Sperm MicroRNA Expression Archives

Ecological adaptation: A new definition of heredity (1)

March 6, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Diseases & Disorders Ecology Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Excerpt: ” …long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans…”
She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity May 29, 2018 | 672 Pages
From the description of the book:

1) We need a new definition of what heredity is…

2) …Zimmer ultimately unpacks urgent bioethical quandaries arising from new biomedical technologies, but also long-standing presumptions about who we really are and what we can pass on to future generations.

The long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans. For comparison to the long-standing presumptions, see:
Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants May 11, 2012
Evolution and functional impact of rare coding variation from deep sequencing of human exomes May 17, 2012
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants November 28, 2012
Reported as: Past 5,000 years prolific for changes to human genome November 28, 2012

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. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

Akey dismissed everything known about the epigenetic effects of food energy and the metabolism of food to pheromones, which biophysically constrains viral latency in the context of the physiology of reproduction in species from microbes to humans.
See for comparison: A third of Americans don’t believe in evolution January 1, 2014
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

When food energy-dependent pheromone-controlled autophagy (see: Autophagy.pro) fails to protect organized genomes from the virus-driven degradation of messenger RNA, organisms pass on mutations to future generations. Clear evidence of that fact was published in the context of this article: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants January, 2013.

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1, 2 and will help to facilitate the development of new approaches for disease-gene discovery3.

The facts about the age of all mutations have since been placed into the context of:
Sperm epigenetics and influence of environmental factors February, 2018

… epigenetic variation may be genetically selected [41], which is in contradiction with the opposite model in which epigenetic variation is a cause of genetic variation. While both models can cooperate, more experimental evidence, other than computationally-based, should be provided to address the mutagenicity of regions subjected to environmentally-induced epigenetic variation and the evolutionary implications.

Conclusion:

Future research efforts may be able to identify a unified epigenetic remodeling response to lifestyle stress across species. Understanding the role of environmentally-driven epigenetic changes in gametes on the phenotype of the offspring constitutes not only a fascinating biological question on its own but also represents a moral obligation for the health of future generations.

MicroRNA present in mature sperm… may actually serve important regulatory roles in fertilization and early developmental processes.

To see how much experimental evidence of biophysically constrained food energy-dependent pheromone-controlled biologically-based cause and effect has been ignored during the past two decades, see: From Fertilization to Adult Sexual Behavior December 1996

…we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.” Although many, and perhaps most, important sex differences arise from gonadal and hormonal development, also important are sex differences which are neither gonadal nor hormonal. All these factors affect the internal workings of the individual and intervene in structuring how the social environment might or might not modify sexual behavior. This discourse calls attention to features that are central to the so-called nature-nurture discussion.

Our section on molecular epigenetics may have been the first to detail what is now being reported in the context of the cryo-EM technology, which links energy-dependent changes from electrons to ecosystems in all living genera via what is known about pre-mRNAs. Pre-mRNAs are now also referred to as microRNAs in more than 70,000 published works.
See: microRNA and/or pre-mRNA
Clearly, what is known to all serious scientists about biophysically constrained viral latency and healthy longevity has forced Carl Zimmer to suggest that “We need a new definition of what heredity is…”
See also:
7/31/16 From hydrogen atom transfer in DNA base pairs to ecosystems
7/31/16 RNA-mediated physics, chemistry, and molecular epigenetics
7/30/16 What is life when it is not protected from virus driven entropy
7/29/16 RNA-mediated molecular epigenetics and virus-driven entropy
4/10/14 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
8/8/13 Nutrient-dependent / pheromone-controlled adaptive evolution
3/8/13 Nutrient-dependent / Pheromone–controlled thermodynamics and thermoregulation
2/17/13 Nutrient-dependent / Pheromone-controlled Adaptive Evolution
Watch for Philip C. Ball’s newest book: Beyond Weird March 22, 2018

Over the past decade or so, the enigma of quantum mechanics has come into sharper focus. We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information: about what can be known and how.

