Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Virus-driven cystinosis

A friend asked about nephropathic cystinosis, which is a disease caused by the virus-driven theft of quantized energy. All serious scientists have linked viruses from the degradation of messenger RNA to mutations and all pathology.

Nephropathic cystinosis (NC) is the most frequent cause of Fanconi syndrome (FS) in young children. It will be linked from the virus-driven degradation of messenger RNA to azoospermia and/or progressive neuromuscular degeneration via the conserved molecular mechanisms of RNA-mediated cell type differentiation compared to mechanisms that link viruses to mitochondrial degeneration.

See: Impact of atypical mitochondrial cyclic-AMP level in nephropathic cystinosis

Treatment with the non-hydrolysable cAMP analog 8-Br-cAMP restored mitochondrial potential and corrected mitochondria morphology. Treatment with cysteamine, which reduces the intra-lysosomal cystine, was able to restore mitochondrial cAMP levels, as well as most other abnormal mitochondrial findings.

The link to treatment of the atypical mitochondrial cyclic-AMP level has not yet been detailed because biologically uninformed science idiots have linked mutations to evolution. But see: Combating Evolution to Fight Disease  and the preprint: Reappraising the human mitochondrial DNA recombination dogma 

The facts about human mitochondrial DNA recombination, which link quantized energy and supercoiled DNA to viral latency, played a significant role in North Korea’s denuclearization. But that fact may not be accepted until the article on human mitochondrial DNA recombination is published in a peer-reviewed journal.

It will then take several more years for medical practitioners to learn how to effectively treat all diseases with food energy-dependent changes in the microRNA/messenger RNA balance.

See for details: Energy as information and constrained endogenous RNA interference

Until all pseudoscientists accept the facts, there will be many others who try to profit from misinformation or from partial information about virus-driven pathology. Most people will not read my reviews and journal articles like this:  MicroRNA Regulation of RNA Virus Replication and Pathogenesis

Instead, most are willing to accept the claims of others who have “blown the whistle” on vaccines more than two decades after I first published this review of RNA-mediated cell type differentiation in a peer-reviewed journal. From Fertilization to Adult Sexual Behavior

See:  Doctor Blows Whistle on Flu Shot: ‘It’s Designed to Spread Cancer’

Treague confirmed that this year’s flu strain, that has left thousands of citizens dead, was caused by the vaccines itself, saying: “I believe that the low effective rate of the vaccine this year is due to the mutations that the virus made in the processing of the vaccine itself.

Claims that viruses make mutations are the claims of fools who do not know that the virus-driven degradation of messenger RNA has been linked from mutations to all pathology in more than 72,000 published works.

See: microRNA

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

MicroRNA-mediated denuclearization (4)

Summary: Christ’s lab showed that in vivo formation of I-motif structures is pH dependent and helped to put the “fear of God” into atheistic communists.

I-motif DNA structures are formed in the nuclei of human cells (4/23/18)

Reported as: In human cells, scientists find DNA that looks like a twisted knot instead of a double helix (4/23/18)

Also reported as: New Twisted ‘Knot’ Human DNA Structure Discovered—and It Looks Nothing Like the Double Helix (4/23/18)

Christ’s lab showed that in vivo formation of I-motif structures is pH dependent. Clearly, the potential of hydrogen (pH) and pH-dependent cell cycles link the quantized energy of virucidal sunlight to protection from the degradation of messenger RNA that links mutations to all pathology.
In that context, denuclearization has been forced on North Korea and other communist countries by scientific creationists in South Korea. The creationists have indirectly revealed that they could decimate human populations in China via the creation of a virus with one base pair change linked to one amino acid substitution.
See also: Virus-mediated archaeal hecatomb in the deep seafloor

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

Until recently, the pseudoscientific nonsense about vaccines that could protect human populations from the forthcoming viral apocalypse was tightly linked from communism to atheism. For comparison, Christ’s lab appears to have put the fear of God into its proper context; the 1918 Spanish flu.
Previously reported as: Structural diversity of supercoiled DNA (2015) and parodied in:

See also: The Pharmacology of Regenerative Medicine (2013)
See also: Energy as information and constrained endogenous RNA interference (2017)

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

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

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA.

Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution.

