman reported on mutations in bacteriophages. He realized that the mutations link the theft of quantized energy from living organisms to the amino acid substitutions in viruses that cause the degradation of messenger RNA, which links mutations to all pathology. If not for his love of physics and the pseudoscientific nonsense of neo-Darwinian theorists, all serious scientists would have linked quantum physics to quantum souls.

See for example: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: The Sense of Smell Impacts Metabolic Health and Obesity

A PubMed search for microRNA and the disease you wish to prevent or effectively treat will help you to eliminate the foolishness of theorists who have failed to link the de novo creation of microRNAs to all biodiversity via the physiology of reproduction and biophysically constrained viral latency.

For example: microRNA alzheimers

To place your searches into the proper context, see: Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

Biologically uniformed theorists invented the term “enhancer” for ambiguous use in the context of energy-dependent changes in the microRNA/messenger RNA balance. They obfuscate facts about food energy and feedback loops that link pheromones to the biophysically constrained viral latency the enables ecological adaptations via use of “enhancer function.”

See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Natural selection for energy-dependent codon optimality links food energy-dependent changes in the microRNA/messenger RNA balance to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology unless terms such as enhancers and enhancer function are used to obfuscate facts about The phylogenetic utility and functional constraint of microRNA flanking sequences

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

There is no such thing as de novo assemblies of genomes. Food energy must be linked to the pheromone-controlled physiology of reproduction to link ecological variation to ecological adaptation via feedback loops.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison:7/25/13

Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

7/26/13

Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

See also: Researchers find new mechanism for genome regulation

Interestingly, this type of liquid-liquid phase separation is very sensitive to changes in temperature, protein concentration, and pH levels.

The sensitivity is food energy-dependent and RNA-mediated. Pseudosciedntists should stop their foolishness long enough to realize there is nothing new about the mechanisms of genome regulation. The mechanisms controlled by pheromones link the physiology of reproduction and chromosomal inheritance to healthy longevity unless they link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: CSmiRTar: Condition-Specific microRNA targets database

…(Condition-Specific miRNA Targets). CSmiRTar collects computationally predicted targets of 2588 human miRNAs and 1945 mouse miRNAs from four most widely used miRNA target prediction databases (miRDB, TargetScan, microRNA.org and DIANA-microT) and implements functional filters which allows users to search (i) a miRNA’s targets expressed in a specific tissue or/and related to a specific disease…

See for comparison: Creationism support is at a new low. The reason should give us hope.

Stuart Kauffman refutes theistic evolution

rp_levels-of-organization.jpg

Charles Darwin refutes theistic evolution

Charles Darwin wrote:

  1. IF under changing conditions of life…
  2. …variability is generally related to the conditions of life…
  3. …we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life.
  4. …during the process of modification, each has become adapted to the conditions of life…

Charles Darwin placed his energy-dependent “conditions of life” first. He knew that natural selection could not occur outside the context of the conditions of life, which are nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in species from microbes to humans.
For information on how ecological variation is linked to ecological adaptation in the context of what is known about Darwin’s and God’s “conditions of life” see:

FEB 23, 2017 12:00 PM PST
Speaker: James Prudent, PhD
 
Specifically, this talk will focus on proteins that interact with the human Na,K-ATPase (NKA). An active plasma membrane ion pump, the NKA is required for life. Without it, the cell cannot maintain a proper ion potential and the cells dies by a natural death process known as necrosis.
 

See also: DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

See also:

1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
2) Evolutionary drivers of thermoadaptation in enzyme catalysis
3) Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
6) Metabolic theory predicts whole-ecosystem properties
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
13) Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
16) All about the base
17) Chemists know
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
20) RNA-Guided Human Genome Engineering
21) What is Life?
22) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
23) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
24) A Big Bang in spliceosome structural biology
See also:
Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study
Activity-dependent spatially localized miRNA maturation in neuronal dendrites
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

fruit-dove

Happy Darwin Day (2017)

My series of blog posts about the refutation of theistic evolution by George Church led him to contact me via email.

