Alternative splicing of pre-mRNA

Evolution outside the context of "the light of evolution" (2)

See first: Evolution outside the context of “the light of evolution”

How many proponents of Intelligent Design never learned that Darwinian evolution was based on his “conditions of life?”

ch 4 IV. Natural Selection; or the Survival of the Fittest  “IF under changing conditions of life…”

ch 5 http://www.bartleby.com/11/5002.html “…the greater variability of species having wider ranges than of those with restricted ranges, lead to the conclusion that variability is generally related to the conditions of life…”

“…we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life.”

ch 6 http://www.bartleby.com/11/6001.html “By my theory these allied species are descended from a common parent; and during the process of modification, each has become adapted to the conditions of life…

How many biologically uninformed science idiots do not know that conditions of life are nutrient energy-dependent and controlled by the physiology of reproduction?

Intelligent Design – Science & Philosophy Discussion attempt: 

https://lh3.googleusercontent.com/M3lHqwXQtKTjApLzM1L43lyjhKKtNHviQEu8EJvcvH2PwjUxJIfzFY4JsND9Nb2b2Uv1crMERBWlRBGu4FTOG837c1H1ULTAE8BPdG1NaPYK9tNYMMcJVdu-xFjUCz7I8FWHRVj1
 

Food energy-dependent RNA-directed DNA methylation alters the shifting of membrane helices. The alterations prevent the virus-driven degradation of messenger RNA and all pathology via fixation of amino acid substitutions in organized genomes. The physiology of reproduction and pheromone-controlled chromosomal inheritance link the fixation of amino acid substitutions in all cell types of all living genera to all biodiversity.

Andréia Silva James Kohl you won the Nobel prize for refuting evolution, correct?

Yoshinori Ohsumi won last year for doing that: A protein conjugation system essential for autophagy

This [energy-dependent] conjugation can be reconstituted in vitro and depends on ATP.

Ben Feringa also won last year: Dynamic control of chirality and self-assembly of double-stranded helicates with light

Did you not get the memo? They linked the speed of light on contact with water from energy-dependent changes in chirality to all biodiversity via ATP, which is required for the creation of RNA.
 
The link from self-assembly to autophagy includes a light-activated endogenous substrate that links the innate immune system of all species to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 

All serious scientists are waiting for all pseudoscientists to realize the level of ignorance they have displayed for at least the past 50 years and take responsibility for the unnecessary suffering and premature deaths their ridiculous theories have caused.

Thank God, some serious scientists have taken the lead.

See:  Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.

Reported as: Common use of antibiotics in cells grown for research could distort tests

“…we treat cells with antibiotics all the time in cell culture and nobody’s looked at how this might affect and ,” said Ahituv.

Admitting that you and your colleagues once were biologically uninformed science idiots is the first step towards recovery. The antibiotic treatment caused the constraint-breaking mutations that all serious scientists have linked to all pathology. Food energy and the pheromone-controlled physiology of reproduction link biophysically constrained viral latency to healthy longevity.

The worst part of all this is that it clearly indicates Carl Woese was wrong. There is one domain of life and the virus-driven degradation of messenger RNA links the theft of quantized energy from the creation of bacteria to the creation of archaea.
 
Virus-driven energy theft also links the creation of humans to the creation of non-human primates via the same molecular mechanisms that link the food energy-dependent pheromone-controlled physiology of reproduction in bacteria to healthy longevity in species from microbes to humans.
 
My antagonists will continue to hate me for revealing that fact, but it was first revealed in Biblical Genesis. If I link the virus-driven theft of quantized energy to the creation of L-forms, I may be martyred.
 
But wait, I already did that and so did Paul in 1 Corinthians 15:36. I’m not quoting scripture, even though it parallels facts from what some people might call the book of “nature” even though there is only one book about that. 

Cytosis

The Origin of Information (3)

Summary: I presented two poster sessions during the Labroots virtual conference “Neuroscience,” March 16-17, 2016
One linked sunlight to energy as the origin of information. The other linked energy as information to biophysically constrained viral latency via the pheromone-controlled physiology of reproduction in all living genera.
Additional experimental evidence of top-down causation has since confirmed that the creation of sunlight can be linked from energy as information to all biodiversity via its anti-entropic virucidal effects. The direct quantitative measurement of top-down causation supports the claims made by all serious scientists, and also refutes all the claims made by evolutionary theorists and “Big Bang” cosmologists.
See:  The Origin of Information (1) 7/28/16 From hydrogen atom transfer in DNA base pairs to ecosystems

The Origin of Information (2) 7/28/16 RNA mediated molecular epigenetics and virus driven entropy (working title: The Origin of Information)
 
A good model predicts. See also: Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy

The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs…

Reported on 7/31/17 as: Scientists Decode DNA; See and Touch the Force That Gives Us Life
My summary: Hydrogen (H) t is the most abundant energy source in the Universe. It is also an indispensable source of the energy that is required for life. The energy links nucleic acids (DNA, RNA) and proteins to the creation of life via hydrogen bonds between molecules.
Energy as information is crucial for encoding the secrets of life. Those who cannot understand the concept of energy as information cannot understand anything about the energyd-dependent creation of life or the energy-dependent physiology of pheromone-controlled reproduction, which links energy as information to all biodiversity.
For instance, the biodiversity of all morphological and behavioral phenotypes is food energy-dependent. Richard Feynman put that fact into the perspective of something that many people are intuitively able to understand.

Feynman also presciently placed the measurement of energy into its current context. He somehow knew that technological advances would someday allow serious scientists to measure the energy in a hydrogen atom and link what organisms eat to all biodiversity.
See also: Hydrogen bonds directly detected for the first time

The measured forces and distances between the oxygen atoms at the tip of the atomic force microscope and the propellane’s hydrogen atoms… show that the interaction clearly involves hydrogen bonds. The measurements mean that the much weaker van der Waals forces and the stronger ionic bonds can be excluded.

The fact that experimental evidence established the primacy of the hydrogen bond in the interactions that link energy-dependent changes from chirality to autophagy and from angstroms to ecosystems in all living genera can be placed into the context of the food energy-dependent physiology of reproduction for comparison to: Mutation-Driven Evolution, which was published on the same day in 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The good news is that neo-Darwinian theories have been replaced with Darwin’s energy-dependent “conditions of life.” That is bad news for all theorists.
For example, yesterday, Jay R. Feierman again threatened to ban me from participation on the Human Ethology Yahoo Group. Our history of friction began in 1995 but it was amplified in 2013, when I wrote:

Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.

Feierman responded:
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.
As first author of the award-winning review Human pheromones: integrating neuroendocrinology and ethology, I may be the only former member of the International Society for Human Ethology (1) who still participates on the yahoo group they own (2). See also their FB page (3).

  1. The International Society for Human Ethology (ISHE) promotes ethological perspectives in the scientific study of humans worldwide. We aim to achieve this goal through:
    • Encouraging empirical research in the field of human behavior, using the full range of methods developed in biology and the human behavioral sciences, and operating within the conceptual framework provided by evolutionary theory.
    • Promoting the exchange of ethological knowledge and opinions with the other empirical sciences of human behavior.
  2. The International Society for Human Ethology (ISHE), http://www.ishe.org/, a not-for-profit scientific organization, is the owner of this listserv, whose purpose is to facilitate communication among persons interested in human ethology and to attract new persons to the field. The language is English. The current moderator is Jay R. Feierman.
  3. The International Society for Human Ethology (ISHE) aims at promoting ethological perspectives in the scientific study of humans worldwide. ISHE encourages empirical research in all fields of human behavior.

