Watering Young Plant - Vintage Effect

A single base change refutes theistic evolution

Everyone who failed to learn how light-activated endogenous substrates biophysically constrain viral latency is playing “catch up” to serious scientists. The serious scientists know how quantized energy-dependent RNA-mediated cell type differentiation occurs in the context of the physiology of reproduction in all living genera. Rather than accept the fact that the innate immune system of bacteria (CRISPR) linked the pheromone-controlled physiology of reproduction from autophagy to biophysically constrained viral latency, theorists decided to waste money on virus-assisted gene-editing attempts to repair virus-damaged DNA.

Mammoth Biosciences launches a CRISPR-powered search engine for disease detection

Jennifer Doudna, George Church and many others still refuse to admit that they have refuted theistic evolution. They are just beginning to accurately portray the how detection of changes in the microRNA/messenger RNA balance links virus-driven energy theft to the degradation of messenger RNA. Clearly, however, they know how the degradation of messenger RNA is linked to all pathology.

Had they followed the works of Christ et al. (2013), The Pharmacology of Regenerative Medicine and Christ et al., (2018) Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming, they could intelligently interact with those who are scheduled to present during Schrödinger at 75 – The Future of Biology – September 2018.

(Nick Lane excepted.) He appears to be a biologically uninformed theorist who does not realize that Fast food makes the immune system more aggressive in the long term

Unhealthy eating causes some of these normally hidden pieces of DNA to unwind, similar to a loop hanging out of a ball of wool. This area of the genetic material can then be read much easier as long as this temporary unwrapping remains active. Scientists call these phenomena epigenetic changes. “The inflammasome triggers such epigenetic changes,” explains Dr. Latz. “The immune system consequently reacts even to small stimuli with stronger inflammatory responses.”

The immune system reacts to the proliferation of viruses. The viruses cause the inflammation, which has been linked to all pathology in more than 72,500 published works. See microRNA.

See also: Field-deployable viral diagnostics using CRISPR-Cas13

…the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015–2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

Pardis C. Sabeti’s group already linked the anti-entropic virucidal energy of sunlight from the creation of enzymes to natural selection for energy-dependent codon optimality via the pheromone-controlled stability of organized genomes in a human population in what is now Central China.
See this report from 2013 on fixation of the EDAR V370A substitution.
Following the footprints of positive selection February 15th, 2013.
For comparison to positive selection for food and fixation of the EDAR V370A amino acid substitution, the pseudoscientific nonsense about evolution touted by Pardis C. Sabeti’s group appears in this YouTube video report: 2 Cell Studies Reveal Genetic Variation Driving Human Evolution
In the mouse model of food energy-dependent pheromone-controlled ecological adaptations, they replaced the valine normally found in mouse EDAR with the alanine that’s under selection in humans. They got mice with thicker hair, changes in mammary tissue, and and increased  number of eccrine sweat glands. Those changes parallel phenotypic changes in humans. The phenotypic changes in humans link the quantized energy-dependent creation of microRNAs to biophysically constrained viral latency in all living genera.
In humans, the changes are linked to visual perception of mass and energy and the perception of physical features that are sexually selected.
See: Olfaction Warps Visual Time Perception
A single base change results in the valine to alanine substitution, which changes the ancient mammalian gene EDAR and the EDAR encoded protein.
That fact was reported in the context of links from subatomic particles and all levels of biophysically constrained viral latency and biological organization in my 2014 invited review of nutritional epigenetics.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (unpublished)
Conclusion:

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man

162. Kamberov, Yana G.; Wang, S.; Tan, J.; Gerbault, P.; Wark, A.; Tan, L.; Yang, Y.; Li, S.; Tang, K.; Chen, H., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013, 152 (4), 691-702. doi: 10.1016/j.cell.2013.01.016
163. Grossman, Sharon R.; Andersen, Kristian G.; Shlyakhter, I.; Tabrizi, S.; Winnicki, S.; Yen, A.; Park, Daniel J.; Griesemer, D.; Karlsson, Elinor K.; Wong, Sunny H., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell 2013, 152 (4), 703-713. doi: 10.1016/j.cell.2013.01.035
See also:
161. Rosenberg, S. M.; Queitsch, C., Combating Evolution to Fight Disease. Science 2014, 343 (6175), 1088-1089. doi: 10.1126/science.1247472
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. — Kalevi Kull

Serious scientists from South Korea are the winners. Two recent publications forced the denuclearization of North Korea.
Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events

Compared to the G2 RotaTeq vaccine strain, 17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets. In a subsequent mini-replicon assay, the effect of PA K338R was highlighted by the enhancement of viral polymerase complex activity of both Vc_BR60 and Ym_WI01 viruses. These results suggest that the PA K338R mutation may be a molecular determinant of IBV pathogenicity via modulating the viral polymerase function of IBVs.

Mutations are known to be the molecular determinants of all pathology in species from microbes to humans. See:  Virus-mediated archaeal hecatomb in the deep seafloor
Watch as Hashem Al-Ghaili puts everything known to serious scientists about the virus-mediated archaeal hecatomb back into the context of neo-Darwinian evolution.

See also: Study offers new approach to starve p53 deficient tumors

One major hallmark of cancer cells is their ability to adapt to stressful conditions such as nutrient deprivation. Rapidly growing tumor cells must compete for the ever-diminishing supply of nutrients in the surrounding environment to survive and proliferate. Targeting these adaptive mechanisms represents a promising approach for cancer therapeutics.

It’s a little late to claim that the virus-driven theft of quantized energy is linked from autophagy to adaptations in viruses. All serious scientists know that food energy-dependent pheromone-controlled biophysically constrained autophagy has been linked to viral latency and to ecological adaptations in all living genera. Intelligent people know that viruses have been linked to all pathology.
See also: From Istanbul, Turkey. Respect for all human life has been placed into the context of the energy-dependent de novo creation of microRNAs and the works of an Islamic creationist in Turkey.

Autophagy-Regulating microRNAs and Cancer
Cancer researchers in other countries clearly are approaching the cure for all pathology from a scientific creationist perspective despite being forced to place their claims into the context of evolution to get their works past peer review.
The Trump administration has been working towards world peace with other leaders for more than a year. See for example:
May 3, 2017
LIVE: President Donald J. Trump and Palestinian President Mahmoud Abbas make a joint statement at the White House.
Who does not want World Peace? Why The End of the Korean War Is Bad News for the United States
Alternative splicing of pre-mRNA

From base editing to RNA editing (4)

Summary: To claim evolution, Koonin must link food energy from the pheromone-controlled physiology of reproduction to fixation of a beneficial mutation in the organized genome of one species that evolved into another species.
Search Results for “base editing” = 82 blog posts starting with Cell-type differentiation on February 7, 2014
Search Results for “RNA editing” = 95 blog posts starting with In theory, or supported by experimental evidence? October 22, 2014
See for comparison PubMed: “base editing” (33 citations) and “RNA editing” (4222 citations)
The failure to link energy-dependent base editing to RNA editing and RNA-mediated cell type differentiation in all publications about healthy longevity compared to pathology can be attributed to the pseudoscientific nonsense touted by theorists. In their ridiculous mathematical models, they claimed the emergence of energy could be linked to the evolution of all biodiversity. Their lack of experimental evidence, which is required to link biologically-based cause and effect to biodiversity, was placed into the context of “human idiocy” by Richard P. Feynman.

