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

fruit-dove

Food energy-dependent epigenetic adaptation

Mechanism of transmembrane signaling by sensor histidine kinases, was reported as Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

The researchers from Russia link energy-dependent changes in angstroms to ecosystems in all living genera. See this parody for fun.
Listen for her to repeat the claim that “,,,every angstrom is dynamic from the 5 prime to the three…”

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) and see this invited review of nutritional epigenetics from 2014: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
All adaptive evolution is epigenetically-effected ecological adaptation. In my model, adaptive evolution equates with epigenetic adaptation for claims that can be compared to claims about mutations and evolution. In 2013, I placed my claims into the context of adaptive evolution because many people did not realize that organized genomes must be protected from virus-driven energy theft at the level of energy-dependent changes in the microRNA/messenger RNA balance.
Other researchers have since begun to realize that virus-driven energy theft causes the degradation of messenger RNA. Every level of examination links the loss of quantized energy from angstroms to ecosystems via mutations, which are linked to all pathology. If my invited review had not been returned without review, other researchers probably would have linked the peer-reviewed publication from 2013 and virus-driven energy theft from the hecatombic evolution of pathology in archaea to all pathology via the degradation of messenger RNA and negative supercoiling of DNA.

See for example: Structural Dynamics and Mechanochemical Coupling in DNA Gyrase

Gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex. Here we present a current understanding of mechanochemical coupling in this essential molecular machine, with a focus on recent diverse biophysical approaches that have revealed details of molecular architectures, new conformational intermediates, structural transitions modulated by ATP binding, and the influence of mechanics on motor function. Recent single-molecule assays have also illuminated the reciprocal relationships between supercoiling and transcription, an illustration of mechanical interactions between gyrase and other molecular machines at the heart of chromosomal biology.

It has also become clear that no experimental evidence links the degradation of messenger RNA from mutations to evolution via natural selection or any other claims that have been made by biologically uninformed theorists. No experimental evidence that supports evolution via natural selection has been published in a peer-reviewed journal.
Natural selection for energy-dependent codon optimality is the experimental evidence-based link to healthy longevity and all biodiversity. Theorists might complain that their absence of experimental evidence is not evidence of absence. But that is how theorists try to keep serious scientists waiting for pseudoscientists to make a contribution to what is known about energy-dependent biologically-based cause and effect. Theorists are pseudoscientists who cannot do that.
For instance, and for an example, in the conclusion of Mutation-Driven Evolution, which was published on the same day as my 2013 review, Masatoshi Nei suggested that other theorists and everyone else should simply ignore the need to consider teleological elements.
Teleology is the philosophical attempt to describe things in terms of their apparent purpose, directive principle, or goal. For instance, in 2012, Thomas Nagel proposed a neo-Darwinian account of evolution that incorporates impersonal, natural teleological laws to explain the existence of life, consciousness, rationality, and objective value.
So far as I know, Nei is still biologically uninformed and Nagel is still looking for his Darwin. See: Awaiting a New Darwin
For comparison, here is an example of what happens when other researchers from Russia included a link from the teleological elements to the purpose of life. Keep in mind that every aspect of neo-Darwinian theory must eventually incorporate “Laws of Biology” that link energy from quantum physics to ecological adaptation via quantum physics and the chemistry of biophysically constrained pheromone-controlled reproduction. For example, in my model of how to link angstroms to ecosystems, Kohl’s “Laws of Biology” are Darwin’s “conditions of life.”
The term “epigenetic adaptation” suggests that others have accepted all the facts about RNA-mediated cell type differentiation. The facts link nutrient energy-dependent changes from angstroms to ecosystems via food energy and the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.

Here’s an example of how the “Laws of Biology’ are linked to energy-dependent ecological adaptation: Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to marine and freshwater conditions

The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution – adaptation to a freshwater environment. While genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, ATP4A were deferentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment.

Although they try to separate microevolution and macroevolution, the authors refute every aspect of neo-Darwinian pseudoscientific nonsense. They inadvertently link the quantized energy of sunlight to the creation of ATP, which links food energy-dependent biophysically constrained RNA-directed DNA methylation biosynthesis  from RNA to cell type differentiation in all living genera via my series of blog posts here. See: Search Results for “rna directed DNA methylation”
Anna Di Cosmo’s group linked all invertebrates to all vertebrates via my model in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:
Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).
RNA-directed DNA methylation links the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum in P. fluorescens to all biodiversity on Earth via conserved molecular mechanisms of controlled cell type differentiation in all living genera. From a teleological perspective, supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA, which links virus-driven energy theft to all pathology in all living genera. See: Structural diversity of supercoiled DNA
See also: Engineering RGB color vision into Escherichia coli, which was reported as Bacterial Photography Goes Technicolor http://mobile.the-scientist.com/article/49481/bacterial-photography-goes-technicolor
The requirement for a light-activated endogenous substrate in all cell types has been known to serious scientists who have linked chromosomal inheritance to all biodiversity during the past century. The de novo creation of the endogenous substrate links the de novo creation of G protein-coupled receptors to all energy-dependent cell type differentiation via chemotaxis and phototaxis, which link the ability of microbes to find food to the creation of supercoiled DNA. The supercoiled DNA protects all living genera from the virus-driven degradation of messenger RNA, which is linked from mutations to all pathology.
Indeed, the success of optogenetics is based on the fact that femtosecond blasts of UV light were been linked to RNA-mediated DNA repair. The light activated DNA repair has been linked to the weekend resurrection of the bacterial flagellum in P. fluorescens. That fact refutes all claims about mutation-driven evolution.
Facts that refute mutation-driven evolution are a nightmare for theorists who failed to link sunlight to the life-sustaining energy that Richard Feynman and others placed into the context of food energy. Feynman used that fact as an example of how to “get” physicists who present themselves as know-it-alls. See the video clip, below.
See also: Advances in Non-Viral DNA Vectors for Gene Therapy