See: 5/8/17 Energy as information and constrained endogenous RNA interference May 8, 2017
See also: New Giant Viruses Further Blur the Definition of Life

“The gap between cellular organisms and viruses is starting to close,” Deeg said. “Which then brings us back to: What is a virus, and what is life?”

Has anyone else linked biophotonics to the energy-dependent proton motive force via the cryo-EM technology?
See for instance: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase.
And preview, Schrödinger at 75 – The Future of Biology – September 2018
Nobel Laureates, Linda Buck, Ben Feringa, Michael Rosbash are among other Nobel Laureates who are scheduled to present.
See also: Are Humans “Smeller Underachievers?” Not So Fast…

…they will share their data and experience on the psychological influences on eating and behavior, the chemosensory properties of food and how we experience them, the role of food as medicine, and the history and evolution of flavor and flavor perception.

No experimental evidence of energy-dependent biophysically constrained top-down causation suggests that flavor perception “evolved.” See: Feedback loops link odor and pheromone signaling with reproduction

The MicroRNAome Strikes Back: A Sokalian hoax (6)

January 25, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology RNA Directed

The nature of nurture: Effects of parental genotypes Science January 26, 2018

…nontransmitted alleles can affect a child through their impacts on the parents and other relatives, a phenomenon we call “genetic nurture.”

It doesn’t matter what they call it, since there is no defined boundary between genetics and epigenetics.
Reported as: You Are Shaped by the Genes You Inherit. And Maybe by Those You Don’t by Carl Zimmer January 25, 2018

A calf may inherit those milk-boosting variants from its mother. But just because the calf carries them doesn’t mean they directly make the calves bigger.

Compared to other mammals, Dr. Bijma observed, human children are especially dependent on their parents — not just for food and other essentials, but for social development. So it stands to reason that they’d experience similar effects.

“Humans provide substantial care to their offspring, and so the nurture they create is very likely to have a genetic component,” said Dr. Bijma.

Dr. Harden said that taking account of genetic nurture could improve research on the effects of poverty on how children do in school, as well as studies of methods to improve educational attainment.

“It’s so obvious in retrospect, and so elegant,” she said. “A lot of people are going to say, ‘I can see my data in a new light with this.’”

See for comparison: No Boundary Really Between Genetic and Epigenetic

…evolutionary science has now “moved on to such an extent” that she and Peter Saunders don’t really care anymore about trying to convince the neo-Darwinists.

The reporting on genetic nurture by Carl Zimmer appears to be a ploy to soften the impact of his past misrepresentations and the misrepresentations of all theorists and most so-called science journalists. He now reports on biophysically constrained energy-dependent events that link ecological variation to ecological adaptation in all living genera. See for example the The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression.
Included in the New York Times online article is a picture of a cow and a calf that tells less than half of what we detailed in From Fertilization to Adult Sexual Behavior (1996). The remaining details include how molecular mechanisms of RNA-mediated cell type differentiation are conserved in the bull.
Without food energy-dependent changes in the bull’s microRNAome, no one, including Carl Zimmer can get from the energy-dependent zinc spark at fertilization to the microRNAs in cow’s milk. And now, Carl Zimmer knows it!
See: The zinc spark is an inorganic signature of human egg activation (2016)
See also: MicroRNAs: Milk’s epigenetic regulators (2017)
See also: Maternal BRG1 regulates zygotic genome activation in the mouse (2006)

Genes involved in transcription, RNA processing, and cell cycle regulation were particularly affected. The early embryonic arrest is not a consequence of a defective oocyte because depleting maternal BRG1 after oocyte development is complete by RNA interference (RNAi) also resulted in two-cell arrest. To our knowledge, Brg1 is the first gene required for ZGA in mammals.