See Richard P. Feynman’s lecture on: Food energy. See for comparison see: Energy as information and constrained endogenous RNA interference.

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

The failure to link energy-dependent base editing and energy-dependent RNA editing to healthy longevity predicted the failure to link the virus-driven degradation of messenger RNA to all pathology. See for instance: The Science of Personalized Nutrition

A single nucleotide polymorphism (SNP) or change occurs in nearly 1 in 1,000 base pairs and accounts for much of an individual’s uniqueness. Research on SNPs and other genetic variations like deletions, inversions, duplications and copy number variations (CNV), which represent up to 9.5 percent of the human genome, have changed the face of human nutrition and validated the concept that nutrition could and should be personalized. (Mullally, 2007)

A single nucleotide polymorphism (SNP) is a single base-pair difference in the DNA sequence of individual members of a species. SNPs in genes may lead to variations in the amino acid sequence, but SNPs can also occur in noncoding regions of DNA. Base editing of A•T to G•C in genomic DNA was linked from RNA editing to the physiology of pheromone-controlled reproduction and fixation of amino acid substitutions in organized genomes. The amino acid substitutions differentiate all cell types in all individuals of all living genera.
See: Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Reported as: Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

Bioengineer Feng Zhang of MIT’S Broad Institute notes in an email that the team employed “a comprehensive and creative approach” to achieve such precision. “As a field, we have been looking for ways to precisely rewrite parts of the genetic code,” writes Feng, whose own, CRISPR-based method to edit single bases in RNA was published today in Science. “Base editors move us closer to this goal.”

The CRISPR-based editing of single base pairs in RNA links the energy-dependent function of the innate immune system to all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction, which biophysically constrains viral latency. Natural selection for energy-dependent codon optimality, links the editing of single base pairs in RNA to every aspect of healthy longevity via RNA editing.
See: RNA editing with CRISPR-Cas13
Reported as: RNA Editing Possible with CRISPR-Cas13

“This work is an impressive study from a highly productive research group that suggests the possibility of editing RNA transcripts to alter their coding potential in a programmable manner,” David Liu…[who] has a report out today in Nature describing specific nucleotide editing of DNA by a similar method.

Feng Zhang (base editing) gives a pat on the back to David Liu (RNA editing), and Liu reciprocated, or vice versa. Taken together, they are making face-saving attempts that ignore everything known to serious scientists about biophysically constrained viral latency.

The tool itself could be further developed, adds computational biologist Eugene Koonin of the National Center for Biotechnology Information who also was not involved in the study. “This paper is not the end of the road,” he says. It’s possible that Cas13b could be fused to a variety of editing enzymes that would allow a range of different sequence changes. The possibilities are numerous, Koonin says, and “the best is still to come.”

Koonin is a biologically uninformed science idiot who has followed in the footsteps of others like him. Their computations link mutations to evolution across millions of years. The computational biologists are evolutionary biologists who have failed to link food energy from the creation of enzymes and the the RNA-mediated editing of the enzymes, which is required to link differences in sequence changes from fixation of RNA-mediated amino acid substitutions in organized genomes to the prevention of virus-driven messenger RNA degradation. All serious scientists have linked the virus-driven degradation of messenger RNA from mutations to all pathology. Koonin’s claim that “the best is still to come” is moronic.
Every link to energy-dependent RNA-mediated cell type differentiation via the pheromone-controlled fixation of amino acid substitutions has been detailed in the context of experimental evidence. But, Koonin (2016) made this ridiculous claim:

The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

To claim evolution, Koonin must link food energy from the pheromone-controlled physiology of reproduction to fixation of a beneficial mutation in the organized genome of one species that evolved into another species.
If Koonin and others like him cannot provide an example of how biologically-based evolution occurs, there is only the pseudoscientific nonsense of their mathematical models for comparison to facts about: How flu shot manufacturing forces influenza to mutate

“Now we can explain — at an atomic level — why egg-based vaccine production is causing problems,” said TSRI Research Associate Nicholas Wu, Ph.D., first author of the study, published recently in the journal PLOS Pathogens.

Clearly, an explanation — at the atomic level — of how viruses adapt to the cell types of one species during the production of an egg-based vaccine must be linked from atoms to ecosystems in all living genera via adaptations in the host.
See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

The genesis of variation is manifested in ecological variation, which confers the ability to adapt via nutrient-dependent epigenetically-effected pheromone-controlled ecological, social, neurogenic, and socio-cognitive niche construction. Niche construction is manifested in organismal complexity. Everything about ecological adaptation appears to make sense in the light of what is currently known about molecular biology. What is currently known about the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA can now be compared to any forthcoming explanations that attempt to make sense of how mutation-driven evolution might occur.

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

From base editing to RNA editing

Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

“Nature conveniently provides us with cytosine deaminase enzymes that operate on DNA,” Liu tells The Scientist.

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
See for comparison: All about that base (video parody)
See also: RNA Editing Possible with CRISPR-Cas13

Introducing specific sequence changes into RNA molecules could allow researchers to answer questions about alternative splicing mechanisms, translation, and even editing, he says. “There’s a lot of scope.”

The entirety of that scope was addressed in the context of energy-dependent RNA-mediated cell type differentiation in our section on molecular epigenetics from this 1996 Hormones and Behavior review. 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.
All biophysically constrained RNA-mediated energy-dependent cell type differentiation has since been linked from the pheromone-controlled physiology of reproduction to supercoiled DNA via the fixation of amino acid substitutions and chromosomal rearrangements.
The facts about the amino acid substitutions in the context of transgenerational epigenetic inheritance link electrons to ecosystems via the cryo-EM technology that won the 2017 Nobel Prize in Chemistry.
See: Chemists know (video parody)
See also:

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

Alternative splicing of pre-mRNA

Thanks again for asking about DNA methylation

Re: RNA-directed DNA methylation (1996) See: From Fertilization to Adult Sexual Behavior

Molecular epigenetics. It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes.

See also: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity (2014)
See also:  Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity (2017) reported as: Humans and sponges share gene regulation
See also: Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability
Reported 10/2/17 as: Unexpected findings uncover new understanding of gene expression

What is it about the whole body of the enzyme itself that functions in development and its mutations that can result in cancer?

Thanks again for asking. It is the fact that RNA-directed DNA methylation is energy-dependent and the fact that virus-driven energy theft causes the degradation of messenger RNA, which serious scientists have linked to all pathology.
Everything known to serious scientists about energy-dependent increasing organismal complexity has been portrayed by pseudoscientists in the context of mutation-driven evolution.
The pseudoscientists are not going to stop until serious scientists force them to start helping those who are “Combating Evolution to Fight Disease.”
See for comparison: Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity

…there is evidence that some of the selected genes may contribute to the formation of different cell types. One route might be through the modification of stem cell activity in response to a greater functional diversity of the proteins that modulate epigenetic status to either maintain or promote differentiation [35,36].