If I am the only person who has detailed the facts about the Origin of Information, and Jay R. Feierman bans me from participation in the ISHE’s group, he will help to eliminate discussion of empirical research such as  Feedback loops link odor and pheromone signaling with reproduction.
There are a few other people like Jay R. Feierman, who have helped prevent the dissemination of accurate information about the Origin of Information and all biodiversity in the context of our visual perception of energy and mass, which has been placed into the context of everything known about the space-time continuum. See: Olfaction Warps Visual Time Perception.
But, to my knowledge, no one besides Jay R. Feierman has claimed that “Variation is not nutrient availability and the something that is doing the selecting is not the individual organism.” According to Feynman, Jay R. Feierman exemplifies “human idiocy.”
But, see also this comment from James Gray (August 1, 2017):

Jay,

I just want you to note my support for your warning to Jim Kohl.  Too bad that his attempts at comments are so incomprehensible.

After Feierman blocked another one of my posts to the group, I wrote:

It can only get worse from here, Jay. Even if you will not admit to the fact that you were dead wrong, others will learn that you caused the death of their loved ones via your ignorance and arrogance.
You are an example of what Feynman’s referred to as human idiocy.
 

Feierman responded (to the group)

This is warning #1. Say something equally offensive again to me in a personal email or on the group and you will be permanently banned from the Yahoo Human Ethology Group.
Sadly, no one ever responds to your posting because they are incomprehensible. I post them out of human compassion for you. But that does not give you license for being rude and flaming.
I’m copying this to the human-ethology group as well, so other members will know why you are gone from the group, if your flaming re-occurs.

Jay

Jay R. Feierman, Moderator Yahoo Human-Ethology Group

See for comparison: http://www.odedrechavilab.com/About.aspx

Our principle aim in the lab is to attack scientific dogmas. Mainly, we aim to use powerful genetic tools to discover novel biological principles by which RNA affects formation and inheritance of complex traits. While linking rare Mendelian traits to specific sequence variations has been accelerated, the genetic basis of many common diseases is not understood despite the undertaking of many genome wide association studies. It appears that our current genetic models fall short of faithfully explaining the inheritance of most complex traits.

Replaced by: Laboratory for radical science
See also: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

…how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.

The changes to histone marks are energy-dependent and they link hydrogen-atom transfer in DNA base pairs to the food energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which prevents virus-driven energy theft from causing the degradation of messenger RNA that links mutations to all pathology.

On August 1, 2017 Jay R. Feierman wrote: 88186 “A genetic correlate of attachment and personality”

This is not a genetic correlate. The COMT VaL158Met amino acid substitution exemplifies the facts detailed in the context of: Hydrogen bonds directly detected for the first time The facts about hydrogen-atom transfer in DNA base pairs in solution have since been linked to all energy-dependent pheromone-controlled biodiversity in: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

…how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.
 

The changes to histone marks are energy-dependent and they link hydrogen-atom transfer in DNA base pairs to the food energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA. The substitutions prevent virus-driven energy theft from causing the degradation of messenger RNA that links mutations to all pathology.

See for comparison: How to teach evolution when students hold creationist views

Teaching evolution is pointless.

See: Cytosis

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

Anyone ten years old or older will learn that natural selection for energy-dependent codon optimality is the key to healthy longevity and that the virus-driven degradation of messenger RNA links mutations to all pathology.

fruit-dove

Theories vs facts about polycombic adaptation

See: Demoncrats fight polycombic ecological adaptation

Exosomes as miRNA Carriers: Formation–Function–Future

Important aspects will be highlighted as a take-home message (THM) at the end of each paragraph.

THM: Extracellular vesicles transport miRNA in a paracrine and endocrine manner. Questions regarding the cellular options of producing either microvesicles or exosomes and their difference in miRNA composition and number are still unknown.

In my 2014 invited review, the four F’s, Formation–Function–Future and Copulation were included in details about how the nutrient energy-dependent de novo creation of microRNAs must be linked to nutritional epigenetics. My invited review was returned without review by the guest editors of a special issue of “Nutrients.”
I realized the guest editors had “baited me” into providing them with all the available current information and published my submission to Figshare. That’s how I show the level of deception that biologically uninformed theorists still use to obfuscate what is known to serious scientists about biologically-based cause and effect.

See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (April 10, 2014)

Abstract: “This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.”

Lynnette Ferguson, was one of two guest editors that invited my review.
 
She is the co-author of The Interaction between Epigenetics, Nutrition and the Development of Cancer This article belongs to the Special Issue NutritionalEpigenetics
 

Conclusion:

…it is imperative to understand the implications of diet on epigenetic modifications, and the effect of those modifications on the development of cancer today and in future generations. Such an understanding and an appropriate resultant response would help decrease the level of risk in future generations.

There would be no future generations if diet could not be epigenetically linked from metabolism to the pheromones that control the physiology of reproduction in species from microbes to human via energy-dependent changes in the microRNA/messenger RNA balance. The microRNA/messenger RNA balance biophysically contrains RNA-mediated protein folding chemistry.

Protein folding chemistry links energy-dependent changes from angstroms to ecosystems in all living genera via the innate immune system and fixation of RNA-mediated amino acid substitutions in supercoiled DNA. Supercoiled DNA exemplifies natural section for energy-dependent codon optimality, but theorists will not accept that fact. They would rather believe that the mutations in DNA are naturally selected and that mutation-driven evolution automagically occurs outside the context of energy or the virus-driven energy theft that causes all mutations and all pathology.

See also: The developmental basis for the recurrent evolution of deuterostomy and protostomy

This scenario challenges the assumed value of extant blastoporal behaviours for explaining the evolutionary origin and diversification of Bilateria that has been presumed for over 100 years4,5,6,7,9,10,11. Freeing the constraint that the mouth and anus have a necessary association with the embryonic blastopore will help in understanding the developmental events underlying the evolution of an alimentary canal5,20,21,50, and ultimately the appearance and diversification of bilaterian body plans.

All scenarios that failed to link energy-dependent behavior to the physiology of reproduction and also failed to link virus-driven energy theft to all pathology have always been based on questionable assumptions. The assumptions fall outside the context of Darwin’s “conditions of life,” which require links from what organisms eat to signaling and sensing and the behavior of other organisms.

For example, Schrodinger (1944) linked excretion from mammals to sunlight as the source of anti-entropic virucidal energy used to support all ecosystems. All serious scientists have done that since Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for linking chromosomes to transgenerational epigenetic inheritance long before most people understood what the term autophagy means.

Filtering light through a prism to identify tissue type

RNA-mediated physics, chemistry, and molecular epigenetics (3)

Summary of the metabolic pathways altered in cancer that are described in this review

Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism

My comment: Metabolic networks are linked to genetic networks by the normal metabolic landscape, which is linked to healthy longevity. Virus-driven energy theft links changes in the metabolic landscape to changes in the physical landscape of supercoiled DNA, which typically maintains healthy longevity across the lifespan by preventing virus-driven entropy. When no consideration is given to facts about virus-driven entropy, you are stuck with theories about brain evolution.
See for example: Metabolic acceleration and the evolution of human brain size and life history 5/4/16 reported as: Humans have faster metabolism than closely related primates, enabling larger brains

My comment: Place that claim into this regression.

Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum 1/15/16
My comment: Copy number variation is nutrient energy dependent
Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants 2/28/16
My comment: MicroRNA flanking sequences link hydrogen atom transfer in DNA base pairs in solution to nutrient energy-dependent copy number variation.

An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers 4/1/16
reported 4/14/16 as: Scientists document rare DNA transfer between animals and plants
My comment: “Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals. For example, ingested plant microRNAs influence gene expression across kingdoms (Zhang et al., 2012). In mammals, this epigenetically links what mammals eat to changes in gene expression (McNulty et al., 2011) and to new genes required for the evolutionary development of the mammalian placenta (Lynch, Leclerc, May, & Wagner, 2011) and the human brain (Zhang, Landback, Vibranovski, & Long, 2011).” — Kohl (2012)
My comment: Place all claims (above) that link nutrient-dependent ecological adaptations into the context of healthy longevity. Place all claims (below) into the context of  virus-driven energy theft and all pathology.
Wolbachia Blocks Currently Circulating Zika Virus Isolates in Brazilian Aedes aegypti Mosquitoes 5/4/16

reported 5/4/16 as: Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing 5/3/16

reported 5/1/16 Australia to spend over $11mn to eradicate carps by releasing herpes virus into rivers

My comment: Place all claims about nutrient energy-dependent cell type differentiation and all claims that link virus-driven energy theft into the context of physics and chemistry linked to the conserved molecular mechanisms of cell type differentiation in twin studies. For example,  NASA’s Twins Study Explores Space Through You: Videos Highlight Omics  4/20/16

What does it take to detect entanglement with the human eye?
reported 5/3/16 as  An experiment seeks to make quantum physics visible to the naked eye

RNA splicing is a primary link between genetic variation and disease 4/29/16

3/31/16 Carl Zimmer Episode 5: Everything you thought you knew about the shape of DNA is wrong

4/24/16 Sea Slug Senses 1/15/13 The sea slug that eats the sun (video)

Saturation of recognition elements blocks evolution of new tRNA identities 4/29/16

reported 5/2/16 Discovery of a fundamental limit to the evolution of the genetic code

Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity and Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPRmt

reported 5/2/16  Genetic switch could be key to increased health and lifespan

The Role of Correlation and Solvation in Ion Interactions with B-DNA 1/19/16

delayed reporting till 5/3/16 A new model for simulating DNA’s ‘atmosphere’ of ions

5/3/16 Part I: Epigenetics: Why Your DNA Isn’t Enough C. David Allis

5/3/16 Part II: Epigenetics in Development and Disease C. David Allis

Genomic instantiation of consciousness in neurons through a biophoton field theory 6/13/14
4/18/16 Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb and 5/1/16 Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy 
collectively reported 5/2/16 as Unraveling complex neuronal networks
My comment: The de novo creation of G-protein coupled receptors (GPCRs) links the epigenetic landscape to the physical landscape of supercoiled DNA via olfaction and the innate immune system.

Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons. Delgado-Peraza F, Nogueras-Ortiz C, Acevedo Canabal AM, Roman-Vendrell C, Yudowski GA. Methods Cell Biol. 2016;132:25-33.
Chapter 1 – Localization and signaling of GPCRs in lipid rafts

Chapter 2 – Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons
Chapter 4 – Single-molecule resolution of G protein-coupled receptor (GPCR) complexes
Chapter 13 – Resonance Energy Transfer-Based Approaches to Study GPCRs
My comment: Place everything known about nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation into the context of virus-driven energy theft and cancer.

Deletion of Amino Acid Transporter ASCT2 (SLC1A5) Reveals an Essential Role for Transporters SNAT1 (SLC38A1) and SNAT2 (SLC38A2) to Sustain Glutaminolysis in Cancer Cells (4/26/16)
reported on 5/5/16 Starving cancer the key to new treatments
Excerpt:

The research team blocked gateways through which the cancer cell was obtaining the amino acid glutamine and found the cells almost completely stopped growing.

My comment: They prevented the viruses in the cancer cell from adapting. Otherwise, energy theft enables amino acid substitutions in the virus that would link ecological variation to healthy longevity when nutrient-stress or social stress is biophysically constrained. Links from the epigenetic landscape to the physical landscape of supercoiled DNA biophysically constrains energy-dependent RNA-mediated cell type differentiation. They have been placed into the context of mutation-driven evolution by theorists who have killed millions with their ridiculous theories.

See for comparison:

reported 5/2/16 We are pleased to announce that today marks the formal release of our latest title: Amber Palaeobiology by Dr David Penney.

Physics

Confusing effects and affects of visual input

Their report indicates that these researchers never learned to differentiate between epigenetic effects on RNA-mediated cell type differentiation compared to the experience-dependent affects on behavior of amino acid substitutions.

Experience Affects Critical Period Plasticity in the Visual Cortex through an Epigenetic Regulation of Histone Post-Translational Modifications

Excerpt:

We show that the early exposure of rat pups to enriching environmental conditions accelerates the critical period for plasticity in the primary visual cortex, linking this effect to increased histone acetylation, specifically at the BDNF gene level. Moreover, we report that the exposure of adult animals to environmental enrichment enhances histone acetylation and reopens juvenile-like plasticity.”

My comment: Nutrient-dependent microRNAs link chemotaxis to phototaxis in species from microbes like Pseudomonas florescens to mammals. MicroRNA flanking sequences link hydrogen-atom transfer in DNA base pairs in solution from the nutrient-dependent physiology of reproduction in all living genera to supercoiled DNA, which protects organized genomes from virus-driven entropy.

For example, the BNDF Val66Met and COMT Val158Met amino acid substitutions alter the stability of organized genomes during life history transitions in the mouse to human model.

Also, the bull sperm microRNAome links soil bacteria to plant growth and nutrient-dependent microRNAs in mammalian milk that alter brain development in human infants by protecting them from Zika virus-damaged DNA.

See also: Increased vitamin C in the diet could help protect against cataracts

Excerpt:

…participants who had a higher intake of vitamin C were associated with a 33 per cent risk reduction of cataract progression and had ‘clearer’ lenses after the 10 years than those who had consumed less vitamin C as part of their diet.

My comment: They add this caveat:  “… the participants are predominantly of UK-origin and female, reflecting cataract progression between the ages of 60 and 70 years on average, so may not be generalisable.” The caveat suggests that everything known to serious scientists about the links from the nutrient-dependent stability and virus-driven entropy of all organized genomes in species from microbes to humans may not include their results.

Filtering light through a prism to identify tissue type

Energy-dependent purpose vs teleophobic telorexia

I’m not getting any responses to an attempt to discuss  On epigenetics: We are not just our DNA. That suggests I should use the claims and my attempt to discuss them in a blog post. If no one else wants to discuss the links from atoms to ecosystems in the diagram above, at least there will be a record to show they ignored them, again.