…synthetic messenger RNAs (mRNAs), which are delivered to the cell and translated in vivo, offer potential for expressing proteins. The nucleotides in these mRNA molecules must be modified to avoid immune detection through pattern recognition receptors…

The fact that synthetic amino acids have been used to create vaccines that may prevent all pathology, links current technology and teleology to pattern recognition across all species that must find food to reproduce.
See: Generation of influenza A viruses as live but replication-incompetent virus vaccines, which was reported as: Engineered virus has artificial amino acid allowing it to serve as a vaccine
See also: A semisynthetic organism engineered for the stable expansion of the genetic alphabet, which was reported as: Scientists create first stable semisynthetic organism

“We can now get the light of life to stay on,” said Romesberg. “That suggests that all of life’s processes can be subject to manipulation.”

If all of life’s processes were not energy-dependent, the processes could not be manipulated by light in the context of Dobzhansky’s claims in 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).”

Similarly, if all of life’s processes were not nutrient energy-dependent and pheromone-controlled, this research could not link pheromones to the control of antibiotic resistance, which is caused by virus-driven energy theft.
See:

Drugs which affect bacteria’s “sense of smell” could potentially be used as substitutes for modern antibiotics. They do not kill bacteria; they simply give them signals that render them harmless to the human body. In theory, in this case it would be impossible for resistance to be developed.

See also:
Bacterial Quorum-Sensing Network Architectures
Social Evolution Selects for Redundancy in Bacterial Quorum Sensing
Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation
Unfortunately for you and all your dying or deceased loved ones, mathematical model of evolution failed to link nutrient energy-dependent pheromone-controlled ecological adaptations in all genera to healthy longevity. Fortunately, the creation of vaccines via substitutions with artificial amino acids attests to the fact that all of life’s processes are energy-dependent. That may be sufficient proof that RNA-mediated amino acid substitutions protect supercoiled DNA from virus-driven energy theft and the degradation of messenger RNA, which links mutations to all pathology. If not, there will be more proof each day.
See: microRNA
Earlier today, this appeared on my alert. The evolutionary origin of plant and animal microRNAs
The idea that microRNAs automagically evolved appears to be linked to the foolishness of theories that tried to link mutations from natural selection to evolution.  For comparison, see: Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes

It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host’s immune system, while increasing the host’s risk for cancer development.

See also: viral microRNA
For example: Presence of Viral microRNA in Extracellular Environments

Many human viruses of clinical importance including polyomaviruses, hepatitis B virus, hepatitis C virus, human papillomavirus, human immunodeficiency virus produce viral miRNAs (Louten et al., 2015). These specific viral miRNAs have likewise been explored as potential diagnostic platforms (Lagatie et al., 2014, Zhu et al., 2017, Takahashi et al., 2013, Kumar Gupta and Kumar, 2015, Dahiya and Atreya, 2014).

See also: Modified mRNA Vaccines Protect against Zika Virus Infection, which was reported as: More evidence that Zika mRNA vaccines can stop viral replication in mice
The potential for side effects of the vaccines can be evaluated in the same context as the potential for detrimental uncontrolled ecological adaptation of viruses that could be caused by the CRISPR Cas9 gene-editing technology.
See: Obama Advisers Urge Action Against CRISPR Bioterror Threat 

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

The CRISPR Bioterror Threat links all current technology to refutations of every aspect of neo-Darwinian pseudoscientific nonsense and the pseudoscientific nonsense touted by “Big Bang” cosmologists. That fact has forced those who once led the scientific advances in technology to place them into a teleological perspective.
For example, I suspect that is what George Church and others are trying to do.
See: Human Genome Project 2: Synth meeting takes place in Boston16 May 16

Yes, the meeting was behind closed doors, but it’s not quite what you’d call a ‘secret meeting’. Word has it, that the organisers have a high impact publication in the works that they can’t talk about openly yet.

See: “This is not a secret meeting” – George Church 29 Jun 2016
See: George Church refutes theistic evolution 9 Feb 2017
See also: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

Harvard biologist George Church burst into the headlines (yet again) last week when he helped organize a closed-door meeting of scores of top scientists to discuss accelerating efforts to create synthetic DNA — including a complete human genome.

Begley reports that a meeting held last year was held last week. I think I can explain why placing her report into the context of George Church’s business practices is good business for people like her. For example, George Church already refuted every aspect of neo-Darwinian pseudoscientific nonsense when he and others filed the patent for ‘RNA-guided human genome engineering,’ which is an energy-dependent naturally occurring RNA-mediated process. It links natural selection for energy-dependent codon optimality to supercoiled DNA and every aspect of biodiversity.
That fact forces many of the world’s top experts to acknowledge that Darwin’s ‘conditions of life’ are nutrient energy-dependent and pheromone-controlled. That fact links quantum physics to quantum consciousness via claims made by Richard Feynman. For example, he claimed that theoretical physicists exemplify idiocy by using too many different terms for the measurement of “energy.”

The “…proof that physicists are human…” he claims, “… is the idiocy of all the different units which they use in measuring energy.”