Beneath the surface of what you see reported about organismal complexity in the mainstream media, you can see: Eligo Bioscience Secures $20 Million Series A from Khosla Ventures and Seventure to Bring Precision Medicine to the Microbiome

A growing body of research shows that the microbiome, made up of the ten trillion bacteria residing within and on the human body, sits “at the interface of health and disease.”

The company’s approach uses the innate immune system of bacteria (CRISPR) to edit the genetic material of antibiotic-resistant bacteria.  The microRNAome links the virus-driven degradation of messenger RNA in bacteria from the energy-dependent pheromone-controlled physiology of reproduction to all pathology biodiversity via changes in the healthy microbiome. The concept of endogenous RNA interference is rapidly replacing the nonsense about virus-driven gene editing, which has not yet earned a Nobel Prize for pseudoscientific representations of cause and effect.
See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014)

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

This is what one of my former Facebook friends called “bullspit.” It is about “bull sperm.” It is not what other former Facebook friends say “nobody cares” about. It is the link from energy-dependent changes in soil bacteria to all biophysically constrained life on Earth. It is also what other researchers who are biologically uninformed science idiots tell you is the link from virus-caused mutations to evolution.
See for comparison: Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See for comparison: Nobel Prize in Medicine Awarded to Circadian Rhythm Researchers
I do not expect anyone who has not already linked what is known about quantum physics to quantum souls to understand why this year’s Nobel Laureates in Physiology or Medicine have abandoned all experimental evidence of biophysically constrained top-down causation to continue touting their ridiculous gene-centric theories.
Do you? But, I understand why they do not want to admit to the facts.

Military-related trauma tied to eating disorder symptoms

…when they controlled for other trauma types, military-related trauma was the only trauma type that was uniquely associated with eating disorder symptoms. Examination of different types of military-related trauma indicated that the association was not driven by exposure to combat.

Predictably, it was an exposure-driven association with the stress-linked failure to adapt to virus-driven changes in gut microbiome and behavior that lead veterans who have served overseas to commit suicide.

See also: Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms

Reported as: The dust storm microbiome

The researchers found that during a dust storm the concentration of bacteria and the number of bacterial species present in the atmosphere rise sharply, so people walking outdoors in these storms are exposed to many more bacteria than usual.

Greg Bear put this into the perspective of Homeland Security in his techno thriller “Quantico.” At times, all that serious scientists can do is laugh about the pseudoscientific nonsense touted by theorists. Bear checked the facts from “Darwin’s Children” with me before he sent the manuscript for publication. And then came this interview with Jon Stewart.

See for comparison the simple-minded misrepresentations of human ethologists in Human Ethology Bulletin » 2017 »
HEB 32(3)
For example: “Y/Our Vocal Sounds – Towards an Ethological Classification of Human Vocalizing Behavior and Sounds
by Jay R. Feierman 

This article is a first attempt at an ethological classification of human vocalizing behaviors and the sounds they make. Lastly, how human ethologists could study these two different types of human vocalizing behaviors, using the sounds they make as proxies, will be discussed.

Summarized in part in Ourselves Explained link opens pdf

A Review of the book

THE SECRET OF OUR SUCCESS. HOW CULTURE IS DRIVING HUMAN EVOLUTION, DOMESTICATING OUR SPECIES, AND MAKING US SMARTER By Joseph Henrich. 2016

The key to this book’s 18-word title can be summed up in five: Cumulative culture drives
human evolution.

The failure of this book to explain any aspect of biophysically constrained biologically-based cause and effect can be summed up in seven words. No species evolved from any other species.
Energy-dependent RNA-directed DNA methylation links ecological variation from biophysically constrained viral latency to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
 
 

Cytosis

Your indifference is killing you and others (3)

Summary: The speed of light on contact with water links the creation of microRNAs to Optical control of membrane tethering and interorganellar communication at nanoscales MicroRNA flanking sequences are linked to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. The physiology of reproduction links energy-dependent changes in the microRNA/messenger RNA balance to the fixation of amino acid substitutions in supercoiled DNA. Supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA.
See also: Combating Evolution to Fight Disease
See also: Biblical Genesis
…in the Garden of Eden but instructs them not to eat the fruit of the tree of knowledge of good and evil.

Tree of the knowledge of good and evil

…when God forbids the man to eat from that particular tree, he says that if he does so, he is “doomed to die”.
I am fascinated by the facts that link the Biblical metaphors from eating a virus-infected “fruit” to the death of everyone who will ever live and die.  That fact can be placed into this context: Past 5,000 years prolific for changes to human genome.

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

See also: Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy
Reported by Exiqon as: Robust one-day ISH protocol for disease microRNA biomarker development

ISH of biopsy material has become routine pathology procedure for monitoring gene expression and sample characterization. This could be of microRNAs which prove excellent as biomarkers for disease diagnosis, patient stratification and treatment efficacy.

A fast and robust microRNA ISH protocol well-suited for clinical biomarker studies has just been published in Methods Mol Biol using DIG or FAM double-labeled microRNA-specific LNA™-enhanced detection probes in formalin-fixed, paraffin-embedded (FFPE) tissue sections.

Monitoring gene expression and sample characterization via natrurally occuring microRNA biomarkers is the key to developing biomarkers for use in “…disease diagnosis, patient stratification and treatment efficacy.”
The microRNAs need only be linked from flanking sequences to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution and the physiology of reproduction, which links energy-dependent changes in the microRNA/messenger RNA balance from the fixation of amino acid substitutions in supercoiled DNA to protection from the virus-driven degradation of messenger RNA.
See: Optical control of membrane tethering and interorganellar communication at nanoscales

All the observed interactions seem to require the presence of at least two consecutive positively charged residues (‘KK’ or ‘KR’). Replacement of a single lysine with alanine in such dyad motifs could lead to pronounced reduction in puncta formation; whereas KK-to-AA substitutions often abrogate the PB-lipid/PM associations (Fig. 4 and S4†). Further structural studies on the interaction between PB domains and PIs will likely provide a definitive answer by pinpointing the exact molecular determinants.

The temporal and spatial control that connects subcellular compartments to interorganellar communication, which links energy-dependent changes from angstroms to ecosystems in all living genera is RNA-mediated and biophysically constrained by the pheromone-controlled physiology of reproduction. The temporal and spacial control is linked to our visual perception of mass and energy via the sense of smell in bacteria and RNA-mediated amino acid substitutions in the organized genomes of all living genera.
See also: Mechanism of metabolic puncta formation and its functional significance

Many metabolic enzymes have recently been shown to assemble into multi-component puncta in cells, and this assembly is though to play some role in controlling metabolic flux. For example, substrate channeling within these structures could play an important role in metabolism, enabling intermediates to be directly fed from one enzyme to another without dilution. Therefore the assembly of enzymes into these puncta could be an important mechanism for cells to manipulate their metabolism in response to different signals. However, the mechanism of formation of these puncta is completely unknown.

If the energy-dependent formation of these puncta was not known to be linked from differences in the microRNA/messenger RNA balance to the pheromone-controlled physiology of reproduction in all living genera, I could not have found the obvious link from food energy to all biodiversity in this PubMed search.
puncta formation microRNA

For example, food energy is the obvious link from changes in chirality to autophagy. Autophagy protects all organized genomes from the virus-driven degradation of messenger RNA. Simply put, biophysically contrained energy-dependent autophagy protects all living genera from the mutations that serious scientists have linked to all pathology.
See also:
MicroRNA-141 Targets Sirt1 and Inhibits Autophagy to Reduce HBV Replication.
C. elegans Dicer interacts with the P-granule component GLH-1 and both regulate germline RNPs.

