An evolutionary theory killer

A single base change refutes theistic evolution (2)

Announcing publication of a model that links the creation of quantized energy from changes in subatomic particles to biophysically constrained viral latency and sympatric speciation in all living genera.

Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans.

The invited review of nutritional epigenetics was returned without review and the preprint was posted 4 years ago as:

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

The only significant change to the manuscript was a change in the title. Atoms to ecosystems became Angstroms to Ecosystems when quantized energy-dependent changes in angstroms were linked to ecological adaptation by what is known to all serious scientists in this 2014 parody.
All About that Base (Meghan Trainor Parody) 12/10/14
Repeat after them (and me): “… every angstrom is dynamic from the 5 prime to the three…”
See also the 2015 publication: Structural diversity of supercoiled DNA

DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases.

See also: RNA-Guided Human Genome Engineering

George Church and others may have been the first to place the naturally occurring biophysically constrained energy-dependent processes of ecological adaptations into the context of a patent. (It is extremely unusual for anyone to attempt to patent a naturally occurring process.) That explains why there is no patent litigation, which still plagues those who claimed to discover the CRISPR-Cas 9 innate immune system of bacteria, which biophysically constrains viral latency and prevents the degradation of messenger RNA that links the energy-dependent creation of bacteria to the virus-driven creation of archaea and L-forms. All biophysically constrained virus-driven pathology has since been placed back into the context of embryogenesis and the dynamics of energy-dependent gene expression at the level of single-cell resolution as if bacteria somehow evolved into humans.

See:

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
Chronicling embryos, cell by cell, gene by gene
Reported as: How one cell gives rise to an entire body
See for comparison our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior (1996)
Watch pseudoscientists continue to make ridiculous claims that fail to link the creation of biophysically constrained thermonuclear energy to autophagy and all biodiversity in the context of the cell biology game Cytosis and most of the forthcoming presentations during Schrödinger at 75 – The Future of Biology – September 2018.
Remember to note that at the end of the parody All About that Base, the research group politely refers to Neil deGrasse Tyson as a big ass (er, a bass). Try not to use the acronym ROTFLMAO in attempts to discuss what is known to all serious scientists with theorists.

Alternative splicing of pre-mRNA

Energy is information. Objections over ruled. You're fired!

Objection: In the law of the United States of America, an objection is a formal protest raised in court during a trial to disallow a witness’s testimony or other evidence which would be in violation of the rules of evidence or other procedural law.
Americanism (ideology) links the laws of United States of America to God’s “Laws of Biology.”  Pseudoscientists violated the rules of evidence that link Darwin’s “conditions of life” from God’s “Laws of Biology” to all nutrient energy-dependent biophysically constrained pheromone-controlled biodiversity on Earth.
Laws of biology: why so few? (2010)

…every biological decision is optimal in a given environmental context. However, due to complex nature of biological organization it is difficult to think of a universal law or a theory in biology connecting all the levels, from atoms to ecosystems.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (excerpts)

  1. In Section One, the focus is on links between atoms and ecosystems via amino acid substitutions. In Section Two, the focus is on examples of links across a continuum of nutrient-dependent, pheromone-controlled, epigenetically-effected, receptor-mediated ecological adaptations via amino acid substitutions and changes in the microRNA/messenger RNA balance.
  2. Nutrient-dependent pheromone-controlled ecological adaptations exemplify how sensing nutrients and secreting the metabolites of nutrients accomplishes different tasks. Efficient circuits enable the functional flexibility that is required in ever-changing ecologies that cause species diversity. Biophysical constraints on ecological adaptations are exemplified in physical proof which suggests that Kohl’s Laws of Biology (Kohl’s Laws) represent what Darwin called ‘conditions of life.’

Natural selection for nutrient energy-dependent codon optimality is exemplified in species from archaea to humans. See for example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2015)

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

That perspective on sequence changes between paralogs in evolution and human disease placed endogenous RNA interference into the context of Intelligent Design after Darwin and all other serious scientists had linked it from sunlight to all biodiversity on Earth via their observations and experimental evidence of biologically-based cause and effect.
See for example: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

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

Wells recognizes that various well-established processes like alternative splicing and RNA editing often determine the amino acid sequence of proteins.