The apparent corruption among evolutionists may simply be another example of what Richard Feynman placed into the context of idiocy. In any case, we will continue to see attempts to make it appear that neo-Darwinian theorists have not displayed that same level of idiocy.
They have failed to link ecological variation to energy-dependent ecological adaptation via the physiology of pheromone-controlled reproduction in all living genera. The report by Begley could be “spin-doctoring” at its finest, or it could simply be her mistake.
In either case, those who have been caught touting alternative facts about evolution must now try to make it appear that they have not done that during the past year. During the past year many academics and liberals have been fighting against the claims of corruption made by the Trump administration when the corruption obviously extends to academia.
The fact that reports from researchers in Russia and researchers in China consistently have linked what is known about energy-dependent changes in the microRNA/messenger RNA balance from ecological variation to ecological adaptation or to pathology is not well known to all researchers in the United States. That problem led to accusations that the Russians had hacked the election of our President.
Those accusations can now be placed into the context of Combating Evolution to Fight Disease and support for the State of Israel.
See:  Israeli Middle Schools School to Include Theory of Evolution

 …learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

For review see: Virus-driven energy theft Archives and RNA directed DNA methylation Archives
Finally see: The phylogenetic utility and functional constraint of microRNA flanking sequences (2015) reported as: All in the (bigger) family
My comment: 

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

I will add that the number of terms that could be reduced to link claims about energy to claims about cell type differentiation increasing. Attempts to avoid making claims that link energy-dependent changes in microRNAs from RNA-directed DNA methylation to amino acid substitutions and healthy longevity are prevented by researchers use these different terms for the same thing.
MicroRNAs are contextualized as enhancers, promotors, quantitative trait loci, RNA-based switches. mobile elements, extra-coding RNAs, CRISPR effectors, Oncocers, oncomiRNA, regeneration enhancer elements, isomiRs, regulatory polymorphisms, c-fos enhancers, potential signatures of environmental exposure or effect, key triggers of neuronal cell fate, and many other terms for the same thing.
Alternative splicing of pre-mRNA

Theistic evolutionists fight back and lose

A giant neuron found wrapped around entire mouse brain

Yuste and Eberwine would like to see 3D reconstructions of individual neurons compared to analyses of the genes expressed in those neurons. This may offer clues as to the type and function of each cell.

The nutrient energy-dependent structure and function of all cell types in all living genera links biodiversity from the physiology of pheromone-controlled reproduction in C. elegans to the predatory behavior of P. pacificus, a predatory nematode with teeth.

See: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans

All ecological adaptations, such as teeth, exemplify what is required to link energy-dependent endogenous RNA interference to supercoiled DNA, which protects all organized genome from virus-driven energy theft and genomic entropy.
Predictably, Paul Allen will be the next to start funding works that might help to prevent the viral apocalypse, now that Bill Gates is mentally prepared to do so.

See: Bill Gates refutes theistic evolution

Malnourished children can be getting enough calories, but not the right nutrients.

See for comparison: Mathematics supports a new way to classify viruses based on structure

“Our work is the first to tie structural lineages to sequences so comprehensively,” says Professor Sinclair.

See for comparison: Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

The antigenic changes are clearly nutrient energy-dependent, as are all changes in all cell types of all living genera. Their results link virus-driven energy theft to all pathology, which is why Sinclair et al (2017) must put his mathematical model back into the context of evolution across billions to millions of years.

 
They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others with critical thinking skills to challenge their ridiculous claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
 

They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.

The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
 

Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.

The energy-dependent coding sequence links the physiology of reproduction to RNA-mediated amino acid substitutions and cell type differentiation in all living genera.

See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic effects of food odors and pheromones are involved in neurogenic niche construction as exemplified in nematodes (Bumbarger, Riebesell, Rödelsperger, & Sommer, 2013), and in flies (Swarup et al., 2013).

See for comparison:

What Came First—the Virus or the Egg? 

Three recent studies find that the single-pass transmembrane protein HAP2 mediates gamete fusion and is remarkably similar to class II fusion proteins found in viruses such as dengue and Zika.

Mutational Processes Shaping the Genome in Early Human Embryos

In-vitro-fertilized human embryos often acquire large structural and numerical chromosomal abnormalities. Liu et al. now show that multiple smaller copy number variations may also arise in in-vivo-conceived embryos. Analysis of these variations provides insight into the DNA mutational processes occurring in early embryos and the mechanisms underlying them.

I repeat: “…evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.” Similarly, “DNA mutational processes occurring in early embryos…” cannot shape the genome because mutations prevent biophysically constrained protein folding chemistry.

For comparison: Linking Protein and RNA Function within the Same Gene

Exposure to ultraviolet light leads to a cell-wide DNA damage response that includes a global reduction in transcription. Williamson et al., identify a protein involved in this process as well as a noncoding RNA produced by alternative processing of RNA transcribed from the same gene that promotes recovery from the repressed state.

Femtosecond blasts of UV light have already been linked to DNA repair via alternative processing of RNA transcribed from the same gene.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

See also: Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer

The fact that UV-light induced charge transfer states in DNA control pH responsive RNA-mediated DNA repair seems to have escaped the notice of those who tout selective repair via effective gene transfer without mentioning the source of energy for the transfer.

It’s the anti-entropic virucidal energy of sunlight!

What is Life? 

…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.)