The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

Witzhany2018

Sympatric speciation vs pseudoscientic nonsense (2)

This is how intermittent fasting protects us from viruses in the context of using stored fat for quantized energy-dependent RNA-mediated DNA repair.
Fat cells converted into stem cells can repair any damaged tissues (video 3:48)
Some whales use the molecular mechanisms of quantized energy-dependent RNA-mediated DNA repair during their migration, which is when they may not eat anything until after completing their route.
See for details: Energy as information and constrained endogenous RNA interference (video 6:46)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution.

The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

Whales are often reported to be the largest creatures on Earth. Some some whales eat large amounts of small creatures. That fact links the sympatric speciation of microbes to the sympatric speciation of all life on Earth via the biophysically constrained energy of sunlight and physiology of reproduction in cyanobacteria.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

Long-range coherence and energy storage in biological systems (1968) Published in: International Journal of Quantum Chemistry

The supplied energy is thus not completely thermalized but stored in a highly ordered fashion.

This notice just appeared in my email inbox with the new title from Aeon: Weekend Reads: Quantum biology and what life wants.
See for comparison: What life wants (2012)

…given that this sense of purposefulness is how we identify life in the first place, perhaps we should resist conclusions that seem to wave it away too easily.

I don’t pretend to have answers to any of these questions. On the other hand, the speed of progress in fields that cross the boundaries between natural sciences – not least quantum biology – makes me optimistic that we will get some, sooner or later.

Aeon magazine continues to attempt to obfuscate their history of horrid misrepresentations exemplified in articles like this:
Quantum common sense (2017)

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

See the sidebar:

“We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking”

See also: Schrödinger at 75 – The Future of Biology – September 2018
See also: What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry (2)

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Neo-Darwinian theorists dispense with Darwin’s food energy-dependent  “conditions of life.” They link mutations and disease to evolution via mathematical models. They exemplify human idiocy.
See for example: Neopterygian phylogeny: the merger assay
Reported as: Adaptive radiations in the Mesozoic

Bony fishes are the most diverse of all extant vertebrate groups. A comprehensive phylogenetic analysis of the group now provides new insights into its 250-million-year evolutionary history.

The claim about the 250-million-year evolutionary history can be compared to what happens when food energy-dependent fixation of a single RNA-mediated amino acid substitution occurs across a vertebrate lineage.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is very surprising and fascinating that the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.

Evolution does not select amino acids. Natural selection for food energy-dependent pheromone-constrained viral latency links the substitution of achiral glycine in position 6 of the GnRH decapeptide to the biodiversity of all morphological and all behavioral phenotypes in all vertebrates.
See also: Handbook of Biologically Active Peptides (2013) Chapter 106 GnRH (LHRH)
Page 794 Figure 2 shows that food energy-dependent substitution of achiral glycine at position 6 stabilizes the folded conformation; increases binding affinity; and decreases metabolic clearance.

This feature is incorporated in all agonist and antagonist analogs.

Simply put, the substitution of achiral glycine in the GnRH decapeptide biophysically constrains viral latency in the context of ligand-receptor interactions and the physiology of pheromone-controlled reproduction.
See also: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The facts that link vertebrates to invertebrates via olfaction and the 2013 model will almost undoubtedly be restated when Tuning Insect Odorant Receptors is published.
Until then, see:Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity (2005)
Biophysical constraints link feedback loops from odors and pheromones to the functional structure of the GnRH decapepetide via achiral glycine in position 6. The link from food to the de novo creation of energy-dependent receptors is required in all organisms. They must select the right food, which helps to ensure their ability to reproduce.

5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry

Summary: Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth
Stop this nonsense about de novo gene birth and you will help to stop the school shootings without more gun control.
See my presentation at the 2017 Precision Medicine Virtual Conference (2/15/17) Energy as information and constrained endogenous RNA interference
See also: Pat Sweeney et al (3/13/2017) Protein misfolding in neurodegenerative diseases: implications and strategies. 

A notable development is the creation of collaborative ecosystems that include patients, clinicians, basic and translational researchers, foundations and regulatory agencies to promote scientific rigor and clinical data to accelerate the development of therapies that prevent, reverse or delay the progression of neurodegenerative proteinopathies.