Like all pseudoscientists before him, Wells failed to recognize the most important fact of all. That fact was expressed in the context of the fact that gene expression is energy-dependent in DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION”(1964)

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

The pseudoscientists that failed to acknowledge that fact are among the losers that were placed into the following perspective:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.Kalevi Kull (2016)
The losers can now be recognized in the context of the failure to provide the free delivery of God’s “billion dollar baby” to  healthcare practitioners. Simply put, many healthcare professionals were not told how to link energy from endogenous RNA interference (RNAi) to healthy longevity in all living genera. They were not told that natural selection for energy-dependent codon optimality and endogenous RNAi have always linked angstroms to ecosystems in all living genera via RNA-mediated amino acid substitutions in supercoiled DNA. Why didn’t all medical practitioners learn that supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.
See for examples of what was missing:
Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection…

RNA-triggered gene silencing (1999)
RNA-Guided Human Genome Engineering (2015)

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).

Alnylam Pharmaceuticals: RNAi Failure Could Catch Monsanto Investors Off Guard ? (2016)

The other technology besides CRISPR gene editing, which is the subject of this post is called RNAi technology. See link in references below as to the differences between CRISPR & RNAi technologies.

…something went horribly wrong, they don’t really know what it was other than it failed, caused death of some patients and so they discontinued the experimental drug. This has an uncanny similarity to and is reminiscent of the Tryptophan disaster – GM Potato & Árpád Pusztai affair & the GM pea causes allergic reactions to name a few.

“Deep inside its labs, Monsanto is learning how to modify crops by spraying them with RNA rather than tinkering with their genes”

Spraying crops with RNA causes RNA interference in the same way that the CRISPR/Cas9 technology replaced virus-altered RNA interference via use of other viruses that caused the innate immune response to link amino acid substitutions to DNA repair if the missing amino acids were again made available. It is like fighting fire with fire, which sometimes works to extinguish the life of one fire that is out of control but does not prevent other fires from emerging and destroying other properties, or the same property at a later date. The ominous prophecies from the Holy Bible now loom larger if, like all other prophecies, they are correct. Those who survive the next viral apocalypse seem likely to live long enough to die a fiery death that clearly will be linked to the sun’s biological energy from the protection of supercoiled DNA that once helped to ensure our healthy longevity.

See for comparison:  A Christian Worldview & Mental Health (2011)

Christian concern for the whole person includes both mind and body, so this volume encourages readers to think about theoretical and spiritual issues within Christian mental health care. Views are collected from various disciplines such as ethics, psychology, theology, counseling, and psychiatry. In its consideration of a Seventh-day Adventist spiritual identity in mental health theory and practice, this text will prove very valuable to mental health education.

The Christian worldview links what organisms eat to natural selection for energy-dependent codon optimality and healthy longevity, which links supercoiled DNA from the physiology of reproduction to all morphological and behavioral diversity in species from microbes to humans. The Christian worldview has typically been one in which peaceful coexistence is the desired goal. That goal is based on what is known about energy-dependent symbiosis and homeostasis in species from microbes to humans. The atheistic worldview is shared by proponents of Intelligent Design and others who are biologically uninformed. They seem to think that Darwin replaced the Laws of Biology, when what he repeated asserted was that “conditions of life” come first. Only pseudoscientists have continued to link mutations from natural selection to the evolution of one species from another across millions of years.
The pseudoscientists have organized a “March for Science” in an attempt to keep forcing their pseudoscientific nonsense on the biologically uninformed masses in the United States of American who were taught that they could break any of God’s Laws that they chose to break, after the Laws were broken by those who chose to believe in, and to teach, their ridiculous theories to several generations of children that grew up to become liberals.
But wait, here are a few more claims that can be placed into the context of the Laws of Biology, but not into the context of mutation-driven evolution.
Worm gene could be key to developing obesity treatment
Nutrient energy-dependent changes in the microRNA/messenger RNA link endogenous RNA interference to biophysically constrained biodiversity in nematodes that is exemplified in differences between C. elegans and P. pacificus, a predatory nematode with teeth. The physiology of reproduction is controlled by pheromones in all living genera and the pheromones link microRNAs from supercoiled DNA to chromosomal inheritance in different species.
See also from 2013: Extracellular Regulation

During Caenorhabditis elegans development, the hermaphrodite-specific neurons (HSNs) migrate and then extend axons toward their functional targets. Posttranslational modification of heparan sulfate proteoglycans are important for HSN development, and so Pedersen et al. (p. 1404) tested the effect of disrupting or reducing chondroitin and heparan sulfate synthesis during C. elegans development. The results suggest that proteoglycan biosynthesis is tightly regulated by a microRNA pathway to shape the cell surface glycosylation architecture required to direct neuronal migration.