————————

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? (Roger Penrose 8 August 1991)

See also: Theistic evolutionists fight back and lose (2)

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

Alternative splicing of pre-mRNA

Bill Gates refutes theistic evolution (sequel)

See: Bill Gates refutes theistic evolution
See also: Gate-controlled conductance switching in DNA

Conclusion:

Our work demonstrates one can introduce an active control to DNA conductance by modifying a base with a redox group, and switch the DNA conductance reversibly between two levels by oxidizing or reducing the redox group with an EC gate. This strategy could be implemented in more sophisticated DNA nanostructures for active device building blocks. As the DNA conductance is an indicator of the molecule in the reduction or oxidation state, it is possible to study redox reaction kinetics at the single-molecule level by monitoring the DNA conductance.

Reported as: Switched-on DNA: Sparking nano-electronic applications

…the engineered DNA provides a nice tool to examine redox reaction kinetics, and thermodynamics the single molecule level…

This means they can examine virus-driven energy theft in the context of redox reaction kinetics and thermodynamics at the single molecule level, which links nutrient energy-dependent changes from angstroms to ecosystems via the physiology of pheromone-controlled reproduction in species from microbes to humans. Simply put, they can link virus-driven energy theft from mutations to all pathology in species from archaea to modern humans.
See for comparison: Actor Steven Kearney reads excerpts from Greg Bear‘s 1985 novel Blood Music.

The virus is made up of tiny biological computers called “noocytes,” where were intended to improve the human body — giving it routine maintenance and maximizing human potential. Instead, it wiped out most of North America.

See also: Donald Trump’s abortion funding ban condemned by Bill Gates

“The US is the number one donor in the work that we do. Government aid can’t be replaced by philanthropy,” the 61-year-old told the Guardian.

Under the order, which is also known as the Mexico City Policy after it was first unveiled at a UN conference there in 1984, no government funding for family planning services can be given to clinics or groups outside the US that offer abortion or counselling services.

Why is Bill Gates condemning any of President Trump’s foreign policies before the Bill and Melinda Gates foundation stops funding research that is irrelevant to prevention of the viral apocalypse. Does Bill Gates decide who gets the vaccine and who doesn’t at the time the apocalypse begins, or will other billionaires like George Soros dictate all foreign policies? Who are you going to trust with the lives of your loved ones?

See also: Leakers beware: Trump has utterly defeated the disloyal coteries of the US intelligence community with my emphasis

The Trump administration exposed the false flag terrorism in the media.

Donald Trump posed as a hit man. He made sure that the leakers in the IC knew that their actions were illegal. He WARNED them. Then he launched his sting.

Donald Trump gave a press conference in which he admitted to the sting. He said that the leaks are real, but the news is fake.

It was his tactic, and he had to expose how he used it. That exemplifies Trump’s brilliance. Any intelligent disloyal Democrat from the intelligence community should have seen it coming. That suggests none of them are intelligent adversaries.
The biased media reporting on the press conference attests to lack of intelligence among the media representatives who reported the claims of Trump’s ignorant adversaries. The media representatives continue to look more foolish every time they speak out against the President of the United States.
The media representatives won’t be charged with any crimes. How many disloyal Democrats from the intelligence community will be prosecuted for treason?
How will President Trump deal with disloyal billionaires and others who waste his time attempting to influence the people of the United States and cause them to challenge him on topics they know nothing about?
Who will be the next billionaire to inadvertently refute theistic evolution by linking what is known about nutrient energy-dependent RNA-mediated amino acid substitutions to healthy longevity and linking virus-driven energy theft to all pathology?
Will Mark Zuckerberg eliminate the false flag terrorist groups from Facebook?
Will Paul Allen stop funding brain research that does not link the speed of light on contact with water to all energy-dependent cell type differentiation in all living genera via biophotonics and optogenetics?
See also: Billionaires say they’ll end disease. Evolution suggests otherwise

Darwin introduced a viewpoint that was radically unsettling: we don’t progress to a more perfect form, but adapt to local environments. If humans are machines, then we can simply repair the broken parts. But if there is something more fundamental to the crisis of life than mere mechanisms of biology, then risk, and an element of danger, will always be with us.

Humans are not machines. Bill Gates probably knows that. And he probably knows that theistic evolution is the threat that can now be placed into the context of Non-theistic evolution

The major criticism of theistic evolution by non-theistic evolutionists focuses on its essential belief in a supernatural creator. These critics argue that by the application of Occam’s razor, sufficient explanation of the phenomena of evolution is provided by natural processes (in particular, natural selection), and the intervention or direction of a supernatural entity is not required.[42] Evolutionary biologist Richard Dawkins considers theistic evolution a superfluous attempt to “smuggle God in by the back door”.[43]

God doesn’t need to be smuggled in. He’s always been with those who believe. Believers know that natural selection for energy-dependent codon optimality occurs in the context of the physiology of pheromone-controlled reproduction. The physiology of energy-dependent reproduction links natural processes to fixation of amino acid substitutions in supercoiled DNA that differentiate the cell types of all living genera.

Supercoiled DNA protects all organized genomes from virus driven energy theft, which is linked to all pathology by mutations. Theistic evolutionists may continue to claim that they believe in mutation-driven evolution, but that’s because they known nothing about energy-dependent top-down causation.

Ask Bill Gates or a theistic evolutionist where the energy comes from, and see for comparison.