  1. He asked why he would get credit for or against the refutations
  2. He claimed he was trained in quantum physics.
  3. He claimed that he has authored peer reviewed papers on protein folding, biodiversity, supercoiling, etc.
  4. He wanted to know more but did not know enough about my target audience to realize why I included information about the viral hecatomb.
  5. He also claimed to have written more on what is known about endogenous RNA interference than on exogenous RNA interference.

I invited him to discuss this further on my FB group, or on this domain. He declined. That was a great end to my 2017 Darwin Day.
See Evolution-guided optimization of biosynthetic pathways, which was co-authored by George Church and published December 1, 2014.
There is no such thing as evolution-guided optimization. Natural selection for energy dependent codon optimality is the only link from ecological variation to ecological adaptation in all living genera. That means we can move forward without George Church and still place his comments into the context of “Trust me, I’m a biologist.
I think that most serious scientists agree that you can’t trust evolutionary theorists For comparison, you can trust Darwin’s “conditions of life.”
Darwin’s “conditions of life” link the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera. Can you trust anyone who claims evolution did that?
See: RNA-Guided Human Genome Engineering 

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Nutrient energy-dependent microRNAs link natural selection for energy-dependent codon optimality to viral latency and protection of organized genomes from endogenous viral elements. Targeting endogenous viral elements with RNA-mediated amino acid substitutions is the key to biophysically constrained cell type differentiation. Fixation of amino acid substitutions prevents problematic nearly identical copies. There is no need for uncontrolled copies if there is no need to find another energy source. Uncontrolled copies link virus-driven energy theft from mutations to all pathology in all genera.
For example, energy theft from bacteria links messenger RNA degradation to morphological and behavioral phenotypes of archaea. Similarly, messenger RNA degradation in humans links the transgenerational epigenetic inheritance of Zika virus-damaged DNA to craniofacial morphology and brain development in infants.
Taken together with what is known about differences in energy-dependent endogenous RNA interference in nematodes, all ridiculous misrepresentations of Darwin’s works must be reversed to show the truth about what virus-driven energy theft does. It links RNA-mediated cell type differentiation from the energy-dependent creation of bacteria to the energy-dependent creation of humans and it links virus-driven energy theft to all pathology.
Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… 

Is Eugene Koonin joking about what was left out? If not, big bang cosmologists and neo-Darwinian theorists have never tried to support their ridiculous theories with any experimental evidence of biologically based cause and effect. They never examined the role of energy-dependent microRNAs or virus-driven energy theft. Instead, they invented gene-centric theories of mutation-driven evolution.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.

A 16 page monograph with 12 pages of citations is an unparalleled achievement for anyone who is not a polymath or someone who has not already linked physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation in all living genera via fixation of nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA.
None of the cited works appear to link what is known about virus-driven energy theft to all pathology. Again, it is time to move forward.
See: Charles Darwin’s Ocean Upwelling

It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory [natural selection]. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Changes in coral reefs are nutrient energy-dependent and controlled by the physiology of reproduction. De vries defined “mutation” in 1902, which means that Darwin could not have had a transmutation theory. Also, Darwin repeatedly asserted the claim that his “conditions of life” must come before any claims about natural selection.
Darwin Day 2017 may become known as the day George Church refused to publicly discuss evolution or to admit there is no such thing as evolution outside the context of virus-driven energy theft and the evolution of  pathology. On the same day, The Smithsonian National Museum of Natural History blog site published a post that misrepresented everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and healthy longevity.  Who could ask for a better Darwin Day than one during which Darwin’s “conditions of life” clearly triumphed over the ridiculous claims made by neo-Darwinian theorists and others who refuse to admit to the facts that link energy-dependent changes in chirality from autophagy to endogenous RNA interference and to supercoiled DNA, which prevents virus-driven energy theft from causing the mutations that all serious scientists have linked to all pathology?
 