  1. Thanks for reporting on the symposium presentation.
    In the early 1990’s Bruce McEwen told me to start with gene activation if I wanted anyone to validate my mammalian model. It developed into a model that now links energy-dependent hydrogen-atom transfer in DNA base pairs in solution from RNA-mediated DNA repair to supercoiled DNA that protects the organized genomes of all living genera from virus-driven entropy.
    The symposium validated my model in the context of what has since been learned about transgenerational epigentic inheritance of the Zika virus, and the virus-driven pathology of Alzheimer’s disease.
    Simply put, the nutrient-dependent innate immune system links RNA-mediated DNA repair to healthy longevity or virus-driven energy theft to all pathology via what is currently known about biophysically constrained protein folding chemistry and the physiology of nutrient-dependent reproduction.
    1. See also the molecular epigenetics section of our 1996 Hormones and Behavior review:
      From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html
      Excerpt: “Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”
      If you haven’t read any of the ~48,000 publications that link the pre-mRNAs (microRNAs) from nutrient-dependent flanking sequences to the biophysically constrained chemistry of RNA-mediated protein folding and RNA-mediated amino acid substitutions that stabilize all organized genomes when fixation occurs in supercoiled DNA, you may not be linking the physiology of reproduction from ecological variation to ecological adaptation.
      1. See also: Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687119/
        Excerpt: “Milk is a highly specialized nutrient and signaling system of mammalian evolution that apparently shapes the epitranscriptome of the milk recipient via FTO-mediated modifications of RNA nucleotides. Future research should unravel milk´s biological impact on the recently recognized dual axis of coordinated regulation between the genome and the epigenome and the transcriptome and the epitranscriptome, respectively [336].”
        My comment: When placed into the context of neo-Darwinian evolution, it makes no sense to place any highly specialized nutrient or any signaling system into the context of a dual axis of coordinated regulation. You cannot simply make claims about the magic of evolution. First, someone must explain how they defined the boundary between epigenetics and genetics outside the context of nutrient-dependent supercoiled DNA that protects all organized genomes from virus-driven entropy.
        For example, how could the protection of the innate immune system “evolve.”
        How could ecological variation be linked to ecological adaptation if the innate immune system did not fine-tune the balance of nutrient-dependent
        1) microRNAs,
        2) adhesion proteins, and
        3) RNA-mediated cell type differentiation that links
        4) hydrogen-atom transfer in
        5) DNA base pairs
        6) in solution to
        7) thermodynamic cycles of protein biosynthesis
        8) and degradation in the context of changes in
        9) oxygen,
        10) pH,
        11) carbon dioxide,
        12) salinity,
        13) other chemical cues,
        14) all integrated sensory input,
        15) and the physiology of reproduction, which is controlled by pheromones in species from microbes to humans?
        —————————————

For comparison: Watch paleoartist John Gurche’s vision of his own direct ancestry in under 2 minutes. Learn how he draws on fossil discoveries and forensic techniques to create transfixing reconstructions of long-lost human ancestors.

Yale University Press made this video to promote Shaping Humanity: How Science, Art, and Imagination Help Us Understand Our Origins in which paleoartist John Gurche uses fossils and forensics to create reconstructions of long-lost human ancestors.

See below: For contrast, researchers who report that an amino acid substitution linked to 180 disorders of cell type differentiation; to pathology; and to human facial characteristics are placing their findings into this misrepresentation of biologically-based cause and effect.

Prolegomenon to patterns in evolution

Excerpt:

In outline: Newton and Laplace created a view of the world whose becoming is entirely entailed by “the laws”, plus the initial and boundary conditions. This view is in a deep sense not altered by quantum mechanics on at least some of its interpretations. In this world view, there can be no “true creativity”.  All is already entailed from the start, for example, the Big Bang.

See also: Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries

Few living scientists are as ambitious in their choice of problems as Stuart Kauffman. He is a polymath, with a degree in medicine and training in biochemistry, genetics, physics, philosophy and other fields.

Excerpt:

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

My comment: Predictably, the anti-entropic force links atoms to ecosystems. Predictably, when it is rediscovered, it will embarrass anyone who has ignored Schrodinger’s claims about biologically-based cause and effect in “What is Life?”
Excerpt:

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

See also: Deriving time-dependent diffusion and relaxation rate in porous systems using eigenfunctions of the Laplace operator
Abstract:

Porous systems are investigated using eigendecomposition of the Laplace matrix. Three parameters; tortuosity, surface-to-pore volume ratio and relaxation rate are derived from the eigenvalue spectrum of the Laplace matrix and connected to the parameters in the Padé approximation, an expression often used to describe the time-dependent diffusion coefficient in porous systems. The Padé length is identified for systems with large pore to connector volume ratio. The results are compared with simulations.

For comparison, see:

What is Life?: With Mind and Matter and Autobiographical Sketches (Canto Classics) Reprint Edition with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking

Excerpt:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

My comment: Too often! How often do we hear about models like this: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Excerpt:

Animal models are often used to model human physical and mental disorders. The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

For comparison see:  Human brain networks function in connectome-specific harmonic waves

Excerpt:

The dynamics of the oscillatory cortical networks is thought to emerge from the interplay of excitation; for instance mediated by glutamatergic principal cells, and inhibition; for instance mediated γ-aminobutyric acid GABAergic interneurons29.

See for comparison: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
Abstract:

Excitatory amino acids play a key role in both adaptive and deleterious effects of stressors on the brain, and dysregulated glutamate homeostasis has been associated with psychiatric and neurological disorders. Here, we elucidate mechanisms of epigenetic plasticity in the hippocampus in the interactions between a history of chronic stress and familiar and novel acute stressors that alter expression of anxiety- and depressive-like behaviors. We demonstrate that acute restraint and acute forced swim stressors induce differential effects on these behaviors in naive mice and in mice with a history of chronic-restraint stress (CRS). They reveal a key role for epigenetic up- and down-regulation of the putative presynaptic type 2 metabotropic glutamate (mGlu2) receptors and the postsynaptic NR1/NMDA receptors in the hippocampus and particularly in the dentate gyrus (DG), a region of active neurogenesis and a target of antidepressant treatment. We show changes in DG long-term potentiation (LTP) that parallel behavioral responses, with habituation to the same acute restraint stressor and sensitization to a novel forced-swim stressor. In WT mice after CRS and 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.

My comment: McEwen’s group does not link the ubiquitous mathematical framework referred to as the “eigendecomposition of the Laplace operator” to any theory. His group knows how heat, light, sound, electricity, magnetism, gravitation, and fluid mechanics predict human cortical activity. They may also know that hydrogen-atom transfer in DNA base pairs in solution must link atoms to ecosystems at the macroscopic scale via the circulating blood delivered to the brain.
So far as I know, Bruce McEwen has always used a model of nutrient-dependent epigenetically-effected biologically-based cause and effect to link ecological variation and ecological adaptation. His group now attests to the fact that the link can be one nutrient-dependent RNA-mediated amino acid substitution: BDNF Val66Met.
They have also linked what they know about BDNF Val66Met to what is known by others about COMT Val158Met and behavior during the life history transitions from adolescence to adulthood. The link is a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution). The base-pair substitution leads to a methionine (Met) valine (Val) amino acid substitution at codons 108/158 (COMT Val158Met).
Carriers of the Met amino acid substitution are reported to have an allele that is linked to display of a fourfold decrease in enzymatic activity compared to Val allele carriers. The Met amino acid substitution is accompanied by increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995). But, the link between the amino acid substitution, increased prefrontal DA activity and behavior is reported only as a link from an allele, as if a different gene was linked to differences in behavior outside the context of epigenetic effects on hormones that affect behavior.
See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
Excerpt:

…our findings are in line with a genetically-informed schizophrenia model derived from an orphan disease (Gothelf et al. 2005, 2013). In velo-cardiofacial syndrome (VCFS), a rare disorder with an increased risk of schizophrenia resulting from a microdeletion in 22q11.2, patients are known to lack one copy of COMT. In this patient group available evidence suggests that genotype effects of COMT Val158Met on cognitive performance are critically dependent on the maturational stage of the brain (Gothelf et al. 2005).