Charge-altering releasable transporters (CARTs) for the delivery and release of mRNA in living animals

CARTs are structurally unique and operate through an unprecedented mechanism, serving initially as oligo(alpha-amino ester) cations that complex, protect, and deliver mRNA and then change physical properties through a degradative, charge-neutralizing intramolecular rearrangement, leading to intracellular release of functional mRNA and highly efficient protein translation.

Reported as: A new way Forward for Gene Therapy

Sickle-cell disease is caused by a mutation that links the transgenerational epigenetic inheritance of virus-driven energy theft to failed nutrient energy-dependent RNA-mediated DNA repair. Hemoglobin S is a naturally occurring hemoglobin variant — one of more than 1200 other variants. The variants link RNA-mediated amino acid substitutions in the cell types of populations of ecologically adapted humans. Clearly, their lineages adapted to ecological variation in the parts of the world where they were raised. Researchers have delivered nutrient energy-dependent messenger RNA (mRNA) into cells that use the mRNA to make proteins. What’s missing from this report on gene therapy are facts about how nutrient energy-dependent viral latency must be linked to healthy longevity via energy-dependent changes in the microRNA/messenger RNA balance linked to amino acid substitutions in supercoiled DNA, or from virus-driven energy theft to all pathology.
I continue to encourage comments from those who are not Combating Evolution to Fight Disease, especially if they are willing to tell others what they like about virus-driven energy theft and all pathology. Now that Bill Gates has clearly stated that virus-driven energy theft is not likely to be a good thing for humanity, perhaps he will join the serious scientists and/or help to fund their works.
See for example: The 2000 T. H. Morgan Medal Essay: H. J. Muller and the Nature of the Gene and works published by Ruth Ann Luna.
For example,  The Brain-Gut-Microbiome Axis: What Role Does It Play in Autism Spectrum Disorder? and her presentation from February 22, 2017:
The Microbiome-Gut-Brain Axis: Linking Gastrointestinal and Neurobehavioral Processes in Autism Spectrum Disorder
She graciously answered these three questions:
Q: Is the gut microbiome the most likely link from nutrient energy-dependent metabolic networks to genetic networks and Precision Medicine via the National Microbiome Initiative?

Ruth Ann Luna PhD, MB (ASCP) CM

It’s certainly a key player in the crosstalk, but there’s still much to uncover about these pathways.

Q: Have you placed the 2016 publication of “Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition” into the context of natural selection for energy-dependent codon optimality and transgenerational epigenetic inheritance in your works?

Ruth Ann Luna PhD, MB (ASCP) CM

No we have not. We are working from functional gut microbiome up the gut-brain axis at this point and hoping to weave in as many other factors as possible.

Q: Who else is addressing the bidirectional communication besides your group?
Ruth Ann Luna PhD, MB (ASCP) CM

There are many other groups evaluating the gut-brain connection in general, but not necessarily exclusive to ASD. I’d suggest a quick search in Pubmed for the latest groups involved in this area.

See: Search Results for “autism” and Search results for “autism microrna”
Her expressed intent to “weave in other factors that already are known to me and to Teresa Binstock inspired me to perform this search for the terms autism and microRNA
See for example from February 17, 2017: Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain
Conclusion:

Our analysis thus indicated that MeCP2-mediated alternative splicing might influence neuronal functions via two different strategies: one is to regulate protein diversity by coding exons, and another is to regulate protein expression by non-coding exons. Our studies not only systematically explore the mechanisms underlying MeCP2-mediated alternative splicing, but also provide insights into the roles of MeCP2-mediated alternative splicing, which could influence both protein diversity and protein expression level in neurons.

Our 1996 Hormones and Behavior review explored the molecular mechanisms of RNA-mediated alternative splicings and nutrient-dependent pheromone-controlled biophysically constrained protein folding chemistry in the context of the physiology of reproduction in species from microbes to humans.
See our molecular epigenetics section in From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

If my co-authors and I had been funded to link what was known about biologically-based cell type differentiation in all species to their origins and from ecological variation to ecological adaptations in all living genera, you would not need to ask whether or not some or all of your loved ones will survive the viral apocalypse.
Nutrient energy-dependent sexual differentiation in yeasts at the advent of sexual reproduction has been linked to all cell type differentiation in all individuals of all species via the conserved molecular mechanisms of pheromone-controlled reproduction that we began to detail two decades ago.
See also: Possible sexually dimorphic role of miRNA and other sncRNA in ASD brain

Our findings of sexual dimorphism in sncRNA levels underscore the importance of considering sex, in addition to age, when interpreting molecular findings on ASD brain.

The interpretation of molecular findings on ASD brain can be placed into the context of virus-driven energy theft and all pathology via the transgenerational epigenetic inheritance of Zika virus-damaged DNA in humans. For comparison see how Greg Bear used information on nutrient-dependent pheromone-controlled RNA-mediated protein folding chemistry to ecological adaptations in a new human subspecies.
See also: Association Between the Probability of Autism Spectrum Disorder and Normative Sex-Related Phenotypic Diversity in Brain Structure

…etiological models suggest that the biological male phenotype carries a higher intrinsic risk for ASD than the female phenotype. To our knowledge, this hypothesis has never been tested directly, and the neurobiological mechanisms that modulate ASD risk in male individuals and female individuals remain elusive.

The neurobiological mechanisms link sex differences in the cell types of yeasts to sex differences in virus-driven energy theft and all pathology.
Reviewed as: Evolution rising from the grave

Bear goes a little further in suggesting that such change can occur over about a generation, an idea that might be a little too radical at the moment. However, he does mention data suggesting that fruitflies can adapt to a new environment in just a few generations of selection.