See also:  Bridging Length and Time Scales in Cell Organization

For comparison, see: “For the past century some people have regarded natural selection as “that secular God.” Now, that title belongs to CRISPR. “— Jay R. Feierman
Feierman has not learned that natural selection for energy-dependent codon optimality links a light-activated endogenous substrate from the innate immune system in bacteria: CRISPR, to the biophysically constrained physiology of pheromone-controlled reproduction in all living genera. That fact is proof of God’s energy-dependent Creation. The claim that the title of “secular God” belongs to CRISPR is as ridiculous as this claim.
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.
See also:  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.
CRISPR is the only obvious link from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the theft of quantized information that links mutations to all pathology via the degradation of messenger RNA.
See also: Your indifference is killing you and others (4)

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Robert Sapolsky's legacy of atheistic pseudoscientific nonsense

Summary: Not only does everything known to serious scientists about energy link RNA synthesis to life, everything McEwen and others have published links nutrient stress and/or social stress to the virus-driven degradation of messenger RNA and all pathology.
As moderator of the International Society for Human Ethology (ISHE), a not-for-profit scientific organization that consistently touts pseudoscientific nonsense in the context of neo-Darwinian evolution, Jay R. Feierman’s attacks on the works of serous scientists are increasing in frequency and in magnitude. Yesterday, he posted this link to a series of 25 lectures by Robert Sapolsky.  You could spend ~25 hours to learn what Sapolsky was teaching to students until 2011, or ignore everything he has claimed because he has been teaching atheistic pseudoscientific nonsense in the context of neo-Darwinian theory.

Today, Jay F. Feierman’s attacks on the works of serous scientists began with this:
Examining non-LTR retrotransposons in the context of the evolving primate brain

Although all mutational types have worked in concert with evolutionary forces to generate the current human brain, in this review we will explore the impact of mobile elements…

Robert Sapolsky may be responsible for many of these ridiculous reports on the evolving primate brain. Sapolsky studied under Bruce McEwen, but Sapolsky failed to link energy as information from an endogenous substrate in all cell types to the light-activated creation of ATP and the creation of RNA in microbes like P. fluorescens.
With exposure to ultraviolet light, this species (P. fluorescens) fluoresces. The weekend resurrection of the bacterial flagellum was also reported in this species. The energy-dependent physiology of pheromone-controlled reproduction links the creation of the sun from the creation of ATP and the creation of RNA to the weekend resurrection of an irreducibly complex functional structure and all biophysically constrained biodiversity on Earth via McEwen et al., (1964). Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Not only does everything known to serious scientists about energy link RNA synthesis to life, everything McEwen and others have published links nutrient stress and/or social stress to the virus-driven degradation of messenger RNA and all pathology.
Sapolsky is reported to be an atheist in a Wikipedia entry. That should not matter to anyone who is capable of linking quantized energy from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum. See: Olfaction Warps Visual Time Perception But, for those of us who have followed McEwen’s lead, and done that, Sapolsky’s lectures attest to his atheistic ignorance of biologically-based cause and effect.
His lectures can be viewed as examples of the human idiocy that Feynman mentioned in the context of the different measures used to make claims about energy as information. The origin of information still appears to come from the sun despite the fact that Feynman used the example of food energy. The history of publications on how the virus-driven energy theft of quantized energy has been linked from mutations to all pathology now includes information about how human endogenous retroviruses must be biophysically constrained.
The information is linked from energy as information to the physiology of pheromone-controlled reproduction in Bombyx mori to the control of cellular processing in mammals by everything I have published since 1995 and everything known about the creation of the innate immune system in bacteria (CRISPR). The works of those who claim that the emergence of energy and “evolution did it” can be compared to the works of serious scientists.
See for examples: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors (2012)
Transposable-element associated small RNAs in Bombyx mori genome (2012)
Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses (2012)
Control of mammalian retrotransposons by cellular RNA processing activities (2014)
Protein-Coding Genes’ Retrocopies and Their Functions (2017)
Identification and characterization of two putative microRNAs encoded by Bombyx mori cypovirus (2017)

This is the first report that an insect double stranded RNA virus may generate miRNAs and the results obtained will benefit the future study of the functions of BmCPV-encoded miRNAs on viral replication and virus-host interaction.

Pheromones (Ectohormones) in Insects (1959)

Independently of Butenandt & Hecker (14, 50), the fractionation of Bombyx extracts and purification of the pheromone was also reported on by Makino et at. (71).

Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) by FRITZ, IRVING B. and MCEWEN, BRUCE
Since 1959, McEwen and many others have linked food energy and pheromones to the biophysically constrained viral latency that ensures the survival of all species.  See also: Feedback loops link odor and pheromone signaling with reproduction
Since the time I met him in 1995, Jay R. Feierman has contributed to the unnecessary suffering and premature death of thousands via his misrepresentations of the facts about food energy-dependent pheromone-controlled RNA-mediated cell type differentiation.
See: Environment and Neurodegenerative Diseases: an Update on miRNA Role
I’m beginning to think that the most obvious way to prevent the deaths by suicide of our veterans is not something that will be discussed in any scientific forum or on most forms of social media.
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.

Hard Science vs the neo-Darwinian "magic box"

Summary: Identical nucleotide sequences link energy-dependent changes in binding sites to different amino acids in different proteins. The binding sites are conserved in the orthologous mammalian genes.

  1. The in vivo structure of biological membranes and evidence for lipid domains
  2. Scientists investigate how the sense of smell works in bacteria
  3. Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

As presciently predicted in the works of Richard Feynman and Bruce McEwen, bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction. The link from a light-activated endogenous substrate in all cell types must be viewed in the context of energy-dependent feedback loops that link sunlight to the anti-entropic constraint of atomic energy in uranium isotopes. Chromosomal inheritance prevents the evolution of one species into another.


at futurism.com

See:  Scientists Have an Experiment to See If the Human Mind Is Bound to the Physical World

What it could mean is this: that the human mind (consciousness) isn’t made up of the same matter governed by physics. Furthermore, it could suggest that the mind is capable of overcoming physics with free will. This could potentially be the first time scientists gain a firm grasp on the problem of consciousness. “It wouldn’t settle the question, but it would certainly have a strong bearing on the issue of free will,” said Hardy.

The idea that the mind isn’t made up of matter, which is governed by the Laws of Physics is ridiculous. You cannot take such a ridiculous idea and make it meaningful via experiments. The experiment would be meaningless. All experiments must start with a rational hypothesis or something that is known. Then you must attempt to add scientific support for extending what is known to something that becomes known via your experiment. Otherwise, you start with a theory and add nothing more than another theory. You don’t get answers to any questions.
See for example: Did humans evolve in Europe rather than Africa? We don’t have the answer just yet

Charles Darwin believed that humans evolved in Africa, because that’s where our closest ape relatives the chimpanzees and gorillas live. And during the twentieth century he was vindicated through a combination of fossil and genetic discoveries.