Females More Prone to Disease Due to Key Immunological Difference
This means the sex difference in cell types can be linked to the advent of sexual reproduction in yeasts via the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior
See for comparison: Today on Darwin Day, Trey the Explainer Sends a Gift. He Power Owns Dr. Ben Carson! (Video)
The “Explainer” dismisses facts about energy-dependent endogenous RNA interference and pretends that the variants in the fossil record support the ridiculous theories of neo-Darwinian theorists. There is no way to explain his ignorance, or why he flaunts it.
See also: Team develops tool that maps functional areas of the genome to better understand disease

…sections of DNA called “enhancers” dictate where and when the gene information is read out.
 

Energy as information dictates gene expression in the context of established links from chirality to autophagy in species from microbes to humans.

See: Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.
 

All pathology is caused by virus-driven energy theft. The barrage of misinformation you are being subjected to is increasing each day.

See:How evolution alters biological invasions
also reported as:

Superspreader phages transfer drug resistance
Lucky for us, bacteriophages infect bacteria, not humans. That doesn’t mean they don’t have profound effects on us, however. A new report in the journal mBio from researchers at the University of Miami and the National Cancer Institute describes “superspreader” bacteriophages that promote DNA transfer from one bacterium to another – and some of this DNA codes for antibiotic resistance genes.

Does life have a purpose?
 

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?
 

rp_levels-of-organization.jpg

The tipping point? 50,000 publications (5)

For review see my blog posts “The tipping point? 50,000 publications” with follow-ups: (2) (3) & (4).

There are now more than 52,000 published works that link microRNAs to cell type differentiation in the context of healthy longevity or virus-driven energy theft, which has been linked from viral latency to all pathology.

At the rate of ~1000 more publications per month that link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity or link virus-driven energy theft to all pathology, it won’t be much longer until public outcry puts an end to the money-grabbing evolution industry and big bang cosmology industry support of theories.

Combating Evolution to Fight Disease is the next step forward to altering the progress of pathology. Others have learned enough about RNA-mediated cell type differentiation to move science forward by leaving neo-Darwinian pseudoscientific nonsense behind.

See: Life’s Greatest Secret: The Race to Crack the Genetic Code

Excerpt from:

 “Information” was about to enter science, but had not done so when Schrödinger gave his lectures. Without that conception of the content of the code, Schrödinger’s insight was merely part of the zeitgeist, a hint of what was to come rather than a breakthrough that shaped all subsequent thinking.– Matthew Cobb (2015)

See for comparison:

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. — Jay R. Feierman (2013)

My comment: Schrodinger’s published claims (1944) set the stage for discussions about energy as information in the context of reality. His equation helped those who were interested in discussion. His claim about the link from sunlight as the source of fuel for all biodiversity is rarely mentioned. Feierman, for example, seems to think that random mutations can somehow be linked from natural selection to all biodiversity.

See for comparison:What is Life?

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

See also the forward by Roger Penrose

Excerpt:

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?

My comment: If you can link the anti-entropic virucidal energy of the sun to hydrogen-atom transfer in DNA base pairs in solution, you can link ultraviolet light to RNA-mediated DNA repair via the innate immune system, the physiology of reproduction, and supercoiled DNA, which typically protects us from all virus-driven energy theft and pathology.
The energy as information is linked from RNA methylation to learning and memory at the cellular and organismal level is the basis for this patent application: RNA-Guided Human Genome Engineering
Excerpt:

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).

My comment: Latent viruses (i.e., endogenous viral elements) are the obvious source of all pathology.  See: “…viral latency is responsible for life-long pathogenesis and mortality risk…” Paul M. Lieberman
If a patent is issued for RNA-Guided Human Genome Engineering, the technology may never be available to all those who need it.
Indeed, the people who need the technology most may never be told why they need it. They will need it because the nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction has been altered by the use of viruses to genetically modify the nutritional value of plants that people eat for food. Now others have learned that virus altered nutrient stress and social stress make the largest contribution to how and why viral latency becomes life-long pathogenesis and mortality risk.  Apparently, they intend to make billions with technology that uses RNA to repair DNA, which is what our innate immune system always has done. The RNA-mediated repair is their  RNA-Guided Human Genome Engineering.
See also: N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression
Excerpt:

These findings suggest that adenosine methylation plays an important role in regulating the ability of HIV to thrive and multiply in T-lymphocytes, which are an important target for HIV. Since the RNAs of other human viruses, such as influenza virus, can also be modified by adenosine methylation, drugs that target this pathway could have the potential to be used to fight a variety of viral illnesses.

My comment: The fact that they have linked energy-dependent RNA methylation to RNA-directed DNA methylation and healthy longevity via prevention of virus-driven energy theft is presented in the context of drug development, which is typical. No one makes much money by reporting how energy-dependent cell type differentiation is linked to healthy longevity.  For comparison, the RNA-Guided Human Genome Engineering patent may be worth billions.