Reviewed as: Living with the Neanderthals

Bear’s two Darwin novels were not written just to entertain. He also seeks to teach readers about science, to highlight our utilitarian politics and our inability to get along with each other, and to provide a quasi-rational basis for theology and morality. He advances a world view in which we are all part of the vast neural network of life, cutting across ethnic borders, species divides and the chasms between taxonomic kingdoms, in balance, and in two-way communication, with the ecosystem.

Bear qualifies to win the next Nobel Peace Prize, or minimally, the Prize for Literature. When you realize whose information is being used as a basis for the claims by Bill Gates that support young earth creationism, see also: Viral Genome Junk Is Bunk

…in an ironic twist, 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

Where else would viruses get their genes, and what else would force organisms to use the sun’s anti-entropic virucidal energy to adapt?

Alternative splicing of pre-mRNA

Bill Gates refutes theistic evolution

See: Bill Gates refutes theistic evolution (prequel)

See for comparison: Our 2017 Annual Letter Warren Buffett’s Best Investment

Reported as: Scientists create first stable semisynthetic organism

 “We can now get the light of life to stay on,” said Romesberg. “That suggests that all of life’s processes can be subject to manipulation.”

Life’s processes are manipulated by nutrient energy-dependent endogenous RNA interference in the context of the physiology of pheromone-controlled reproduction in all living genera. Supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. But, someone will make billions of dollars on vaccines like this one, which will cost millions and be delivered only to those who can pay for them.

Alternatively, here’s another money-maker: Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy 

But wait. What about nutrient energy-dependent endogenous RNA interference in the context of the physiology of pheromone-controlled reproduction in all living genera. As a computer software developer, Bill Gates knows what can go wrong when a virus steals the energy as information that is required to run the central processing unit, which has sometimes been compared to the human brain.

See also: Bill Gates warns tens of millions could be killed by bio-terrorism  February 18, 2017

The next epidemic could originate on the computer screen of a terrorist intent on using genetic engineering to create a synthetic version of the smallpox virus … or a super contagious and deadly strain of the flu.

The creation of a synthetic virus and/or the virus-driven energy theft that leads to the creation of a deadly strain of the flu links the failure of nutrient energy-dependent endogenous RNA interference to protect organized genomes from virus-driven energy theft.

For example see: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

I placed that claim into the context of The Quest to End the Flu with this comment.

SARCASM ALERT

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.

The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.

If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).

If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.

Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

People with a background in biophysics or computer models of biophysically constrained top-down causation have addressed the confusion about random mutations and natural selection in mutation-driven evolution. Simply put, there is no such thing as natural selection for random mutations, which means there no such thing as the evolution of one species from another.
Francis S. Collins, author of The Language of God: A Scientist Presents Evidence for Belief may not like the facts, but
See for comparison:The Darwin Code by Greg Bear

Perhaps the most intriguing method of gene swapping in bacteria is the bacteriophage, or bacterial virus. Bacteriophages–phages for short–can either kill large numbers of host bacteria, reproducing rapidly, or lie dormant in the bacterial chromosome until the time is right for expression and release.

Ask where Bill Gates got the idea that virus-driven energy theft could cause the death of 30 million people.
Also, see this Google search for “virus-driven energy theft.”
My claim follows the claims Greg Bear has been making during the past 2-3 decades. All energy-dependent changes, which link angstroms to ecosystems in all living genera, are biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.
Is it coincidental or providential that Bill Gates finally admits to what serious scientists have known for more than 2 decades about the forthcoming viral apocalypse?
The viral apocalypse will not be prevented by vaccines because viruses adapt to quickly. The facts about the energy-dependent adaptations of viruses compared to hosts are known to all serious scientists. For comparison, whose works have been funded by the Bill and Melinda Gates Foundation? Is philanthropy wasted on pseudoscientists?
See: Bill Gates refutes theistic evolution (sequel)
 

rp_levels-of-organization.jpg

Pseudoscientists fail to refute theistic evolution

Darwinism for the Genomic Age: Connecting Mutation to Diversification

…the chief cause of our natural unwillingness to admit that one species has given birth to other and distinct species, is that we are always slow in admitting any great change of which we do not see the intermediate steps. (Darwin, 1859)

Darwin put energy-dependent “conditions of life” before what is now known about natural selection for codon optimality. That is the chief cause for ignoring anything that neo-Darwinists claim about mutations and diversification.
Energy-dependent codon optimality links the epigenetic landscape to the physical landscape of supercoiled DNA in all living genera via endogenous RNA interference and fixation of amino acid substitutions. The energy-dependent fixation of amino acid substitutions differentiates all cell types in all living genera in the context of the pheromone-controlled physiology of reproduction and supercoiled DNA
For comparison: Virus-driven energy theft has been linked from mutations to all pathology.

See also: Circulating Plasma and Exosomal microRNAs as Indicators of Drug-Induced Organ Injury in Rodent Models

…circulating plasma and exosomal miRNAs can be used as potential biomarkers specific for drug-induced liver, kidney or muscle injury.

The circulating microRNAs typically link nutrient energy-dependent changes in the microRNA/messenger RNA balance from endogenous RNA interference to supercoiled DNA via RNA-mediated DNA repair.

For comparison, see: DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

Reported as: Study shows higher than expected sequencing errors in public databases

…the accuracy of public databases has been called into question by work done by the team at NEB, which in turn calls into question the accuracy of the cancer datasets.