For consideration of protein folding in the context of my life’s works, see: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

Claudio Casola refers “… to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.” Use of the term ‘de nono’ to refute Pat Sweeney’s neo-Darwinian pseudosceintific nonsense is brilliant! For instance, all serious scientists know that protein folding chemistry is energy-dependent.
 
 

The structural diversity biophysically constrains viral latency and the constraints are referred to in the context of RNA-mediated autophagy. Autophagy clearly makes “de novo” gene creation a no-no term. That is why serious scientists are not likely to use the term de novo. It is like claiming that something automagically occurs.

In the context of what is known about energy-dependent cell type differentiation, see also:

Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis (2011)

and

Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone (2017)
The fact that food odors and pheromones biophysically constrain physical and mental pathology via alternative splicings of RNA has been addressed in published works since 1990.
See for a recent example: RNA splicing is a primary link between genetic variation and disease (2016)
See for examples of constraints:
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (E-pub 2014)
The catechol-o-methyltransferase Val158Met polymorphism modulates the intrinsic functional network centrality of the parahippocampal cortex in healthy subjects (2015)
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb (2016)
The COMT Val158Met polymorphism exerts a common influence on avoidant attachment and inhibited personality, with a pattern of positive heterosis (2017)
In the context of energy-dependent constraints, the COMT VaL158Met amino acid substitution exemplifies the facts detailed in the context of: Hydrogen bonds directly detected for the first time (2017). 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 (2017)
See also: Catechol O-methyltransferase (COMT) functional haplotype is associated with recurrence of affective symptoms: A prospective birth cohort study (1/15/2018)
Analysis of COMT Val158Met polymorphisms and methylation in Chinese male schizophrenia patients with homicidal behavior (2/20/2018)
Adjunctive nutrients in first‐episode psychosis: A systematic review of efficacy, tolerability and neurobiological mechanisms (3/21/18)
Reported as: Antioxidants and amino acids could play role in the treatment of psychosis 3/22/2018
See for comparison: March for Our Lives 3/24/18

Theme Gun violence awareness
Support of gun control

The focus on support of gun control ignores everything known to all serious scientists about biophysically constrained mental health and the virus-driven constraint-breaking mutations in the killers with guns. The future of school shootings depends on mental health treatment.

Why nutritional psychiatry is the future of mental health treatment

…29 clinical trials of antidepressant use in young people found no benefits at all. These trials revealed that instead of relieving symptoms of anxiety and depression, antidepressants caused children and young people to feel suicidal.

See for comparison: 7/25/13 Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

My understanding of biology is linked to my understanding of physics and chemistry via 40 years testing experience as a medical laboratory scientist (ASCP emeritus). Simply put, all organisms must eat and reproduce or species do not survive. The discovery of bacteria that eat electrons and create uranium ore was place into the context of this news:
Biologists discover electric bacteria that eat pure electrons rather than sugar, redefining the tenacity of life (2017)
The link from eating electrons to hydrogen-atom transfer in DNA base pairs in solution appears in the context of energy delivery to all cell types in organisms that have blood in their circulatory system. The claim that the human circulatory system evolved incorporates ‘de nono’ gene creation.
There is no such thing as de novo gene creation and ‘de nono gene creation’ can now be used in the context of post-publication ridicule of this model:
Basic Science Model of Blood as an Electron-Delivery Circuit Describes the Evolution of the Human Circulation (2017)
The anti-entropic virucidal energy of sunlight is the link from ecological variation to ecological adaptation in the context of the physiology of reproduction and biophysically constrained viral latency. Pseudoscientists will not stop trying to place that fact into the context of ridiculous neo-Darwinian theories.
Thankfully, ages 10+ can learn how energy-dependent life is biophysically constrained by playing the cell biology game “Cytosis” and the game that links energy-dependent changes from electrons to ecosystems in all living genera: “Subatomic“.
See my attempt to deliver that message in: There is no such thing as de novo control of electrons or the self-assembly of genes. (11/21/17)
But see: Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth
Stop this nonsense and you will help to stop the school shootings without more gun control.

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Ecological adaptation: A new definition of heredity (3)

Excerpt:
Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

OMCD: OncoMir Cancer Database

Dysregulation of miRNAs is commonly observed in cancers and it largely cancer dependent.