Darwin placed his energy-dependent “conditions of life” first. .

While our place in the tree of life is now well established – chimpanzees being our closest relatives – the beginning of the human line millions of years ago continues to be shrouded in mystery.

Charles Darwin had a theory about how his “conditions of life” might be linked to biodiversity via natural selection. Others thought that his theory could be linked from natural selection to the evolution of humans from ape relatives. They claimed that Darwin thought humans evolved during millions of years of natural selection for small changes. De Vries (1902) defined the small changes as mutations. Biologically uninformed neo-Darwinian theorists still claim that mutation-driven evolution is supported by the fossil record and genetic discoveries.
See for comparison: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
Svante Paabo is one of the paleoanthropologists who has a grasp of cell biology, which links energy to RNA-mediated biodiversity via the sense of smell. When someone with his level of expertise refutes all neo-Darwinian nonsense with experimental evidence of biologically-based cause and effect, how can others justify their lack of acceptance for the facts? Paabo’s facts link natural selection for energy-dependent codon optimality to all biodiversity via the claims in Feedback loops link odor and pheromone signaling with reproduction.

See also: Engineering RGB color vision into Escherichia coli reported as: Bacterial Photography Goes Technicolor

Genetically engineered “disco bacteria” sense and respond to different colors of light, creating both stunning art in the culture dish and new possibilities for synthetic biology.

See for comparison:Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates
Who engineered the energy-dependent acquisition of RGB color vision in E. coli and full trichromatic RGB color vision in primates? What prevents the biophysically constrained loss of the engineered receptors for RGB color vision in E. coli that are linked from the de novo creation of olfactory receptor genes to the loss of the genes that coincides with the advent of RGB (Trichromatic) color vision in primates?
Pseudoscientists might claim that evolution engineers the acquisition of all morphological and behavioral traits, but they won’t make verifiable claims about biophysical constraints or loss of the genes after the genes are created. Instead, see: Mutation-Driven Evolution.
Theorists start with genes that were somehow created and then claim:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations…

After the energy-dependent de novo creation of genes, genomic conservation continues to be nutrient energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in all living genera. Chromosomal inheritance prevents the evolution of one species into another — unless it occurs via magic traits. In the context of mutation-driven evolution species must have magic traits.
See for example: Evolution on the fast lane—One flounder species became two

“The answer may lay in so called magic traits, meaning traits that are under selection which at the same time cause reproductive isolation as a byproduct. In theory, selection on such traits could play a central role in rapid speciation events. The mating strategies and reproductive traits of the two flounder species could act as magic traits,” clarifies Momigliano.

See for comparison: Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

Reported as: Living fossil challenges thinking on brain evolution

Despite its appearance, amphioxus is not a fish. It has a primitive spinal cord which runs down its back, but no clearly defined face, no bones or jaws and a small brain with a single light-sensing “frontal eye”. It has changed so little for hundreds of millions of years that it has been described as a “living fossil”.

See for comparison to the report of a hundreds of million years-old “living fossil:” Bacteria evolve over a weekend  (video)
Serious scientists know that the bacteria that reportedly “evolved” adapted to ecological variation in their food supply. Adaptation is nutrient energy-dependent and pheromone controlled via the physiology of reproduction in all living genera. It occurs over-the-weekend in P. fluorescens, but it is still reported to be mutation-driven evolution by biologically uninformed theorists.
Biologically uniformed theorists also make claims like those found here: The Physics of Everything

For comparison: This is the Physics of Everything, outside the context of the magic of evolution in the context of magic traits.

See: The in vivo structure of biological membranes and evidence for lipid domains

This approach relies on tuning the isotopic content of hydrogen within the membrane, and other parts of the bacterium, to generate neutron scattering spectra exclusively from the membrane. Using this approach, we confirmed that the structure of the B. subtilis membrane is lamellar and has an average hydrophobic thickness of 23.9 ± 0.9 Ångstroms (Å).

Average hydrophobic thickness cannot be linked from energy-dependent changes in the cell membrane to biophysically constrained cause and effect via the pheromone-controlled physiology of reproduction in any organism.
See for comparison: 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.

Serious scientists do not link average hydrophobic thickness from the sense of smell in bacteria to all biophysically constrained energy-dependent biodiversity via the physiology of reproduction in species from microbes to humans. Serious scientists link the energy-dependent changes from angstroms to ecosystems in the context of RNA-mediated amino acid substitutions in supercoiled DNA.
See: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

The metabolic processes are energy-dependent and biophysically constrained.

For another example of biogenic metabolic processes, see: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

This was reported as: A new twist on uranium’s origin story, by CSU scientists

In recent years, scientists had uncovered new evidence that bacteria – living microorganisms – could generate a different kind of reduced uranium that is non-crystalline and has very different physical and chemical properties.

…using new techniques including synchrotron radiation-based spectroscopy and isotope fingerprinting. They found that up to 89 percent of the uranium from their 650-foot-deep samples wasn’t crystalline uraninite at all, but rather, a non-crystalline uranium that was bound to organic matter or inorganic carbonate. Most of the uranium they found in that unmined site is estimated to be 3 million years old, and formed via reduction by microorganisms – microbes that respire not on oxygen, but on uranium.

They linked the nutrient energy-dependent pheromone-controlled physiology of reproduction in bacteria and all other living genera to the creation of differences in the 238U to 235U isotope ratio. The differences in the 238U to 235U isotope ratio discriminate between the abiotic and biotic transformation of uranium. But, they placed their findings on abiogenesis into the context of ridiculous theories of evolution and ignored everything  known to serious scientists about the energy-dependent biotic transformation of uranium and all energy-dependent biogenesis.

For any example of how placing their results into the context of abiogenesis supports ridiculous theories about emergence and evolution, see: Uranium–lead dating

The method relies on two separate decay chains, the uranium series from 238U to 206Pb, with a half-life of 4.47 billion years and the actinium series from 235U to 207Pb, with a half-life of 710 million years.

For comparison, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

This was reported as: Evolutionary Rewiring: Strong selective pressure can lead to rapid and reproducible evolution in bacteria

NtrC shares 30 percent amino acid identity with FleQ… the re-evolved flagella enabled the bacteria to access food supplies…

Natural selection for food energy-dependent codon optimality links ultraviolet light (UV) to the nutrient energy-dependent pheromone-controlled physiology of reproduction in P. fluorescens, which links UV light to the weekend resurrection of the flagellum because P. fluorescens fluoresces with exposure to UV light.

Differences in the nutrient energy-dependent RNA-mediated amino acid substitutions link differences in supercoiled DNA to the protection of all organized genomes from viruses. Virus-driven energy theft causes the degradation of messenger RNA, which links mutations to all pathology.

See Feynman’s comments about food energy:

Could any other physicist but Feynman have guessed that bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction?

Could any other molecular biologist but Bruce McEwen have linked an endogenous substrate from the energy-dependent biophysically constrained pheromone controlled physiology of reproduction to all biodiversity in all living genera?

See also: The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes

Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes.

CONCLUSIONS:(with my emphasis)

The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes.