poster-from-jesse

A single amino acid substitution differentiates cell types of E. coli

Rare amino acid influences E. coli infection

Excerpt: “They found that E. coli O157 is unable to attach itself to host tissue in high concentrations of D-Serine. Other strains, such as those that cause meningitis, thrive in the presence of the amino-acid.”
My comment: Three steps are required to link the amino acid substitution in E. coli to RNA-mediated stability of the DNA in the organized genome of a nutrient-dependent strain.
1) nutrient-dependent potentiation makes a trait possible;
2) receptor-mediated actualization makes the trait manifest via nutrient uptake and metabolism;
3) pheromone-controlled refinement fixes the amino acid substitution, which makes it effective.
Effectiveness of the amino acid substitution in manifested when RNA-directed DNA methylation links thermodynamic cycles of protein biosynthesis and degradation from metabolic networks to genetic networks that stabilize protein folding in the DNA of organized genomes.
In the words of Blount, Barrick, Davidson, & Lenski, the three-step process “…is probably typical…” of how many new functions arise. Evolutionary theorists typically replace that 3-step process and claim that Lenski’s experiments proved beneficial mutations cause evolution. See, for example: The Man Who Bottled Evolution See for comparison Combating Evolution to Fight Disease
In the context of combating evolution, it is important to note that Dobzhansky (1973) was aware that a single amino acid substitution differentiated the blood cell types of humans, gorillas, and chimpanzees. “…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.”
This research report links microbes (E. coli) to man (humans) via the conserved molecular mechanisms we first detailed in our 1996 Hormones and Behavior review “From Fertilization to Adult Sexual Behavior
Everything learned about physics, chemistry, and the conserved molecular mechanisms of cell type differentiation attests to the fact that nothing about RNA-directed DNA-methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species has changed during the past 18 years. That suggests it has never changed. That means conserved molecular mechanisms link ecological variation to ecological adaptations without this pseudoscientific nonsense: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199) “Mutation-driven evolution
See also: Natura non facit saltus (Latin for “nature does not make jumps”)
This was an essential element of Charles Darwin’s treatment of natural selection. Erwin Schrödinger’s objections to de Vries quantum jumps, which led to the definition of mutations, supported Darwin’s claims that “conditions of life” must come before any consideration for natural selection. Erwin Schrödinger’s support for Darwinian natural selection without the definition of mutation was dismissed along with Darwin’s “conditions of life,” which theorists seem to think somehow followed from whatever was naturally selected. The “cart before the horse” bastardization of Darwin’s theory by population geneticists is still more popular among evolutionary theorists today. They were taught to believe that natural section occurred and that it established the “conditions of life” and evolution of biodiversity by eliminating mutations despite no experimental evidence of biologically-based cause and effect to support their ridiculous claims.
“In the biological context, the principle [that nature does not make jumps] was used by Charles Darwin and others to defend the evolutionary postulate that all species develop from earlier species through gradual and minute changes rather than through the sudden emergence of new forms. Modern evolutionary biology has terminology suggesting both continuous change, such as genetic drift, and discontinuous variation, such as mutation. However, as the basic structure of DNA is discrete, nature is now widely understood to make jumps at the biological level, if only on a very small scale.”
Open access article: The host metabolite D-serine contributes to bacterial niche specificity through gene selection
Excerpt: “This locus codes for a D-serine deaminase (DsdA), a D-serine inner membrane transporter (DsdX) and an essential LysR-type regulator of the system (DsdC).
My comment: The biologically uninformed may continue to portray the three step process above as if the amino acid substitution could be called a mutation. However, this research on E. coli refutes the concept of jumps that have been reported as mutations since the invention of neo-Darwinism.
Nutrient-dependent energy is obviously the only way to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. The sun’s biological energy is linked from light-induced amino acid substitutions in plants and animals to nutrient-dependent pheromone-controlled fixation of amino acid substitutions in organisms from microbes to man.
Although amino acid substitutions clearly link jumps in energy, which are exemplified in the ecological speciation via amino acid substitutions in viruses, yeasts, nematodes, invertebrates, and vertebrates, the example of a single amino acid substitution that differentiates cell types in E. coli  is a welcome addition.