The virus-driven theft of quantized energy as information has been linked from changes in the microRNA/messenger RNA balance to all pathology. That fact replaces the circular logic that links cancer-dependent dysregulation of miRNAs to cancer.  Simply put, the proliferation of viruses cause cancer. The proliferation of viruses is energy-dependent in the context of established links from atoms to ecosystems in all living genera.
See: Subatomic: An Atom Building Board Game

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!

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

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.

Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

My “Disqus” comment (and nearly 2000 others): Gene expression is energy-dependent, RNA-mediated, and biophysically constrained.
See: FUS Regulates Activity of MicroRNA-Mediated Gene Silencing.

MicroRNA-mediated gene silencing is a fundamental mechanism in the regulation of gene expression.

MicroRNAs do not create themselves.
See also:  Energy as information and constrained endogenous RNA interference
8 of my 9 most recent comments to Disqus have been removed.
See for comparison: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Reported as: In nature, an imperfect immune system drives the evolution of deadly pathogens

…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.

…lower virulence strains could be their own worst enemies, creating a population of hosts that are resistant to them but not the higher virulence strains that remain.

By removing my Disqus comments, the moderators limit discussion of the facts about virus-driven energy theft, which links mutations to all pathology.  That allows the biased reporting on preprints that continue to try to support the ridiculous concept of neo-Darwinian evolution.
It also prevents the realization of goals by serious scientists who have linked the biogenic creation of uranium ores to the prevention of radiation sickness via microRNA therapy. See, for examples: miRNA-mediated therapies
A miRNA-145/TGF-beta1 Negative Feedback Loop Regulates the Cancer-Associated Fibroblast Phenotype

…miR-145 is a key regulator of the CAF phenotype, acting in a negative feedback loop to dampen acquisition of myofibroblastic traits, a key feature of CAF associated with poor disease outcome.

See also: Microhomology-assisted scarless genome editing in human iPSCs

Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.

Reported as: Gene Editing Is Now Precise Enough to Modify a Single Letter of DNA

To make these very precise edits, an SNP modification is first inserted alongside a fluorescent reporter gene that helps researchers to identify modified cells. The researchers engineered a duplicate DNA sequence known as a microhomology (hence the technique’s name) on each side of the fluorescent gene, targeting sites for CRISPR to go in and cut DNA. The researchers were then able to use a DNA repair system known as microhomology-mediated end joining (MMEJ) to remove the fluorescent gene. That left only the single-base edit, in the form of an SNP, behind.

See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Nuclear envelope-derived autophagy (NEDA) appears to be a cellular stress response, which is triggered late during HSV-1 infection. An energy-dependent single nucleotide repeat (SNR) might compensate for the viral alteration of the macroautophagic response. At this level of hydrogen-atom energy transfer in DNA base pairs in solution, the link to supercoiled DNA and viral latency becomes increasingly important.
Theorists are angry because they have been left behind. They know very little about what is important. That was expected by all serious scientists, especially those who have accumulated decades of testing experience while working in medical laboratories.
See for example: Applications of ligation-mediated PCR

Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:

The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.
The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.

It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.

Biologically uninformed theorists cannot even speak the same language. They do not start with a molecular energy source for base pairing and microRNA-mediated amino acid substitutions that differentiate all cell types. Instead, mutations are linked to increasing organismal complexity via the magic of evolution.

5th-6th Sept 2018 Dublin, Ireland

Ecological adaptation: A new definition of heredity (1)

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
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.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression December, 2014

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

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (5)

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)


The list of those scheduled to present has changed. Michael Rosbash has been added. John E. Walker is not scheduled, which suggests that everyone else already knows that the creation of the sun’s anti-entropic virucidal energy is the link from the creation of ATP to the creation of RNA and all biophysically constrained viral latency via feedback loops and the physiology of reproduction.
Rosbash, as all serious scientists know,  started with energy-dependent changes in cycles of RNA biosynthesis. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990). Pseudoscientists failed to link the energy from feedback to biophysically constrained viral latency.
But see: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM).