But wait, there’s more than just RNA interference involved. The energy-dependent zinc spark is linked from the energy-dependent creation of microRNAs to the creation of monoallelic olfactory receptor genes via the biparental contribution to chromosomal rearrangements. If not, Carl Zimmer and other science journalists cannot get from the epigenetic effects of food odors and pheromones to the feedback loops that link chromosomal rearrangements to the protection of all organized genomes from the virus-driven degradation of messenger RNA and all pathology.
If Carl Zimmer appears to have had a sudden epiphany that led him to see the light of evolution is actually sunlight in the context of ecological adaptation, his ability to see the how the facts extend to humans cannot be attributed only to a recent publication.
See also: Fine-scale recombination rate differences between sexes, populations and individuals (2010)

Comparisons of our maps with two LD-based maps inferred from data of HapMap populations of Utah residents with ancestry from northern and western Europe (CEU) and Yoruba in Ibadan, Nigeria (YRI) reveal population differences previously masked by noise and map differences at regions previously described as targets of natural selection.

Human population differences were linked to natural selection and the energy-dependent spark at fertilization. What, besides natural selection for energy-dependent codon optimality, could have been linked to the spark at fertilization? Why would there be any questions about whether the findings in other animals extend to the findings on the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in species from yeasts to mammals that we reported in 1996? See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior.
I wonder if Carl Zimmer was one of the people who may have seen my tweets during the past 28 days (80,000 impressions). There is no way to be certain that the timing of his epiphany is anything more than coincidental. But that doesn’t matter.
He is now well on his way to reporting the facts about biophysically constrained viral latency and biodiversity after decades of reporting on the pseudoscientific nonsense touted by neo-Darwinian theorists.
it seems just as likely that he has been following my blog posts here and is scared to death not to report the facts before the forthcoming conference: Mechanisms of Recombination After that, everyone in the world of intelligent science journalism will know that energy-dependent epigenetic effects link food odors and pheromones from feedback loops to biophysically constrained cell type differentiation and viral latency in all living genera.
See also: Epigenetic modifications poster
Anyone who continues to report findings in the context of neo-Darwinian pseudoscientific nonsense about mutations and/or evolution is unlikely to be employed as a science journalist.

Energy-dependent structure and function: Until death (1)

October 11, 2017

by James Kohl with One Comment Autophagy Diseases & Disorders Human Brain Human Pheromones Model Organisms Neuronal Plasticity RNA Directed RNA-mediated epigenetic regulation of gene expression Variations

The structure-energy landscape of NMDA receptor gating

…using single-molecule Forster resonance energy transfer (smFRET), we map the energy landscape of the first transmembrane segment of the Rattus norvegicus NMDA receptor under resting and various liganded conditions. These results show kinetically and structurally distinct changes associated with apo, agonist-bound, and inhibited receptors linked by a linear mechanism of gating at this site. Furthermore, the smFRET data suggest that allosteric inhibition by zinc occurs by an uncoupling of the agonist-induced changes at the extracellular domains from the gating motions leading to an apo-like state, while dizocilpine, a pore blocker, stabilizes multiple closely packed transmembrane states.

Achiral glycine in position 6 of the gonadotropin releasing hormone (GnRH) decapeptide links the energy landscape from ecological variation to the stability of the 7 transmembrane states in the GnRH receptor to the creation of all biophysically constrained vertebrate biodiversity via feedback loops that link food odors and pheromones to the survival of all species on Earth. Organisms die without food and species become extinct when too many conspecifics die. The virus-driven degradation of messenger RNA, links mutations to all pathology and to death and the extinction of species.
Reported as: Molecule Movements Through Nerve Cells Could Lead to Multi-functional Drugs

The NMDA receptor is set of four protein subunits, each with four domains, and each of those domains has a particular function. Collectively, they span the cell membrane. Each subunit can have many “states,” or shapes, that regulate which electrical signals — and how many of them — pass through. The subunits sit on each side of the channel and activate when they bind both glutamate and glycine neurotransmitter ligands and trigger the signaling pathway that allows positively charged ions to pass into the cell.

The energy-dependent “states” are the functional shapes of receptors that link electrical signals to receptor-mediated behavior and to all biodiversity. Their function can be examined in the context of links from electrons to ecosystems via cryo-electron microscopy (cryo-EM).
All energy-dependent functions in all living genera link top-down causation from food energy-dependent feedback loops to the pheromone-controlled physiology of reproduction in species of microbes to survival of all species. For example, the effects of energy-dependent binding of glutamate and glycine neurotransmitter ligands to their substrates can be examined in the relatively simplistic context of this 2005 review of ecological variation and ecological adaptations.
Feedback loops link odor and pheromone signaling with reproduction

It appears that GnRH neurons integrate a variety of information about the internal state of the animal and its external environment. At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons. Among these are areas involved in odor and pheromone processing, sexual behavior, arousal, reward, and other functions. This suggests that GnRH neurons are poised to modulate reproductive physiology and behavior in accordance with the overall state of the animal.