My comment: There is no mention that COMT Val158Met links an energy-dependent hydrogen-atom transfer of a DNA base pair in circulating blood to the amino acid substitution and the effect on hormones linked to the affect on behavior in the report.  Instead they report their findings in the context of a gene linked from loss of one amino acid substitution to schizophrenia and to abnormal pharyngeal arch development that results in defective development of the parathyroid glands, thymus, and conotruncal region of the heart. Actually, I mentioned the 180 different disorders of cell type differentiation (above) because there are more than 180 different clinical features associated with velocardiofacial syndrome, with no single anomaly present in every patient. Some abnormalities are more common than others. Affected individuals may present with structural or functional palatal abnormalities, cardiac defects, unique facial characteristics, hypernasal speech, hypotonia, and defective thymic development. That means one energy-dependent base-pair change and one amino acid substitution was linked to all those morphological and behavioral phenotypes during life history transitions.
Cause and effect was reported as: Genes exhibit different behaviours in different stages of development
See my comment on that report:

1 / 5 (2) Oct 22, 2014

The study highlights the dynamism of gene effects on brain function throughout the various stages of life such as adolescence or adulthood.

So does everything currently known about nutrient-dependent pheromone-controlled RNA-directed DNA methylation and cell type differentiation via RNA-mediated events and amino acid substitutions in species from microbes to man. See the following two references for information on the honeybee model organism.

Organizational and activational effects of hormones on insect behavior
Honey bees as a model for understanding mechanisms of life history transitions
For the link to conserved molecular epigenetics in mammals see: From Fertilization to Adult Sexual Behavior
Summary: These researchers know that they linked an energy-dependent base pair change to an amino acid substitution. They know that they linked one amino acid substitution to many different human morphological and behavioral phenotypes during life history transitions. Yet they reported their findings in the context of a gene-centric view of evolved phenotypic changes as if “Nature” made more than 180 mistakes associated with velocardiofacial syndrome, which also linked a gene to evolution.
All serious scientists would ask at least two questions:

  1. What prevents the mistakes from causing extinction of a species that accumulates mutations during the life history transitions?
  2. How could primate ancestors mutate and become individuals that somehow established a population of ecologically adapted modern humans?

Dobzhansky (1973) claimed that “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla ( p. 127)”
Can that claim be placed into the context of transgenerational epigenetic inheritance by what is known or suspected about how the Zika virus might be linked to craniofacial morphology and to brain development, which is probably linked to behavior during life history transitions of all invertebrates and vertebrates. What is the best approach to take in attempts to discuss the claims of neo-Darwinian theorists, other theorists, or serious scientists who know how to link physics and chemistry to the conserved molecular mechanisms of nutrient-dependent RNA-mediated cell type differentiation? I’ve tried everything I can think of to help with potential discussions.

Telorexia – Blind to Purpose in Nature

Thanks. It is not so much what I have shown. It is the details of biophysically constrained links from atoms to ecosystems, which are perturbed by viruses.
Ecker (from the human genome project) is senior author of a published work with this line as the first line in the abstract.
RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses.
What I have shown links quantum physics to the de novo creation of genes. What you have shown is that DNA repair mechanisms are required to maintain the virus-perturbed code.
I have shown how RNA-mediated DNA repair occurs in the context of an atoms to ecosystems model. You are still discussing randomness and evolution with people who know nothing about nutrient energy-dependent cell type differentiation.
It may not be possible for them to move forward, but you have the attention of a few other serious scientists who can link your claims across all living genera by what is currently known.
In my opinion, you are excluding their input by not allowing the first part of my submission to be included in the context of the prize.
Thank you for allowing the link to my invited review of nutritional epigenetics. If you include it as part 1 of the prize submission, perhaps others will see why the review was invited, and why the submission was returned without review.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
No one from any camp wants someone like you or like me to destroy their theories. And, no one else from outside those camps will risk their wrath — as you have been told.
Why are you concerned about accepting the review as part 1 of the 2 part submission that will link hydrogen-atom transport in DNA base pairs to cell type differentiation that is perturbed by viruses?
It’s just part 1 of the submission. Perhaps part 2 will be unnecessary, or meaningless. But if you exclude part 1 because of the complexity, no one gets to part 2 who isn’t already nearly there.
And the works of others who are nearly there will not be integrated into the representations made in your book.

January 23, 2016 at 6:45 pm

Thanks. I have demonstrated the well-known need for an anti-entropic force, which must be linked from Schrodinger’s claims to Stuart Kauffman’s claims. I have detailed the links from the anti-entropic force to RNA-mediated DNA repair at a time when Kauffman and Sheldrake are not discussing Lipton’s works and you are not discussing the works that refute Shapiro’s theories.
You have led many others to a point where they can dismiss “Evolution 2.0” as nothing more than another opinion. That’s what folks like PZ Myers want them to do, and that’s why he attacked me for my accurate representation of chromosomal rearrangements.
Others have linked the anti-entropic force from microbes in the guts of octopuses to chromosomal rearrangements and to human cognition via the conserved molecular mechanisms I have helped to detail during the past 20 years.
Simply put, you’re still trying to address the ridiculous claims of people like PZ Myers when it’s time to dismiss their nonsense and move forward using experimental evidence of biologically- based cause and effect.
For example: Feedback from Network States Generates Variability in a Probabilistic Olfactory Circuit and Feedback loops link odor and pheromone signaling with reproduction  are ‘cut from the same cloth.’
The metaphorical cloth emerged in the context of Dobzhansky’s “light of evolution,” which turned out to be the light that linked ecological variation to ecological adaptation in all living genera via nutrient-dependent RNA-mediated cell type differentiation in the context of the physiology of reproduction in all living genera.

3/13/16

I gave up on attempts to discuss anything on Perry Marshall’s sites. Clearly, he does not want to start with nutrient-dependent RNA-mediated protein folding chemistry in an attempt to link what is known to serious scientists to his revision of Darwin’s works.

terrarium-eco-system

RNA-mediated theory killers (4)

DNA methylation and microRNA biomarkers for noninvasive detection of gastric and colorectal cancer

Excerpt:

At this moment, DNA methylation and non-coding RNA including with microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) represent the largest body of available literature on epigenetic biomarkers with the highest potential for cancer diagnosis.

My comment: The SLC19A3 microRNA was mentioned in the context of cancer and brain development in The impact of new technologies on clinical decision-making in health care. The location of the base pair for the  SLC19A3 gene starts at 228549926 and ends at 228582745 bp from pter ( according to hg19-Feb_2009) Also, “According to the NCBI Homo sapiens Annotation Release 106, SLC19A3 is flanked by genes including: ArfGAP with FG repeats 1 (AGFG1), microRNA 5703 (MIR5703), chromosome 2 open reading frame 83 (C2orf83), 5S ribosomal pseudogene 121 (RNA5SP121), and small nuclear ribonucleoprotein polypeptide G pseudogene 8 (SNRPGP8).”