To help differentiate between evolution and adaptation in the context of natural selection for food energy-dependent codon optimality in the context of the physiology of pheromone-controlled reproduciton, see: Metrics of assay accuracy

Neo-Darwinian evolution occurs only in the context of this “Magic Box” example. Each time you look at the “+” sign on the box, you are taught to believe in evolution.

For comparison, see: The Emerging View of Aging as a Reversible Epigenetic Process

This evidence supports the idea that progressive epigenetic dysregulation may be the key driver of organismal aging and challenges the conventional view of aging as an irreversible process. The model of aging as an epigenetic process provides an elegant explanation of a number of age-related processes difficult to explain by conventional theories of aging.

Conventional theories of aging have failed to link the nutrient energy-dependent pheromone-controlled physiology of RNA-mediated protein folding chemistry to all biodiversity via biophysically constrained chromosomal inheritance. That’s how conventional theories left all of humanity waiting for cures that will never become available. Biologically uninformed theorists still do not know how protein folding chemistry is linked from changes in the microRNA/messenger RNA balance to healthy longevity via cell type differentiation or from the virus-driven degradation of messenger RNA to mutations and all pathology.
See: Genome editing: That’s the way the CRISPR crumbles
Review of A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution This title will be released on June 13, 2017.

Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use.

June 14, 2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…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’.

 June 14, 2013 Mutation-Driven Evolution

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.

 

Cytosis

From E. coli to monkeys and mankind: Theories vs models (5)

From E. coli to monkeys and mankind: Theories vs models (4)
CRISPR Is Taking Over Science, Breaks Out Of Labs And Invades Schools (5/29/17)

…used mathematical models to reveal that even in a uniform environment, metabolic competition generally leads to the steady coexistence of distinct microbes, collectively called a “consortium”. In a consortium, distinct microbes organize themselves to create a community-level metabolism that best exploits the nutrients present. The models showed that while growing, a consortium depletes the available pool of nutrients to such low levels that only members of the consortium can survive. The findings suggest that the benefit of metabolic diversity stems from the ability of a consortium to automatically deplete nutrients to levels at which no other microbes can invade.

Taillefumier et al. propose that consortia that arise naturally under conditions where there is a steady supply of nutrients produce the maximum mass of microbes. Future experiments that analyze the impact of fluctuating nutrient supply may help us to understand the benefit of metabolic diversity in real-world microbial communities.

Microbes do not organize themselves into consortia via the automatic depletion of nutrients. Natural selection for food energy-dependent codon optimality links quantum physics to the pheromone-controlled physiology of biophysically constrained viral latency. That is how metabolic networks must link ecological variation to ecological adaptation in all living genera.

Pseudoscientists who know nothing about energy-dependent quorum sensing and RNA-mediated cell type differentiation in microbial consoritia have wasted billions of dollars and nearly all the time that humans have existed on Earth. Now they tout automagically evolved consortia in attempts to subvert what is known about the nutrient energy-dependent protection from virus-driven energy theft, which is built into the molecular essence of all cell types. The pseudoscientists have led us to the brink of a viral apocalypse.

See: CRISPR gene editing can cause hundreds of unintended mutations (5/29/17)

…the genomes of two independent gene therapy recipients had sustained more than 1,500 single-nucleotide mutations and more than 100 larger deletions and insertions. None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.

Division of labor

Competition causes microbes to organize themselves into communities that make the most of the available nutrients.

Where do viruses come from? (2004)

…when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. ‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9

Virus-driven energy theft causes the degradation of messenger RNA that links mutations to all pathology.

Virus-mediated archaeal hecatomb in the deep seafloor (2016)

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

People who believe in mutation-driven evolution are not likely to link virus-driven energy theft in archaea to the morphological and behavioral phenotype of bacteria or from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to Alzheimer’s disease. People who believe in mutation-driven evolution may not be capable of understanding how the conserved molecular mechanisms detailed in the published works of serious scientists must be linked from viruses to the the degradation of messenger RNA that links the mutation-driven evolution of pathology to the increase in Alzheimer’s Deaths.

U.S. Alzheimer’s Deaths Jump 54 Percent

In the video that accompanies this report, the image from a brain scan is paired with the mention of biomarkers. microRNAs are the biomarkers. The changes in energy-dependent microRNA biosynthesis clearly predict the onset and severity of all pathology.

That’s why most people will not seek the most effective and least invasive treatment for Alzheimer’s. They won’t link the loss of olfactory acuity and specificity to the virus-driven degradation of messenger RNA and neurodegenerative diseases, because their physicians don’t understand enough about the creation of G protein-coupled receptors to link chemotaxis and phototaxis to all biodiversity via the physiology of reproduction.

See for comparison: microRNA Alzheimer

See also: Search Results for “alzheimer’s”

Reports about an article that I have not yet seen published in “Nature Methods” attest to facts about cell type differentiation that have been placed into this context:

Crack in CRISPR Façade after Unanticipated In Vivo Mutations Arise

“Researchers… may be missing potentially important mutations,” Dr. Tsang remarked. “Even a single nucleotide change can have a huge impact.”

That fact is not just a “Crack in the CRISPR Facade.” It dismisses all claims about mutation-driven evolution. Those ridiculous claims have been replaced by what is known to serious scientists about how viral latency must be biophysically constrained. It must be constrained by a light-activated endogenous substrate in all cell types of all living genera. The light comes from the sun. For example, the anti-entropic energy of ultraviolet light kills viruses.

SARCASM ALERT: Ask your doctor if sunlight could save your life.

Until the publication of “Unexpected mutations after CRISPR-Cas9 editing in vivo” is available to all serious scientists, watch how the prescient claims about food energy that have been made by people like Richard Feynman have forced theorists to do what they have always done. Expect that some of the censorship will end when the news about the unexpected mutations is linked to what all serious scientists have expected since the time that Thomas Hunt Morgan linked energy-dependent chromosomal inheritance to all biodiversity on Earth and virus-driven energy theft was linked to antibiotic resistance.

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. —  Kalevi Kull

See: Nature Methods May 2017, Volume 14 No 5 pp457-540

For example:

Systems biology guided by XCMS Online metabolomics pp461 – 462

See also: Research Highlights

Defining developmental grammar p465

An iterative clustering approach finds the few genes that mark discrete cell states and their transitions during early mouse development.

It takes two to make an embryo pp466 – 467

In vitro culture of mouse embryonic and extra-embryonic stem cells recapitulates embryogenesis.

A light switch for kinases pp466 – 467

A photodissociable dimer of the Dronpa fluorescent protein can cage kinases, making these important signal transducers controllable by light.

A proteome-wide view of thermal stability p468

Proteome thermal stability is probed using limited proteolysis and mass spectrometry.

Dynamic measurement of membrane charges p471

A FRET sensor enables quantitative characterization of electrostatic potential of membranes in living cells.


See for comparison: 2012 Genome evolution: Unexpected relationship between mutation rate and genome complexity

Contrary to expectation, species that have experienced recently accelerated mutation rates have the largest genomes…

Biophysically constrained food energy-dependent pheromone-controlled viral latency protects the organized genomes of all living genera from the degradation of messenger RNA, which links virus-driven energy theft from mutations to all pathology regardless of the size of the organized genome. The measurement of membrane charges in the context of cryo-EM makes it possible to link virus-driven energy theft in bacteria to the degradation of messenger RNA in archaea and the degradation of messenger RNA in archaea to L-forms, which represent the virus-driven destruction of all created cell types. So far as is currently known, only the anti-entropic virucidal energy of sunlight can prevent the virus-driven death of all life on Earth.