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See for comparison to what is known about the feedback loops: Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence
My summary: Viral persistence (paramyxovirus persistence) and biophysically constrained epigenetically-effected viral latency require the energy-dependent fine-tuning of epigenesis and epistasis that links the pheromone-controlled physiology of reproduction from species of microbes to humans via what is known about soil microbes, fescue toxicosis, and the bull sperm microRNAome.
The most confusing representation of biophysically constrained energy-dependent epigenetically-effected top-down causation I have ever seen was reported as: Team shows how seemingly acute viral infections can persist

…our cells are wired to survive if they are engaged in an antiviral response…

One expert from the report, which is about the well known aspects of food energy-dependent autophagy attests to all the facts known to serious scientists. The facts refute the pseudoscientific nonsense touted by most theorists. For example, see the three articles that link the food energy-dependent pheromone-controlled physiology of reproduction in soil bacteria to all biodiversity in mammals.

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

The presence of viruses in bacteria (bacteriophages) and in semen attests help to explain how serious scientists have linked the virus-driven theft of quantized energy from the degradation of messenger RNA to mutations and all pathology in all living genera. The facts can now be placed into the context of the fact that other organisms typically do not commit suicide. Energy-dependent autophagy typically links chirality to the protection of all cell types in all individuals of all species from suicide. That fact left me and others with questions about why people commit suicide.
See: Energy-dependent structure and function: Until death (2)
See also: Energy-dependent structure and function: Until death (3)

Thanks again for asking about DNA methylation

October 2, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Cytosis Diseases & Disorders Ecology Human Brain Model Organisms Nutrigenomics RNA Directed RNA editing RNA-directed DNA methylation Variations What's in the News

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.

…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.

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.

The billion dollar baby (revisited)

August 31, 2017

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology Model Organisms RNA Directed RNA-directed DNA methylation Variations What's in the News

Summary: All energy-dependent differences in the microRNA/messenger RNA balance have now been linked from the physiology of pheromone-controlled reproduction to all morphological and behavioral phenotypes by the conserved molecular mechanisms of RNA-mediated cell type differentiation.

FDA Approves Treatment That Modifies Patient’s Own Genes To Fight Cancer

It costs $475,000 and the treatment could kill you.
Discussion attempt

Keep in mind that you could have stopped this. Now, you either continue to play their game, or play the cell biology game “Cytosis” when it becomes available next month.

All pathology, including all cancer is caused by the virus-driven degradation of messenger RNA. If you can’t afford the $475,000 treatment, learn how to prevent all pathology.

See: Cytosis: A Cell Biology Board Game

Biologically uninformed science idiots cannot link CAR-T from microRNAs to the cure for John McCain’s glioblastoma. Only serious scientists and those who play the game “Cytosis” can do that.

See for example: Regression of Glioblastoma after Chimeric Antigen Receptor T-Cell Therapy

It will become obvious to all serious scientist that microRNA therapy is the treatment that will control or cure John McCain’s glioblastoma and that the effective treatment must be placed into the context of the unaffordable CAR-T cell treatment. Otherwise too many people would recognize the fact that all pathology is caused by the virus-driven degradation of messenger RNA.

I’m sure the obfuscation is due to the plan to deliver this billion dollar baby “RNAi has targeted exogenous genes in models of viral infection…” Naturally occurring endogenous RNAi prevents the virus-driven degradation of messenger RNA, which links mutations to all pathology. That fact confirms claims that the “billion dollar baby” is a repackaged CAR-T version of microRNA-mediated treatments. Those treatments clearly link food energy from what organisms eat to all healthy longevity via the physiology of reproduction — not via mutations and evolution.