Those facts suggest to me that the SLC19A3 microRNA link from the nutrient-dependent de novo creation of the SLC19A3 gene could be examined in the context of an atoms to ecosystems model of RNA-mediated cell type differentiation by a team of physicists, chemists and molecular biologists. But first, the team would need to become interested in linking atoms to ecosystems in the context of what is currently known to serious scientists about biologically-based cause and effect. Obviously, the systems complexity of cause and effect that links the epigenetic landscape to the physical landscape of DNA via metabolic networks and genetic networks in all living genera is beyond the capabilities of any one person to detail.  And, the team members would need to know or to learn how to communicated without using the jargon of their disciplines or inventing new terms via definitions to capture the attention of science journalists who link to report “first evidence” as if the evidence had not existed from the dawn of creation.

Perhaps the team could start with what is known about Progress in microRNA delivery

Excerpt:

Viral vectors are efficient delivery agents but toxicity and immunogenicity limit their clinical usage. Herein, we review the recent advances in the mechanisms and strategies of nonviral miRNA delivery systems and provide a perspective on the future of miRNA-based therapeutics.

My comment: That fact can also be placed into the context of RNA-directed DNA methylation and histone acetylation, which is linked to cell type specific changes and healthy longevity by the conserved molecular mechanisms that link RNA-mediated amino acid substitutions to the stability of organized genomes in all living genera. Any team that starts with links from the epigenetic landscape to the physical landscape of DNA in all invertebrates and vertebrates could clarify what is known about the conserved molecular mechanism that link marine invertebrates to insects. But, they would not be the first to do that.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

This appears to have been reported in advance as: All in the (bigger) family

Excerpt:

A flurry of other presentations compared different classes of molecules—respiratory proteins, microRNAs, and the heat shock proteins produced in response to stress—in insects and standard crustaceans.

My comment: The link from nutrient-dependent microRNAs and cell adhesion proteins was removed with publication of the sequencing of the octopus genome. Instead of linking biologically-based cause and effect, they linked theories about the evolution of cephalopod neural and morphological novelties. Team-mates might need to agree to mention the fact that neo-Darwinian theory is not supported by the experimental evidence revealed in the context of the octopus genome sequence. It would take a very special team of researchers who were willing to end their careers by not supporting neo-Darwinian dogma and focusing on experimentally established facts.

See: The octopus genome and the evolution of cephalopod neural and morphological novelties

Excerpt:

We found, amid extensive transcription of octopus transposons, that a class of octopus-specific short interspersed nuclear element sequences (SINEs) is highly expressed in neural tissues (Supplementary Note 4 and Extended Data Fig. 8). Although the role of active transposons is unclear, elevated transposon expression in neural tissues has been suggested to serve an important function in learning and memory in mammals and flies28.

Conclusion:

…these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise ‘typical’ lophotrochozoan gene complement that contributed to the evolution of cephalopod octopus-specific short interspersed nuclear element sequences (SINEs).

My comment: The facts do not change. Octopus-specific short interspersed nuclear element sequences (SINEs) replaced nutrient-dependent microRNAs, but the change of terms does not destroy the team’s efforts to establish links from the molecular mechanisms of cell type differentiation for comparison to claims that appear to link the complexity of octopus-specific short interspersed nuclear element sequences (SINEs) to the evolution of octopus-specific short interspersed nuclear element sequences (SINEs). Pheromones are species-specific, which suggests it doesn’t matter what undefined terms are used to link olfaction to species-specific behaviors.

However, for an example of word games played by evolutionary theorists, see: Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish? Clearly,  no experimental evidence of biologically-based cause and effect supports the claims that DNA elements or nuclear element sequences link novel genes or any other aspect of the links from the nutrient-dependent de novo creation of olfactory receptor genes to the downstream effects on neural complexity and morphological innovations that these researchers also attributed to evolution. They used the terms short interspersed nuclear element sequences, nuclear element sequences, and DNA elements to avoid the use of the term microRNAs (miRNAs). Fortunately, their use of terms was ineffective, since serious scientists already had linked atoms to ecosystems in all living genera via details that were subsequently reported.

See: Structural diversity of supercoiled DNA

Nutrient-dependent microRNAs were linked to cell type differentiation via cell adhesion proteins and supercoiled DNA that protects organized genomes from virus-driven entropy.

See also: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Conclusion:

Taken together, our data untangle the complicated roles of E-cadherin and p120 in the context of distinct junctional complexes, spatially separating their functions and providing an explanation for their conflicting behaviour in cell growth. In addition, they identify PLEKHA7 as a specific marker of ZA that mediates suppression of growth-related signalling. Finally, they reveal an interaction of the ZA with the microprocessor complex, and uncover a mechanism whereby the ZA regulates a set of miRNAs to suppress cellular transformation and maintain the epithelial phenotype.

My comment: The link from nutrient energy to microRNAs and differences in behavior development during life history transitions has also been established in the context of experimental evidence of biologically-based cause and effect.

See also: Mitochondrial function in the brain links anxiety with social subordination

Conclusion:

Limited energy production due to reduced mitochondrial function may impair adaptive neuronal capacity to life challenges (32) and contribute to the development of psychopathologies (9, 10, 13, 14). Therefore, our results highlight differences in mitochondrial function in the NAc as a potential mechanism underlying the susceptibility or resilience to develop depression, and may open new prospects for the advancement of preventive therapeutic approaches to mood disorders.

My comment: It is extremely difficult for a serious scientist to miss the connection from energy-dependent cell type differentiation to healthy longevity. For contrast, it seems to be very easy for evolutionary theorists to ignore the role of energy that is linked to RNA-mediated cell type differentiation via nutrient-dependent amino acid substitutions because they think one species evolves from another species via mutations. Similarly, sex differences in cell types also must somehow be naturally selected in the context of beneficial mutations.

But wait, see for contrast: Mitochondria can orchestrate sex differences in cell fate of vascular smooth muscle cells from rats

Conclusion:

Importantly, this research also suggests that (i) it is essential to indicate the sex of cells and plan experiments on male and female cells, to understand the basics of the observed differences in the male and female pathophysiology, and (ii) the idea that isolated cells could maintain a sort of “memory” of their origin, i.e., a sexual dimorphism, could provide new insight in understanding pathogenesis and outcome of some diseases, including cardiovascular diseases.

My comment: By now the team has arrived at experimentally established links to sex difference in cell types and somatic difference that have been linked from energy-dependent function of mitochondria across species in the context of a single amino acid substitution linked to life history transitions in behavior. Go, team, GO:

See also: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

My comment: The fact that a single amino acid substitution during life history transitions of humans can be linked from the honeybee model organism to life history transitions in all invertebrates and vertebrates via what is currently known about the links from atoms to ecosystems and supercoiled DNA has begun to alter the course of history in social science.

For example see: CAMH to ‘wind down’ gender identity clinic after damning review of services

My comment: Although serious scientists have continued to reassert the need for interdisciplinary collaboration to link sex differences in cell types to somatic differences, I know of only two groups that have moved forward as separate teams. For comparison, sex researchers have stagnated, which is one reason the editor of the Archives of Sexual Behavior was removed from his position at the Centre for Addiction and Mental Health (CAMH).

See also: Infamous Reparative Therapy Clinic For Transgender Youth Set To Close

Excerpt:

GIC’s “developmental model” was backwards. It blamed symptoms like depression and anxiety on the gender non-conforming behavior itself, rather than on the stigma attached to it or the conflict of not being able to fulfill one’s gender identity. This philosophy allowed the clinic to claim it was treating these negative mental health outcomes without affirming the trans behavior.