L-form bacteria

Bacterial morphology is determined by the cell wall. Since the L-form has no cell wall, its morphology is different from that of the strain of bacteria from which it is derived.

The cell wall is important for cell division, which, in most bacteria, occurs by binary fission. This process usually requires a cell wall and components of the bacterial cytoskeleton such as FtsZ. The ability of L-form bacteria to grow and divide in the absence of both of these structures is highly unusual, and may represent a form of cell division that was important in early forms of life.[1]

The failure to recognize the fact that virus-driven degradation of the cell wall is an example of how cell type destruction occurs in all cells that contain a light-activated endogenous substrate, is also an example of pervasive ignorance among all theorists and other pseudoscientists.

See also: Cytosis:

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Cytosis

From E. coli to monkeys and mankind: Theories vs models (2)

Dedicated to Dr. Tom Jordan and Priscilla Jordan on the day of their retirement from the Baptist ministry, May 28, 2017. They always encouraged me to learn more about the “Laws of Biology” and link the Laws from energy as information to all biodiversity on Earth via the physiology of reproduction.

See also: From E. coli to monkeys and mankind: Theories vs models

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding (5/23/127)

…changes in observed association and dissociation, suggesting the possibility of kinetic and thermodynamic tuning of Cas9 behavior.

Simply put, the technology didn’t work. That’s a problem for CRISPR/Cas9 advocates (see the incessant barrage of CRISPR/Cas9 promotion on the closed FB group CRISPR Cas9).

Advocates will be forced to accept the fact that natural selection for energy-dependent codon optimality has always been the link from ecological variation to ecological adaptation via food odors and pheromones.

Suggesting the possibility of kinetic and thermodynamic tuning is akin to telling all serious scientists that, until now, the innate immune system of bacteria and the CRISPR Cas technology has not been examined inside the context of the Laws of Physics and the Basic Principles of chemistry. The Laws and the Basic Principles must link RNA-mediated protein folding chemistry from the physiology of reproduction to all food energy-dependent pheromone-controlled behavior in species from microbes to humans via amino acid substitutions in supercoiled DNA.
 

That fact separates the serious scientists from the pseudoscientists who have refused to examine other facts about biologically-based biophysically constrained protein folding chemistry. The facts start with the sun’s anti-entropic virucidal energy as information and the energy as information has been linked to all cell type differentiation by these researchers.

See: Mechanism of transmembrane signaling by sensor histidine kinases (5/18/17)

Reported as: Scientists investigate how the sense of smell works in bacteria

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.

My summary of the signalling mechanism, which links subatomic particles to cell type differentiation in all living genera via the sense of smell in bacteria:

The active and inactive signaling states link energy-dependent changes from angstroms to ecosystems via slight variations at the nitrate-binding site. When the ion binds to the sensor, a change in 0.5-1 angstroms (approximately one fifth of the size of the ion itself) causes a change in the protein that links input from the sensor to a change in the output that varies by as much as 7 angstroms.

In the context of what is known about food energy-dependent pheromone-controlled quorum sensing in bacteria, the change in 0.5-1 angstroms can be linked from the changes in 7 angstroms to base pair changes and amino acid substitutions that stabilize the organized genomes of species from E. coli to primates in the context of all energy-dependent interactive ecosystems, which appear to have existed from the dawn of Creation.

For example, the link from energy-dependent changes in angstroms to ecosystems in all vertebrates is mentioned in the title of this published work: The zinc spark is an inorganic signature of human egg activation. 

The spark that links inorganic material to organic life was placed into the context of our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. See our section on molecular distance in: From Fertilization to Adult Sexual Behavior.

Molecular distance. As measured in centimorgans, human and other species’ male and female chromosomes, including the autosomes, tend to have different lengths in various segments. To some extent, this suggests a correlation with physical distance but instead the differing lengths are based upon rates of recombination; although sections of most female chromosomes are longer than their homologous counterparts in male chromosomes, in some segments of various chromosomes opposite length-difference occurs, with males having larger centimorgan values than females in those regions (Lawrence, Collins, Keats, Hulten, and Morton, 1993; Murray, Buetow, Weber, Ludwigsen, Scherpbier-Heddema, Manion, Quillen, Sheffield, Sunden, and Duyk, 1994; Straub, Speer, Luo, Rojas, Overhauser, Ott, and Gilliam, 1993). While ramifications of these centimorgan sexual dimorphisms are not yet clearly established, in recent years cis- and trans-acting factors contributing to these recombination length differences have been reported for a specific part of the murine major histocompatibility complex (MHC) (Shiroishi, Sagai, Hanzawa, Gotoh, and Moriwaki, 1991).

Simply put, the cited works linked energy-dependent changes from angstroms to ecosystems via the innate immune system of bacteria, which was linked to sex differences in chromosomes. Note the difference between our accurate representation of biophysically constrained energy-dependent chromosomal inheritance and the claims in: Sex chromosome evolution: historical insights and future perspectives

Conclusion:

…a direct experimental test of the steps in sex chromosome evolution constitutes more robust evidence than a comparative study, especially considering the new manipulative possibilities opened up by the CRISPR/Cas9 system [105]. In any case, the field of sex chromosome evolution seems likely to remain active and dynamic for many years to come.

Reported as: Knowledge gap on the origin of sex

The review shows that the significance of ecology has not been sufficiently noted. Therefore, the biologists in Lund call for more research on how the living environment of a population affects the development and evolution of sex chromosomes. This could include factors such as access to food, age variations within a population or the consequences for sex chromosomes when populations that have lived separately meet and mix.

The fact that others still claim that the origin of sex has not already been linked from factors such as access to food, age variations within a population or the consequences for sex chromosomes attests to the ignorance of theorists. The fact that theorists want to attempt to evoke aspects of the CRISPR Cas9 technology in attempts to explain sexual differentiation attests to the ignorance of those who think more research is required to link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction and chromosomal inheritance.

Energy-dependent changes were linked from angstroms to ecosystems in all living genera in this published work: Structural diversity of supercoiled DNA (10/12/15) and in this parody from 12/10/14.

See also: Origins of Life: A Problem for Physics

The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.

See for comparison: The Chirality Of Life: From Phase Transitions To Astrobiology

A key missing piece is the origin of biomolecular homochirality: permeating almost every life-form on Earth is the presence of exclusively levorotary amino acids and dextrorotary sugars.

Watch as Jeremy England eliminates any discussion of light activated endogenous substrates in the context of microRNAs linked to the energy-dependent creation of exclusively levorotary amino acids and dextrorotary sugars.

A New Physics Theory of Life

You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.

If another ridiculous theory emerged, will it explain anything outside the context of experimental evidence that links energy as information to biophysically constrained cell type differentiation via the physiology of reproduction in all living genera? For example, what theory might emerge to explain how an infection in the throat is linked to mental disorders in adults.