That fact is a problem for medical professionals who make more money from ineffective treatments than from prevention or from effective treatments based on the practice of Precision Medicine. But, it isn’t their fault. They were taught to believe in ridiculous neo-Darwinian theories and can’t accept the facts about Darwin’s “conditions of life” or Schrodinger’s claims in “What is Life?” (1944).

George Church refutes theistic evolution

February 9, 2017

by James Kohl with 3 Comments Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Human Brain Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

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.

Researchers rename, reshuffle, and reveal their ignorance

December 28, 2015

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity Variations

New Species Abound

Re: Researchers renamed, reshuffled, and revealed species…
Evidently, NEW SPECIES is part of a misleading headline placed into the context of some that EMERGED.
Adapted/updated from my comments on Beyond DNA
See: A Cellular System for Spatial Signal Decoding in Chemical Gradients
This cellular system links the sun’s anti-entropic force and the virucidal effect of UV light to the strategic cellular defense system of all cell types.

Researchers began studying this particular molecule because the RNA kicks into action after DNA is damaged; they therefore termed it Noncoding RNA Activated by DNA Damage, or NORAD.

NORAD is another welcome break from neo-Dawinian theory.
See for comparison: DNA Methylation: Insights into Human Evolution
The insights into human evolution ignore everything known to serious scientists. They have linked atoms to ecosystems via nutrient-dependent RNA-mediated events. RNA-direceted DNA methylation links nutrient energy-dependent support of the innate immune system via NORAD to the physiology of reproduction in all living genera.
However, the fact that DNA repair is essential to ecological speciation has been placed back into the context of evolution with the conclusion that:

…the major challenge for the next years is to move beyond mere comparative descriptions and offer insight into phenotypic consequences. To that end, experimental assays are required.

That claim takes us back 50 years to Dobzhansky (1964):

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!

Experimental assays have since linked the speed of light on contact with water and everything known about molecular epigenetics. Clearly, nutrients in chemical gradients are linked from NORAD to all other epigentically-effected RNA-mediated events and cell type differentiation in all cell types of all individuals of all living genera.
Claims that additional experimental assays are required attest to the fact that neo-Darwinian theorists do not look at the experimental evidence of biologically-based cause and effect that has accumulated during the past 50 years. For example, during the past two decades more that 45000 indexed publications mention microRNA, which is something that serious scientists are expected to notice.
Theorists have not noticed the links from atoms to ecosystems at a time when all serious scientists use what is known about differences in the microRNA/messenger RNA balance to link the sun’s biological energy to an answer to Schrodinger’s question “What is Life?”

Life is the nutrient-dependent NORAD-protected biophysically constrained physiology of reproduction that links microRNAs from adhesion proteins to supercoiled DNA, which protects all organized genomes in all living genera from virus-driven entropy.

See for example: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

My comment: Is there something that is not quite clear to you about the links between sunlight, soil bacteria, plant life, and the survival of all species via their innate ability to repair DNA and reproduce in the absence of excessive stress?
Do you not understand how the effects of stress link hydrogen-atom transfer in DNA base pairs to the ecological, social, neurogenic, and socio-cognitive niche construction associated with increasing organismal complexity? Perhaps not, but you could learn to avoid the stress of ridicule (e.g., in front of audience of 200+ serious scientists).
Stress is an RNA-mediated neo-Darwinian theory killer. Stress links viruses that overwhelm the strategic cellular defense system NORAD, to mutations and all pathology via energy theft. That’s why neo-Darwinian theorists cannot link viruses from Darwin’s “conditions of life” to the answer to Schrodinger’s question “What is Life?” Life has nothing to do with death by evolutionary theory or the viruses that cause the mutations that some theorists claim can be linked to the evolution of new species.
See for comparison:
The webinar The Hidden Effects of Epigenetic Discoveries is now available on-demand.