The link to specimen processing to the number of errors helps to explain why only serious scientists have refuted theistic evolution. Pseudoscientists incorporated the specimen processing errors into their ridiculous mathematical models. Their mathematical models failed to link energy dependent changes in base pairs to single nucleotide polymorphisms and endogenous RNA interference. That fact destroyed any chance that natural selection for energy-dependent codon optimality would be linked from supercoiled DNA to protection from virus-driven energy theft and genomic entropy in all living genera.

See for example: 2007 Using genomic data to unravel the root of the placental mammal phylogeny

A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals ∼103 (95–114) million years ago.

Then this: 2013  Making the impossible possible: rooting the tree of placental mammals

…two groups of researchers have scrutinized the largest available genomic data sets bearing on the question and have come to opposite conclusions, as reported in this issue of Molecular Biology and Evolution.

Then this: 2016  Rooting the family tree of placental mammals

“The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other,” said author Dr Mario Dos-Reis of Queen Mary London, UK. “The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago.”

“You don’t always need to overturn the status quo to make a big impact,” said Dr Tarver. “All of the competing hypotheses had some evidence to support them — that’s precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment.”

Nothing about the roots of any family tree has ever been proved in the context of the fossil record and genomic data. The organization of genomes is nutrient-dependent and pheromone-controlled in the context of energy-dependent links from chirality to autophagy and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy, which is clearly the only link to pathology that consistently shows up in the pathology of dead things.

It’s time to admit that many researchers do not know how RNA-mediated cell type differentiation is biophysically constrained in the context of energy-dependent endogenous RNA interference. The magnitude of the problem increases every day for students in the USA who are taught to believe in mutation-driven evolution.

See for comparison: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans

Conclusion:

Our data presented here suggest the intriguing possibility that RNAi pathways may mediate distinct effects on gene expression in postdauer animals that experienced different environmental stresses. Since other animals, such as pea aphids, form polyphenisms due to crowding or starvation as well, we predict that this work may have broader implications for the RNAi-mediated regulation phenotypic plasticity.

My goodness, what an “intriguing possiblity.” It might be possible to link energy-dependent RNAi from chirality to autophagy and all biodiversity on Earth by starting from the anti-entropic virucidal energy of sunlight and linking it to the differences between bacteria and virus-infected archaea in the ocean via the physiology of their pheromone-controlled reproduction.

See also: Dobzhansky 1973 and precision medicine (5)

See also: RNA-Guided Human Genome Engineering

5. 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).

Targeting viral elements with energy-dependent Cas+gRNA systems in microbes, plants, animals, or human cells links energy-dependent RNA-mediated amino acid substitutions to viral latency in all living genera. That fact links these three refutations of theist evolution to the examples of the refutations in this model. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
One George Church refutes theistic evolution (3-part series)
Two Francis S. Collins refutes theistic evolution
Three Stuart Kauffman refutes theistic evolution
See also: Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries

He proposed that our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.

Let me make this perfectly clear:

The anti-entropic order-generating force is sunlight.

 

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?
 

Alternative splicing of pre-mRNA

George Church refutes theistic evolution (2)

See: George Church refutes theistic evolution

George Church may not know that he refuted every aspect of theistic evolution in his presentation on February 8, 2017. Hopefully, someone will tell him how he linked quantum physics from chemistry to biophysically constrained protein folding and all biodiversity, or explain to others how he did that. Here is my explanation of his admissions. I placed the explanation into the context of this poster session submission.

Title: Energy as information and constrained endogenous RNA interference
Abstract:

Sunlight-induces energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Changes in the potential of hydrogen (pH) link quantum physics to classical physics via chirality (manifested in chemistry). Energy-dependent biophysically constrained protein folding chemistry links what is known about molecular epigenetics to what is known about autophagy.  For instance, energy-dependent changes in pH link ecological variation from angstroms to ecosystems via base pair changes and RNA-directed DNA methylation (endogenous RNA interference).  That is how the sun’s anti-entropic virucidal energy is linked from the physiology of reproduction to all life on Earth.

Base pair changes link microbial quorum sensing from the nutrient energy-dependent pheromone-controlled physiology of reproduction to the National Microbiome Initiative. Endogenous RNA interference (RNAi) links the base pair changes from the innate immune system to supercoiled DNA and chromosomal inheritance. Sunlight is linked from the National Microbiome Initiative to the Precision Medicine Initiative via genome wide inferences of natural selection for nutrients and the pheromone-controlled energy-dependent fixation of amino acid substitutions in all organized genomes.

This presentation explains how natural selection for energy-dependent codon optimality links biologically-based cause and effect from the de novo creation of G protein-coupled receptors (GPCRs) to fixation of RNA-mediated amino acid substitutions. GPCRs link metabolic networks and genetic networks to the amino acid substitutions that differentiate all cell types in all individuals of all species.

Ecological variation is linked to energy-dependent metabolic networks and genetic networks, which link alternative RNA splicings from supercoiled DNA to polycombic ecological adaptations.  Ecological adaptations, which are manifested in morphology, are linked from supercoiled DNA and chromosomal inheritance to healthy longevity via energy-dependent differences in behavior.

For contrast, virus-driven energy theft links messenger RNA degradation to negative supercoiling and constraint-breaking mutations. Virus-driven hecatombic evolution links energy theft from biophysical constraint-breaking mutations to all pathology. For example, the viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA in human infants, which typically is repaired by energy-dependent endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

A link to the poster session and narrative summary should be available within the next two weeks.