My comment: They had no developmental model. Philosophy has finally put an end to one career, and the end of many other careers will follow. Serious scientists have linked atoms to ecosystems in the context of morphological and behavioral phenotypes that vary during life history transitions. Others who have failed to pay attention to details that link RNA-mediated cell type differentiation to sexual orientation via links from sexual orientiation in yeasts to mammals, will be among those with the most vocal complaint as the heads continue to roll. But they probably won’t learn anything new about cell type differentiation. Most are at the end of their careers and they probably hope to get out before being thrown out the door, like Ken Zucker.
Personally, I like Ken, but his decision not to publish our study results in 2007 probably led others to ignore facts that link molecular epigenetics to sexual orientation via what is known to serious scientists about olfaction, food odors, and pheromones in species from microbes to primates. Besides, if researchers can’t publish the results of their experiments, they cannot recruit team members who need to publish or perish. That puts individuals up again teams that typically tout pseudoscientific nonsense because they have the strength of numbers to support their theories, which are typically published in the context of mathematical models of population genetics, not biologically-based cause and effect.
See, for example: Deciphered Gorilla Y chromosome shows strong conservation with Human but not with Chimpanzee
Excerpt:

Our results attest to strong conservation in structure and gene content between the gorilla and human Y chromosomes, and portray the chimpanzee Y as an outlier in the hominine Y chromosome evolution, even though chimpanzee and human shared the most recent common ancestor. Compared with the human Y, the chimpanzee Y lost four X-degenerate genes, three ampliconic gene families, and one palindrome, while the gorilla Y retained all these elements with the exception of one gene family. The ampliconic gene family size varies dramatically among the three hominines, as well as intraspecifically for four genes in gorilla. We speculate that the Y chromosome evolution in hominines is associated with their mating patterns. Additionally, the gorilla Y chromosome sequence was used to design polymorphic genetic markers for tracing male-specific dispersal in this endangered species. 

My comment: At this point it is not acceptable for anyone to link evolution to species-specific chromosomal rearrangements. Gene losses and gains exemplify nutrient-dependent RNA-mediated events that link viruses to the loss of genes or to the creation of pseudogenes, which is consistent with everything known to serious scientists about how DNA repair is linked from supercoiled DNA to the protection of organized genomes from virus-driven entropy. Intelligent team members might get angry if biologically uninformed researchers continue to jump across species via links from mutations to chromosomal rearrangements without linking them to nutrient energy-dependent species-specific reproduction that is controlled by the metabolism of nutrients to species-specific pheromones.
See also: The ribosome as a missing link in the evolution of life. The authors “Suggest that DNA and cells evolved to protect and optimize pre-existing ribosome functions.”
My comment: Others who suggest that DNA and cells automagically evolved seem to have not noticed that there is no experimental evidence that links biologically-based cause and effect to the evolution of anything that pre-existed. The automagical link from mutations to chromosomal rearrangement in primates is worse for anyone who knows what was addressed in A universal trend of amino acid gain and loss in protein evolution.
Excerpt:

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

My comment: The trend that emerged appears to be the basis for all the ridiculous claims of evolutionary theorists who link something unknown to whatever happened that biophysically constrains RNA-mediated cell type differentiation via amino acid substitutions, which are linked to all morphological and behavioral diversity via the nutrient-dependent physiology of reproduction that protects organized genome from virus-driven entropy.
And what about those viruses? They were left out of the modern synthesis.
The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
That’s why it will take a good team to unravel the mess that has been left to serious scientists by evolutionary theorists and other social scientists.

rp_levels-of-organization.jpg

Life and death predicted by DNA methylation

The bounce rate here has more than doubled  (from 20% to 44%) during the past week at the same reports continue to support all the claims I have made about RNA-mediated cell type differentiation.
Obviously, pseudoscientists are not willing to examine any evidence of biologically-based cause and effect that refutes their ridiculous claims about mutations and evolution. For comparison, serious scientists will want to read this:
See:

DNA methylation age is associated with mortality in a longitudinal Danish twin study

Excerpt:

In conclusion, we report a leveling off of the correlation between DNAm age and chronological age in old cohorts, which is likely to reflect that individuals reaching advanced ages have a more healthy aging profile. The association with mortality risk seen in the old twins when adjusting for familial factors adds considerable evidence to support the hypothesis that DNAm age can discriminate between slow and fast agers, consistent with the hypothesis that DNAm age is a proxy for underlying mechanisms of aging.

See also: rna directed dna methylation
DNA methylation is nutrient-dependent. It is also RNA directed.
RNA-directed DNA methylation (RdDM) provides a system for targeting DNA methylation to asymmetric CHH (H = A, C, or T) sites.
RNA-directed DNA methylation links the conserved mechanisms of molecular epigenetics to cell type differentiation via amino acid substitutions that differentiate all cell types of all individuals all living genera.

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. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes (Razin and Shemer, 1995; Reik, 1989; Surani, 1991; Zuccotti and Monk, 1995).

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Unconscious affects that are manifested during the development of diversified life and human behavior are, by their very nature, part of life that few people think about (Kohl et al., 2001). Therefore, the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, 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’.

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

 

terrarium-eco-system

Theorists can't understand biology

See also: Neuroplasticity
Thanks to Teresa Binstock for calling my attention to this:
 

Biology is imposssible

Optimizing neuroplasticity by linking atoms to ecosystems

Thanks to Anna Di Cosmo for calling the attention of others to this:

My comment: Attempts to explain the “binding problem” of integration in the context of ecoimmunology and disease ecology compared to emergence and evolution are examples of how much pseudoscientific nonsense has been accepted and touted in the context of the neo-Darwinian “Modern Synthesis.” For comparison, serious scientists have detailed a model of top-down causation that links the design of the brain from the bottom up in an atoms to ecosystems model of cell type differentiation. The model links our experiences from our first breath to our behavior during life history transitions via biophysically constrained protein folding.
Re: “Man is the measure of all things.” Intelligent scientists understand that their measurements from physics, chemistry, and the molecular mechanisms of biologically-based cause and effect must link all other scientific disciplines to biology.
See for example: Oxygen regulation of breathing through an olfactory receptor activated by lactate
Conclusion:

Although ORs [olfactory receptors] were first identified for their role in smell, they may be involved in myriad chemosensory pathways detecting endogenous and exogenous ligands throughout the body.

For comparison to what is known to serious scientists about receptor-mediated cause and effect in the context of chemosensory pathways, evolutionary theorists and theoretical physicists continue to misrepresent all measures of all things. For example, they refuse to explain how “re-evolution” of the bacterial flagellum occurred in four days but claim that an example of no evolution in ~2 billion years supports the claims included in the “Modern Synthesis.”
See: Scientists discover organism that hasn’t evolved in more than 2 billion years
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
My comment: Try to place the evolutionary resurrection of flagellar motility into the context of the binding problem that must link receptor-mediated events to chemosensory pathways after watching this video.