Other serious scientists have consistently linked photophosphorylation from oxidative phosphorylation to all biodiversity via the physiology of pheromone-controlled reproduction in species from soil bacteria to humans
Speakers (new copy-protected list)
Speakers (old list)
See also: Viral Resistance Project
The differences in innate immunity and ecological adaptation are obviously nutrient energy-dependent and transgenerationally inherited in the context of the epigenetically-effected physiology of pheromone-controlled reproduction and the affects of hormones on behavior. For instance, pheromones biophysically constrain viral latency via the fixation of amino acid substitutions.
See for comparison: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
There are several neo-Darwinian theorists who are scheduled to present, which means they may be ready to accept the ridicule from serious scientists.
See for example: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

See also: Why I got rid of my friends
Some of my former friends kept dumping their garbage about evolution on others in the same way that I. King Jordan and Eugene Koonin did it with their comment about the evolution of the amino acid composition of proteins. See for comparison: All About that Base (Meghan Trainor Parody) 12/10/14 and Energy as information and constrained endogenous RNA interference 2/15/17
Help others who are Combating Evolution to Fight Disease

For God and Country

Diet-driven RNA interference and cancer prevention (4)

Excerpt: What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
“micrornas”[MeSH Terms] OR “micrornas”[All Fields] OR “microrna”[All Fields] Items: 1 to 20 of 68871
See:  The tipping point (revisited): 68,000 publications
69,000 published works on microRNAs will be the next “tipping point.” Predictably, it will be reached during the same 28 day period in which my tweets (@jvkohl have received more than 70,000 impressions.
On 1/18/18: Tweet impressions 71.2K 602.0%
The 602.0% increase has not been accompanied by a significant increase in followers or a significant increase in engagements.
What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
See: A curcumin-loaded polymeric micelle as a carrier of a microRNA-21 antisense-oligonucleotide for enhanced anti-tumor effects in a glioblastoma animal model

DP-Cur is an efficient carrier of miR21ASO and the combined delivery of miR21ASO and curcumin may be useful in the development of combination therapy for glioblastoma.

See also: Pharmacological blockade of ASCT2-dependent glutamine transport leads to antitumor efficacy in preclinical models

This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in oncology, representing a new class of targeted therapy and laying a framework for paradigm-shifting therapies targeting cancer cell metabolism.

Reported as: Researchers find a way to ‘starve’ cancer

Glutamine is an essential amino acid for many cell functions including biosynthesis, cell signaling and protection against oxidative damage. Because cancer cells divide more rapidly than do normal cells, they need more glutamine.

A protein called ACST2 is the primary transporter of glutamine into cancer cells. Elevated ASCT2 levels have been linked to poor survival in many human cancers, including those of the lung, breast and colon. Genetic studies that silence the ACST2 gene in cancer cells have produced dramatic anti-tumor effects.

See also: MicroRNA[s] and glutamine Items: 1 to 20 of 65
The facts about food energy-dependent microRNA-mediated RNA-directed DNA methylation and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera were removed from this report. Use off the cryo-EM technology links energy-dependent changes in electrons to healthy longevity in all ecosystems. It is apparent that some researchers do not want more people to learn about that fact.
See: Structural basis of RNA polymerase III transcription initiation

The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.

The information that links the virus-driven theft of quantized energy from the negative supercoiling (unwinding) of supercoiled DNA was removed in this attempt to support the neo-Darwinian pseudoscientific nonsense about the three domains of life. The bastardization of the use of cryo-EM technology occurred in the following context(s).
1) There is no mention of the quantized anti-entropic virucidal energy as information that is required to create ATP and RNA.
2) The energy-dependent creation of ATP and the creation of RNA is not linked to healthy longevity in all living genera via the physiology of pheromone-controlled reproduction.
3) The fixation of RNA-mediated amino acid substitutions that stabilize the differentiated cell types of all living genera are viewed in the context of negative supercoiling that occurs in an ATP-independent manner.
4) A spontaneously formed transcription bubble links the energy-dependent stability of supercoiled DNA to cell type differentiation in species from bacteria to humans.
5) The claim that promoters can be opened without ATP hydrolysis is used to suggest that no energy-dependent supercoiling is required to link the three kingdoms of life — assuming that there are three kingdoms of life.
6) The fact that the virus-driven degradation of messenger RNA in humans causes them to become non-human primates and the fact that it also cause bacteria to archaea and L-forms is ignored.
See: Virus-mediated archaeal hecatomb in the deep seafloor

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

By deliberately removing virus-archaea interactions from the representations reported as: Scientists zoom in to watch DNA code being read, pseudoscientists have reverted to promotion of their ridiculous gene-centric theories.
See for comparison: “Cytosis

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

See also: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.