Alternative splicing of pre-mRNA

George Church refutes theistic evolution

Wednesday Afternoon Lecture Series (WALS) – The future of genetic codes and BRAIN codes

The NIH Director’s Wednesday Afternoon Lecture Series, colloquially known as WALS, is the highest-profile lecture program at the NIH.

The future of genetic codes and BRAIN codes (video)
My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.
Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.
Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
They showed that a single set of light-activated reactions gave rise to most of life’s building blocks simultaneously. Simply put, that fact refutes every aspect of neo-Darwinian nonsense. It also eliminates consideration of any theories proposed by “big bang” cosmologists.
The irony of this is that not one of the young earth creationists I know would fail to link the hydrogen-atom energy-dependent de novo creation of nucleic acid precursors to all biodiversity on Earth via the physiology of biophysically constrained cell type differentiation.
For example, see: Multipurpose Plant Sensors Startle Scientists
Even if a young earth creationist knew nothing about energy-dependent cell type differentiation, he or she would not be likely to link minimal mutational differences, called mutations to the mutation-driven evolution of all biodiversity.
As you can see in the video, George Church has been forced to abide by the rules of serious scientists.
Here is an unavoidable rule: Kalevi Kull: Censorship & Royal Society Evo Event

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.

George Church has, until yesterday, focused his efforts on exogenous RNA interference rather than what is known about endogenous RNA interference, which links supercoiled DNA to the prevention of all virus-driven pathology in all living genera. Most people will not recognize what President Trump has forced the NIH to do before the theistic evolutionist, Francis Collins is replaced. They may read this, but not understand what it means.
Obama Advisers Urge Action Against CRISPR Bioterror Threat

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The likelihood that NIH funding will be used for any studies that do not link prevention from the National Microbiome Initiative to the Precision Medicine Initiative via the microRNAome and energy-dependent microRNA expression can be placed into the context of failed mathematical models, which have not addressed any aspect of energy-dependent biologically-based cause and effect.
Let me help others decipher the content of George Church’s claims in: The future of genetic codes and BRAIN codes
The question (at 54:22) about teratomas is answered with a classic attempt to obfuscate what is known about virus-driven energy theft and all pathology.
How organs assemble in the context of virus-driven energy theft has been placed into the context of energy-dependent viral latency since the time that Sinclair Lewis published “Arrowsmith” in 1925 and Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for his works on chromosomal inheritance.
At 59.00 the question about natural selection for energy-dependent codon optimality leads to another attempt to obfuscate what is known about top-down causation.
At 1:00 he begins to talks about adding a built-in sequencer in your phone.  At this point, you may need some comic relief, which Jon Stewart provided with his question about whether the new technology would be integrated with a camera. See: Jon Stewart interviews Greg Bear.
At 1:04, the question and answer about Alzheimer’s vs cognitive enhancement can be placed into the context of Greg Bear’s works, which were published in 1999 and 2003. They were reviewed by Michael A. Goldman in “Nature.”
Evolution rising from the grave
Living with the Neanderthals
See also: Newly found mechanism for protecting neurons could underlie brain disease

The neurons expel large (4- micron diameter) membrane-bound vesicles (dubbed “exophers”) that are filled with clumped protein and damaged cellular organelles including mitochondria.

The only mention of exopher in the extant literature indexed on PubMed is in the article published yesterday, C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress.  The authors seem to be trying to make everything known to all serious scientists appear to be new information about the biophysically constrained RNA-mediated transgenerational epigenetic inheritance of morphological and behavioral phenotypes.
This is roughly the equivalent of inventing de Vries 1902 term “mutation,” which was used by theorists to dismiss Darwin’s “conditions of life.”
For comparison, there are now 58,887 indexed articles on PubMed that mention microRNA.  For example, see: MCMDA: Matrix Completion for MiRNA-Disease Association prediction
If you do not object to the level of obfuscation that is required for pseudoscientists to continue touting their ridiculous theories, you may not be allowed to join those who are Combating Evolution to Fight Disease.
What career goals will you pursue after the Trump administration ensures that pseudoscientific nonsense is no longer funded?
Activity-dependent spatially-localized miRNA maturation in neuronal dendrites
Reported as: Bright Spots in Brain Cells

Thanks to Anna Di Cosmo for calling attention to more detailed facts about cell type differentiation that link energy-dependent changes in fluorescence from the weekend resurrection of the bacterial flagellum to endogenous RNA interference and the maturation of brain cells in rats.
Everything known appears to link the conserved molecular mechanisms of nutrient-dependent pheromone-controlled physiology of reproduction in species from archaea to humans.
In any case, no one is challenging the perspective that serious scientists like Anna Di Cosmo have added to what is known about everything that links quantum physics to quantum consciousness via energy-dependent “bright spots in brain cells.”
And there is still no other model for comparison to this model of biologically-based cause and effect. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
A good model predicts, and people who understand the need for a good model of biologically-based cause and effect predictably make the most scientific progress.
In 2013 I wrote:

“…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.”

In 2015, Role of olfaction in Octopus vulgaris reproduction, Anna Di Cosmo’s group concluded:

The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). The knowledge of the nature of the factor released by the optic gland could shed light on the role played by this gland in the reproduction: is it a gonadotropin or a trophic factor? Intriguingly, even though the mechanisms and molecules regulating reproduction are the same in both male and female, O’Dor and Wells (1978) observed mature sperms in young O. vulgaris males independently from optic gland hypertrophy.