New discoveries uncover that exposure to current environmental, dietary, behavioral, and medical conditions can significantly affect the future development and health of an individual and their offspring. Which correspondingly means, that the development and health of an individual is influenced by past experiences of that individual’s parents.
Research shows, that enriching environments offer opportunities for improved sensory, motor, cognitive, and social stimulation. This improved stimulation has a multitude of positive effects, from increasing learning and memory, to reducing the possibility of acquiring depression or many brain disorders including Huntington’s diseases, Alzheimer’s and stroke. In this webinar we will talk about how current investigation in Epigenetics can affect patient treatment and impacts research in general.

My comment: Ask yourself, “What has evolutionary theory done for anyone during the past 50 years of scientific progress that has been slowed by neo-Darwinists and other pseudoscientists?” Answer yourself by learning the answer to Schrodinger’s question “What is Life?”
See also: Kulasekara et al. c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility. ELife, 2013;2:e01402
See also: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Reported as: Flagellum re-evolves over the weekend

Filtering light through a prism to identify tissue type

From fertilization to RNA-mediated events and back

September 1, 2015

by James Kohl with No Comment Adaptations Ecology Light Energy Model Organisms Nutrigenomics Pharmacogenomics Physics RNA Directed Variations

My comment: The RNA-mediated events that link all biodiversity from it’s nutrient-dependent origins to the physiology of reproduction in all living genera (from octopuses to insects in this video), were detailed in:
From Fertilization to Adult Sexual Behavior
See also:
Organizational and activational effects of hormones on insect behavior
Honey bees as a model for understanding mechanisms of life history transitions
Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Role of olfaction in Octopus vulgaris reproduction
The octopus genome and the evolution of cephalopod neural and morphological novelties
My comment: For an attempt to make everything known about how ecological variation is linked via RNA-mediated events to ecological adaptation fit into a mathematical model of “emergence,” see:
Stability analysis of a model gene network links aging, stress resistance, and negligible senescence
Excerpt 1)

The most important results of this study are Eq. (4), phenomenologically describing aging of a gene network, and the concept of fundamental genomic instability described by Eq. (6).

Excerpt 2)

Although unstable gene networks exponentially accumulate gene expression errors and eventually disintegrate, the growth exponent is nevertheless small and the characteristic mean lifespans can be made sufficiently large and weakly dependent on genotoxic stress factors in the Gompertz limit. This may be an explanation of the apparent prevalence of Gompertzian aging in Nature.

My comment: Gene expression errors is used instead of mutations in the context of metabolic networks linked to genetic networks that disintegrate, which replaces the term genomic entropy. Their team makes it clear why mathematical models that phenomenolgically describe aging of gene networks have no explanatory power in the context of biologically-based cause and effect.
Biologically based cause and effect must link RNA-mediated DNA repair to healthy longevity via metabolic networks and genetic networks that do not disintegrate due to gene expression errors. The metabolic networks and genetic networks link the conserved molecular mechanisms of RNA-mediated cell type differentiation to the nutrient-dependent origin of life in all living genera.
See also: A Surprise Source of Life’s Code
Excerpt:

In 2006, Begun found some of the first evidence that genes could indeed pop into existence from noncoding DNA.

My comment: That’s phenomenologically ridiculous. Never in history have the simple-minded so greatly influenced young scientists who have learned how to become biologically uninformed science idiots.
The article concludes:

“How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”

My comment: The nutrient-dependent de novo creation of olfactory receptor genes links The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the pheromone-controlled physiology of reproduction via RNA-mediated molecular mechanisms of cell type differentiation that link species from microbes to man.
Duplicate genes that are not required for survival of organisms and species accumulate virus-driven mutations that lead to the formation of pseudogenes or gene loss in the context of biophysically constrained thermodynamic cycles of protein biosynthesis and degradation.
See also: DNA methylation pathways and their crosstalk with histone methylation
Excerpt:

Histone and DNA methylation have important and connected roles in the epigenetic control of gene expression in all three kingdoms of eukaryotic organisms. In some cases the relationships between these two epigenetic marks are linear.

My comment: In cases where the relationships between these two epigenetic marks do not appear to be linear, preventing food acquisition or reproduction would quickly establish a link between biologically-based cause and effect in the context of everything known to serious scientists about top-down causation and biophysically constrained ecological speciation.

Scent of Eros

Posts tagged: Sperm MicroRNA Expression