The bacteria that “re-evolved” their flagella over a weekend exemplify how the nutrient-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation in all living genera via receptor-mediated events that link food odors and pheromones to the physiology of reproduction in all living genera.
For comparison, Simon LeVay challenged my model of ecological adaptation, which resolved issues of the “binding problem” that links receptor-mediated behaviors in the context of sex differences in cell types and differences in sexual orientation.
See: Gay, Straight, and the Reason Why: The Science of Sexual Orientation
Excerpts:

That the odor of gay men is recognizably different from the odor of other people is believable, although the claim hasn’t been independently verified and its chemical basis hasn’t been studied. (p. 209)
It seems unlikely to me, though, that gay men have an innate preference for the odor of gay men over that of straight men because many gay men are attracted to straight men and, given the opportunity, will have sex with them even in preference to gay partners. Thus this finding, if replicable, is more likely to represent a learned association resulting from gay men’s prior history of intimacy with other gay men. (p. 210)
James Kohl, an independent researcher who also markets “human pheromones” to the general public, believes that pheromones may have a primary influence in setting up a person’s basic sexual orientation. Other, more consciously perceived aspects of attractiveness, such as facial appearance, are attached to a person’s basic orientation through a process of association during early postnatal life, according to Kohl. 35 (p. 210)
This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions. (p. 210)
Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (p. 210 – 211)

The chapter 8 notes entry number 36 attempts to show there is “…no compelling evidence for the primacy of one sense over another.” LeVay tries to support that ridiculous claim by citing Spieth (1974) “Courtship behavior in Drosophilia” and Stockinger et al (2005) “Neural circuitry that governs Drosophilia male courtship
Excerpt:

Anatomical differences in this circuit that might account for the dramatic differences in male and female sexual behavior are not apparent.

My comment: In our 1996 Hormones and Beahavior review, From Fertilization to Adult Sexual Behavior, we placed anatomical differences and sex differences in behavior into the context of RNA-mediated cell type differention. The conserved molecular mechanisms we detailed in our section on molecular epigenetics extend across species, regardless of whether LeVay or anyone else can find sex differences in neuroanatomy that correlate with differences in the behaviors of flies and humans.
See for comparison: Courtship behavior in Drosophila melanogaster: towards a ‘courtship connectome’

Excerpt: 

The construction of a comprehensive structural, and importantly functional map of the network of elements and connections forming the brain represents the Holy Grail for research groups working in disparate disciplines.

My comment: None of my former colleagues from the Society for the Scientific Study of Sexuality has since made any attempt to challenge LeVay’s claims about my model. However, LeVay’s claims can be compared in the context of two recent reports from serious scientists:
1) Feedback loops link odor and pheromone signaling with reproduction
Excerpt:

Compelling evidence that links the feedback loops from microbes to humans

2) MicroRNA-encoded behavior in Drosophila
Conclusion:

The results of this study contribute to the understanding of how complex innate behaviors are represented in the genetic program. Our data lead us to propose that other miRNAs might also be involved in the control of behavior in Drosophila and other species.

See also: The protein arginine methyltransferase PRMT5 promotes D2-like dopamine receptor signaling, which was reported as: Receptor methylation controls behavior 
Excerpt:

Likhite et al. found putative arginine methylation motifs in some human G protein–coupled receptors (GPCRs), including the D2 dopamine receptor, and in homologs in the worm Caenorhabditis elegans.

My comment: Nutrient-dependent RNA-directed DNA methylation of GPCRs in nematodes and humans, links the pheromone-controlled physiology of reproduction to the nutrient-dependent pheromone-controlled physiology of reproduction in yeasts and other microbes via the conserved molecular mechanisms of cell type differentiation we detailed in our 1996 review. Serious scientists have linked the facts from our review from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all living genera.
See: DNA twist as a transcriptional sensor for environmental changes (1992) and DNA supercoiling and bacterial gene expression (2006) and Flagellar and global gene regulation in Helicobacter pylori modulated by changes in DNA supercoiling (2007).
Addendum: Only pseudoscientists and other who are among the biologically uninformed have failed to accept the scientific progress that led to publication of Structural diversity of supercoiled DNA (2015).
This parody links what is known to serious scientists about biologically-based cause and effect to the ridiculous claims of theorists in an amusing musical rendition of insults to the theorists that is unlike any other collection of polite insults that you may ever see.

See also: Combating Evolution to Fight Disease
My comment: Help serious scientists to force pseudoscientists to learn about biologically-based cause and effect. Join the fight to stop the pseudoscience and preventable diseases!

Compare what is known to serious scientist to the claims of these pseudoscientists in the context of the most recent attempt to convince others that evolution is true.

Evolution website sets out to tackle great scientific unknowns

Excerpt: 

The site was created by a team led by Simon Conway Morris, Professor of Evolutionary Palaeobiology and a Fellow of St John’s College at the University of Cambridge. “Evolution is true, and if it didn’t happen, we wouldn’t be here,” he said.

My comment: Are you willing to accept that circular logic rather than examine life in the context of Schrodinger’s claims from “What is Life?
Excerpt:

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

My comment: The anti-entropic epigenetic effect of the sun’s virucidal energy on DNA repair links ecological variation to nutrient-dependent ecological adaptation via the physiology of reproduction or to virus-driven pathology in all living genera. That is not circular logic, and molecular mechanisms linked to the physiology of nutrient-dependent reproduction exemplify how the differences between life and death arose.
See also: Consciousness Mechanics: The Movie for more philosophical nonsense than most people have seen integrated into something to entertain the masses.
 

amino acid homeostasis

Receptor methylation controls behavior

The protein arginine methyltransferase PRMT5 promotes D2-like dopamine receptor signaling

Excerpt 1)

The addition of a methyl group to an arginine residue can remove a hydrogen bond donor and decrease the electrostatic surface potential at the residue, resulting in a change in size and hydrophobicity that can affect its interaction with binding partners (21).

Excerpt 2)

Together, these results led us to propose that arginine methylation promotes D2-like dopamine receptor signaling and that this mechanism of receptor regulation is conserved between nematodes and humans. Moreover, our finding that several hundred mammalian GPCRs contain predicted methylation sites within their cytoplasmic domains (Fig. 1A and tables S1 and S2) suggests that methylation may broadly regulate GPCR signaling in a previously unappreciated manner.

My comment: This article links RNA-directed DNA methylation to G protein-coupled receptors via biophysically constrained nutrient-dependent pheromone-controlled protein folding chemistry in species from nematodes to humans. It was reported as:

Receptor methylation controls behavior

D2 dopamine receptors are targeted by antipsychotic agents to regulate behavior. Likhite et al. found putative arginine methylation motifs in some human G protein–coupled receptors (GPCRs), including the D2 dopamine receptor, and in homologs in the worm Caenorhabditis elegans. Methylation of the D2 dopamine receptor by the arginine methyltransferase PRMT5 enhanced D2 receptor signaling in cultured cells. C. elegans lacking prmt-5 had behavioral problems similar to those in worms deficient in the D2-like receptor DOP-3. Thus, methylation of GPCRs may be important for clinically relevant targets such as the D2 receptor.

My comment: The claim that Receptor methylation controls behavior can be placed into the context of MicroRNA-encoded behavior in Drosophila, and all other living genera. For example, Feedback loops link odor and pheromone signaling with reproduction.
Excerpt:

Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons. (p 683)

My comment: The nutrient-dependent microRNA/messenger RNA balance links energy-dependent base pair changes to RNA-mediated gene duplication and fixation of RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all living genera in the context of the physiology of reproduction. Even when the physiology of reproduction does not involve neurons, it involves the conserved molecular mechanisms of nutrient-dependent pheromone-controlled reproduction in species from microbes to humans.
See for details: From Fertilization to Adult Sexual Behavior
Excerpt:

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.

My comment: The alternative splicing of otherwise identical genes links everything known about physics, chemistry, and biology via the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated protein folding to protection against virus-driven genomic entropy, which is ensured by supercoiled DNA.