See: Streptococcal throat infection linked to mental disorders

The researchers found that the risk of any mental disorder was increased for individuals with a positive streptococcal test compared to those without a streptococcal test…

Watch a biologist fail to link physics and chemistry from the strep infection to brain development via the innate immune system and molecular epigenetics as he explains CRISPR at 5 different levels of his ignorance. 5/24/17

 

The speaker is a co-author of: Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis 3/5/15

In all of these experiments, the effect of mutations on primary tumor growth positively correlates with the development of metastases. Our study demonstrates Cas9-based screening as a robust method to systematically assay gene phenotypes in cancer evolution in vivo.

Reported as: In vivo CRISPR-Cas9 screen sheds light on cancer metastasis and tumor evolution

The results highlighted some well-known tumor suppressor genes in human cancer, including Pten, Cdkn2a, and Nf2, but included some genes not previously linked to cancer. Unexpectedly, the screen also implicated several microRNAs — small RNA segments that are functional in the cell.

Neville E Sanjana, has now linked his ignorance from 2015 to assays that link energy-dependent microRNAs to healthy longevity or from virus-driven energy theft to all pathology. Kaveli Kull attests to the fact about what loser must do, when facts replace their ridiculous theories about genome editing.

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. —  Kalevi Kull

Anyone who has tried to explain what humans are made of without linking energy from the light activated endogenous substrate that links ATP to the creation of RNA via microRNAs in the context of what is now being referred to as endogenous RNA interference may not recognize how desperate evolutionary theorists have become in their attempt to make others think that all neo-Darwinian theorists are not losers.

See (link opens .pdf) Participation of glycolysis, and the citric acid cycle, in nuclear adenosine triphosphate synthesis (1963)

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Energy-dependent epigenetic translation to mRNA stability (3)

Energy-dependent epigenetic translation to mRNA stability (2)

Energy-dependent epigenetic translation to mRNA stability (2)


See for comparison this treatise on climate change packaged as information on the evolution of a flying snake.
Fossil ‘winged serpent’ is a new species of ancient snake

At the time that Zilantophis dwelled there, the site was a sinkhole surrounded by forest, attracting a variety of animals. The local fauna included ancient representatives of familiar North American creatures such as bears, beavers and salamanders. Others were more exotic, including unique species of rhinoceros, alligator and the site’s famous red panda.

“This is a time when the world was moving in the direction of a modern climate and modern fauna,” Jasinski said.

For information on the evolution of the flying snake’s behavior see Robert Sapolsky: The biology of our best and worst selves

How can humans be so compassionate and altruistic — and also so brutal and violent? To understand why we do what we do, neuroscientist Robert Sapolsky looks at extreme context, examining actions on timescales from seconds to millions of years before they occurred. In this fascinating talk, he shares his cutting edge research into the biology that drives our worst and best behaviors.

I did not learn anything about cutting edge research from this TED talk. I learned that Robert Sapolsky believes in the evolution of human behavior. That surprised me because Robert Sapolsky is one of the most famous students of Bruce McEwen, who linked a single amino acid substitution (BDNF Val66Met) from nutrient energy-dependent biophysically constrained biologically-based top-down causation to behavior in the dramatically different pheromone-controlled ecosystems of mice and humans.
See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Correction for McEwen, Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

Until Robert Sapolsky helps others to make sense of how the energy-dependent pheromone-controlled de novo creation of olfactory receptor genes is linked to differences in epigenetic effects that link sensory stimuli from hormones to the affects of hormones on animal behavior, his lectures will be of little use to those who study the biology of behavior.
In all vertebrates, the study of behavior begins with the epigenetic effects of food odors and pheromones on gene activation that link changes in microRNAs from gonadotropin releasing hormone to the physiology of reproduction. In the early 90’s, Bruce McEwen told me that my model of biologically-based cause and effect could not be validated unless I found experimental evidence that could be linked to gene activation in gonadotropin releasing hormone (GnRH) neurosecretory neurons.
The late Robert L. Moss provided preprints from his group that now link everything known about energy-dependent RNA-mediated cell type differentiation in all vertebrates to the pheromone-controlled physiology of reproduction in mice and in humans via amino acid substitutions.
The early gene expression of cFos has since linked the Fos protein to proof of the concept that links food odors and pheromones to all receptor-mediated behavior in all living genera via what is known about vertebrate GnRH.
See: Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males
See: A hypothalamic circuit that controls body temperature

…we used cFos staining to identify neurons that are activated by a thermal challenge and found induced expression in subsets of neurons…

See: Researchers discover neuronal targets that restore movement in Parkinson’s disease model

The research group used optogenetics, a technique that turns genetically tagged cells on and off with light.

See also: Hypothalamic microRNAs flip the switch for fertility
See also our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior
More than 60,000 published works on microRNAs link cutting edge research to energy-dependent healthy longevity or from virus-driven energy theft and the degradation of messenger RNA to all pathology. Who is discussing that fact?
See for comparison: Behave: Why do we do the things we do?

Over a decade in the making, this game-changing book is Robert Sapolsky’s genre-shattering attempt to answer that question as fully as perhaps only he could, looking at it from every angle. Sapolsky’s storytelling concept is delightful but it also has a powerful intrinsic logic: he starts by looking at the factors that bear on a person’s reaction in the precise moment a behavior occurs, and then hops back in time from there, in stages, ultimately ending up at the deep history of our species and its genetic inheritance.

And so the first category of explanation is the neurobiological one. What goes on in a person’s brain a second before the behavior happens? Then he pulls out to a slightly larger field of vision, a little earlier in time: What sight, sound, or smell triggers the nervous system to produce that behavior? And then, what hormones act hours to days earlier to change how responsive that individual is to the stimuli which trigger the nervous system? By now, he has increased our field of vision so that we are thinking about neurobiology and the sensory world of our environment and endocrinology in trying to explain what happened.

Sapolsky keeps going–next to what features of the environment affected that person’s brain, and then back to the childhood of the individual, and then to their genetic makeup. Finally, he expands the view to encompass factors larger than that one individual. How culture has shaped that individual’s group, what ecological factors helped shape that culture, and on and on, back to evolutionary factors thousands and even millions of years old.

The result is one of the most dazzling tours de horizon of the science of human behavior ever attempted, a majestic synthesis that harvests cutting-edge research across a range of disciplines to provide a subtle and nuanced perspective on why we ultimately do the things we do…for good and for ill. Sapolsky builds on this understanding to wrestle with some of our deepest and thorniest questions relating to tribalism and xenophobia, hierarchy and competition, morality and free will, and war and peace. Wise, humane, often very funny, Behave is a towering achievement, powerfully humanizing, and downright heroic in its own right.

See also: CRISPR kills HIV and eats Zika ‘like Pac-man’. Its next target? Cancer

Researchers paired proteins with a process that amplifies RNA which could be used to detect cancer cells

One of the most fascinating things that I have repeatedly encountered is the failure to link CRISPR from the nutrient-dependent pheromone-controlled physiology of reproduction to the biophysically constrained viral latency that links ecological variation to ecological adaptation via natural selection for energy-dependent codon optimality in all living genera.
It’s as if the gene-editing technology could not be understood in the context of femtosecond blasts of virucidal UV light and RNA-mediated DNA repair, which has been linked to the prevention of all pathology until stress overwhelms the immune system.