Accurate representations of how natural selection for food energy-dependent codon optimality links the physiology of pheromone-controlled reproduction to the transgenerational epigenetic inheritance of healthy longevity will continue to be attacked from all sides.
Biologically uninformed theorists and philosophers can do nothing else but attack after proclaiming the nonsense of mutation-driven evolution during the past decades. They have failed to link their nonsense to the prevention of all pathology or to effective treatments via optimization of autophagy: the innate antiphage defense mechanism of all living genera.

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Light-activated error free DNA repair

Summary: The same set of microRNAs controls expression of the genes for rate-limiting enzymes, which control differences in the hormone production of different hormones in insects and crustaceans. That fact led to this claim in: The secret to safe DNA repair.

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

The Secret to Long Life? It May Lurk in the DNA of the Oldest Among Us

If unusual patterns in their three billion pairs of A’s, C’s, G’s and T’s — the nucleobases that make up all genomes — can be shown to have prolonged their lives and protected their health, the logic goes, it is conceivable that a drug or gene therapy could be devised to replicate the effects in the rest of us.

The unusual patterns exist only in the context of error-free RNA-directed DNA repair. DNA repair is linked from the energy-dependent creation of one enzyme and the metabolism of food to species-specific pheromones.
The secret to safe DNA repair.

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

The pheromones control the physiology of reproduction. In the mouse model, pheromones have repeatedly been linked to epigenetic effects on gene regulation.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] 1994

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.
 

The virus-driven degradation of messenger RNA has since been linked to all pathology. Food odors and pheromones biophysically constrain the transgenerational epigenetic inheritance of viral latency via the creation of amino acid substitutions that differentiate all the cell types of all individuals of all individuals of all species.
When all serious scientists fully disclose what is known about the biophysically constrained energy-dependent links from 1) base editing and 2) microRNA editing to 3) RNA editing and RNA-mediated DNA repair, pseudoscientists will be put out of the business of drug development. Medical practice will be based on what is known about Precision Medicine, which specifically links the food energy-dependent creation of enzymes to healthy longevity and to the metabolism of the drugs that often do more harm than good.
1)
Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

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

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
2)
Conserved microRNA editing in mammalian evolution, development and disease
MicroRNA (miRNA) editing is a site-specific conserved mechanism that links ecological variation to energy-dependent ecological adaptations via the physiology of pheromone-controlled reproduction, which increases the functional diversity of mammalian miRNA transcriptomes. These authors place microRNA editing into the context of an “evolutionarily stable feature” without explaining how the energy-dependent stability was linked to biophysically constrained viral latency.
3)
RNA Editing Possible with CRISPR-Cas13
Serious scientists moved forward by calling pre-mRNAs “microRNAs.” They linked energy-dependent alternative splicings to all biodiversity via fixation of amino acid substitutions in the context of the pheromone-controlled physiology of reproduction. Now, Zhang and others make the claim that’s akin to saying they rediscovered the innate immune system, which biophysically constrains viral latency.
The so-called secret to the three-step recognition of the pattern linked to longevity may be as simple as this: Learn how anything you eat or drink may be beneficial and do not take drugs that will kill you by stealing the quantized energy as information that McEwen et al. (1964) linked the light-activated creation of ATP to the food energy-dependent creation of RNA.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

See also: Dobzhansky (1964): Biology, molecular and organismic

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

See also: Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, 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.

All serious scientists know that the creation of the sun’s anti-entropic virucidal energy must be linked from ecological variation to ecological adaptations, whether or not they refer to light in the context of evolution. Nothing makes sense when theorists fail to link the speed of light on contact with water from the creation of enzymes to the metabolism of food. And nothing else about food energy makes sense when pseudoscientists fail to link it to the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences (2015)
Reported as:‘Junk DNA’ Used To Sort Species and also as: All in the (bigger) family with my comment:

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400
Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.
Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.
Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.
Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior