5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

Lethal virus kills 5 billion people?

The "walking fish" walks straight from quantum physics to quantum souls (5)

Evolutionary determinants of genome-wide nucleotide composition January 1, 2018
1) They place their thoughts about mutation rates into the context of compatibility with mutational spectra.
2)They claim the mutation rate can be linked to mutational spectra that may be free to wander across evolutionary time.
3) They ignore facts that link the energy-dependent maintenance of a suppressed constant genome-wide deleterious rate that obviously occurs in the context of the Virus-mediated archaeal hecatomb in the deep seafloor
4) They eliminate the need for food energy and the pheromone-controlled physiology of reproduction, which protect all organized genomes from the virus-driven degradation of messenger RNA.
5) They link the mutations caused by the degradation of messenger RNA to increasing organismal complexity via mutational spectra.
Summary, these researchers appear to be biologically uninformed science idiots.
See also Luo lab at CUHK publications Microbial Evolution and Ecology
The fact that microbes do not evolve and the fact that ecological variation is biophysically constrained by the food energy-dependent pheromone-controlled physiology of reproduction does not appear to have occurred to any coauthors of any articles from this group with one notable exception.
Singlecell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

Viruses are the most abundant biological entities on Earth, surpassing the number of their potential host cells by at least one order of magnitude (). In the ocean, viral infections kill ~10–20% of planktonic biomass each day (; ). These infections are believed to have a major impact on microbial community composition, evolution and global geochemical cycles ().

See also: Marine phage genomics: the tip of the iceberg
At some point, all serious scientists expect others to acknowledge the fact that the role bacteriophages play in pathology extends from marine phage genomics to the energy-dependent antiphage defense mechanism referred to as autophagy. Autophagy links food energy from the biophysically constrained pheromone-controlled physiology of reproduction to healthy longevity in all living genera.  The facts about autophagy refute all the pseudoscientific nonsense touted by theorists.
See for instance: Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.

The resolve of the carbon and nitrogen enrichment in P. fluorescens was linked to autophagy via the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The claim about the “evolutionary resurrection” exemplifies the amount of pseudoscientific nonsense that theorists have placed into the context of energy-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all living genera.
A single nucleotide polymorphism (SNP) in ntrB in strain AR2S caused an amino acid substitution [Thr97→Pro97 (T97P)] within the PAS domain of the enzyme sensor NtrB.  Another SNP in the fast-spreading strain AR2F in the σ54-dependent EBP gene ntrC alters an amino acid (R442C) within the DNA binding domain. The alteration in the two amino acids were reported as if they were mutations in the context of evolution, which occurred over-the-weekend.
See for comparison Diet and cancer prevention: Dietary compounds, dietary MicroRNAs, and dietary exosomes October 4, 2017

,,,a variety of dietary compounds such as curcumin, green tea, folat, selenium, and soy isoflavones show a wide range anti-cancer properties. It has been showed that these compounds via targeting a sequence of cellular and molecular pathways could be used as suitable options for cancer chemoprevention and cancer therapy. Recently, dietary microRNAs and exosomes have been emerged as attractive players in cancer prevention and cancer therapy. These molecules could change behavior of cancer cells via targeting various cellular and molecular pathways involved in cancer pathogenesis. Hence, the utilization of dietary compounds which are associated with powerful molecules such as microRNAs and exosomes and put them in dietary patterns could contribute to prevention or treatment of various cancers.

Natural agents mediated autophagic signal networks in cancer

When growth factors are withdrawn, the autophagosome forms to induce autophagy [14].

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
Classical physics cannot explain how Darwin’s “conditions of life” are linked to the biophysically constrained energy that is released during cell type signalling, which appears to be absolutely and precisely quantized in the context of tunnelling. However, nothing known to serious scientists about tunneling has been linked from experimental evidence of top-down causation to the energy-dependent tunneling. The spurious use of the term “evolution” should be placed into that context.
Docosahexaenoic acid–mediated, targeted and sustained brain delivery of curcumin microemulsion

Conclusion: The superiority of CUR DHA ME in enabling targeted brain delivery of CUR by both intravenous and intranasal administration presents this new formulation as a promising and versatile formulation for application in brain cancer.
MicroRNA: A Novel Target of Curcumin in Cancer Therapy

…curcumin has a variety of pharmacological effects such as antioxidant, anti-cancer, anti-inflammatory, and anti-microbial activities. Anti-cancer effects of curcumin are due to targeting of a wide range of cellular and molecular pathways involved in cancer pathogenesis including NF-kB, MAPK, PTEN, P53, and microRNAs (miRNA) network. Multiple lines of evidence have indicated that curcumin exerts its therapeutic effects via regulating miRNA expression (e.g. miR-1, miR-7, miR-9, miR-34a, miR-181, miR-21 and miR-19) which could lead to the regulation of underlying cellular and molecular pathways involved in cancer pathogenesis.

At some point, the facts must be recognized by even the most biologically uninformed researchers in the world. See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Electron cloud superimposed on the yin yang symbol

The "walking fish" walks straight from quantum physics to quantum souls (4)

Excerpt: During the past 21 months, others have either learned nothing about microRNAs or they have ignored the fact that virus-driven energy theft is not the same as energy dissipation in the context of food energy (the quantized energy as information that is used by viruses to create the amino acid substitutions that stabilize their RNA and DNA).

The dark side of the new popularity of cryo-electron microscopy

…we need to stand together as a field, and support our colleagues by accepting to review their papers and grant applications in order to ensure a fair evaluation. In my opinion, we need to collaborate, support and acknowledge each other as best as we can so we can successfully move forward together into a bright future in cryoEM.

This invited review of nutritional epigenetics was returned without review.  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Food energy-dependent changes in base pairs were linked to ecological adaptation in species from microbes to humans via methylation and the fixation of RNA-mediated amino acid substitutions. There is no dark side to cryo-electron microscopy (cryoEM), and Ariane Briegel knows that. See: Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling (2014)

  1. …methylations confer adaptation on the system, modulating its response based on recent environmental conditions (Kleene et al., 1979; Toews et al., 1979; Lupas and Stock, 1989). The architecture of these membrane-bound chemoreceptor arrays is not specific to E. coli, indeed it is universal among bacteria (Briegel et al., 2009). The architecture of these arrays is likely key to the high sensitivity, wide dynamic range, cooperativity, and feedback control of this system…
  2. Interestingly, while transmembrane arrays remain intact upon cell lysis, presumably due to the stabilizing effect of the membrane, cytoplasmic arrays fall apart unless molecular crowding agents are added. This suggests that cellular crowding contributes to the stability of the array and may be an important factor in assembly of these, and likely other, cellular structures (Ellis, 2001; Zhou et al., 2008; Zhou, 2013). We observe the same requirement for molecular crowding (mimicking the cellular environment) in our in vitro preparation from E. coli. This supports the idea that chemoreceptor interactions can be enhanced by membrane binding (Shrout et al., 2003), but in the absence of a membrane, this can be achieved by molecular crowding and sandwiching (Fowler et al., 2010).

Briegel et  al., (2014) reestablished the facts from our 1996 review of biophysically constrained RNA-mediated cell type differentiation. See the molecular epigenetics section of From Fertilization to Adult Sexual Behavior.
Life on Earth exists within the confines of the energy that is required to maintain the functional structure of the cell membrane. The crowding of food energy-dependent microRNAs in the cell membrane is reduced by virus-driven energy theft. 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.

Bacteria become archaea and archaea become L-forms (with no cell wall).
See: L-form bacteria cohabitants in human blood: significance for health and diseases
That significance of L-forms was not placed into the context of this representation of how serious scientists will prevent or begin to effectively treat all virus-driven pathology in the context of what has been revealed by the cryoEM technology.
See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels
The circadian cycling of energy-dependent microRNA-mediated protein biosynthesis and degradation has been linked to healthy longevity via what is known about quantum physics and the link from quantized energy as information to quantum souls via hydrogen-atom transfer in DNA base pairs in solution that link microRNA flanking sequences in exosomes to RNA-mediated DNA repair.
See: Exosomes from human umbilical cord blood accelerate cutaneous wound healing through miR-21-3p-mediated promotion of angiogenesis and fibroblast function (Jan 1, 2018)

It has been shown that exosomes contain large amounts of miRNAs and can serve as vehicles to transfer miRNAs to recipient cells, where the exogenous miRNAs can alter the gene expression and bioactivity of recipient cells [28].

28. Au Yeung CL, Co NN, Tsuruga T, Yeung TL, Kwan SY, Leung CS. et al. Exosomal transfer of stroma-derived miR21 confers paclitaxel resistance in ovarian cancer cells through targeting APAF1. Nat Commun. 2016;7:11150

These data suggest that the malignant phenotype of metastatic ovarian cancer cells can be altered by miR21 delivered by exosomes derived from neighbouring stromal cells in the omental tumour microenvironment, and that inhibiting the transfer of stromal-derived miR21 is an alternative modality in the treatment of metastatic and recurrent ovarian cancer.

All experimental evidence of biophysically constrained viral latency links the food energy-dependent creation of microRNAs from the bioreactivity of recipient cells to healthy longevity via  protection from the virus-driven degradation of messenger RNA, which all serious scientists have linked from mutations to all pathology.

See this presentation from a Precision Medicine virtual conference for review

See also:

Mar 2, 2016  From hydrogen atom transfer in DNA base pairs to ecosystems
Mar 2, 2016  RNA mediated molecular epigenetics and virus driven entropy
Mar 30, 2016 What is life when it is not protected from virus driven entropy
May 3, 2016  RNA-mediated physics, chemistry, and molecular epigenetics

Not only did Telepresence robots let employees ‘beam’ into work (December 24, 2012), telecommuting established my ability to disseminate accurate information about biophysically constrained biologically-based cause and effect to those who want to inform themselves. After I learned about microRNAs during the 2012 Society for Neuroscience annual meeting, I did not waste anymore time or money attending scientific conferences. It became perfectly clear that biologically uninformed theorists ignored the facts that link the creation of energy-dependent microRNAs to healthy longevity — if only because I had never heard of them.

During the past 21 months, others have either learned nothing about microRNAs or they have ignored the fact that virus-driven energy theft is not the same as energy dissipation in the context of food energy (the quantized energy as information that is used by viruses to create the amino acid substitutions that stabilize their RNA and DNA.

See for comparison: Quantum secret sharing for a multipartite system under energy dissipation!

Only the virus-driven theft of quantized energy has been linked to all pathology in all living genera.

That fact makes this fact perfectly clear. Scientific progress toward the prevention or effective treatment of all pathology has been delayed at every level of examination by theorists. See for example:

 Complex Mutations can Help Drive Evolution

“This study is the first of its kind in complex organisms like the fruit fly. With this unique resource in hand, we have already characterized several candidate structural variation which show evidence for phenotypic adaptation, which can function to drive species evolution,” explained Emerson.

Species do not evolve. Natural selection for energy-dependent codon optimality links food energy from ecological variation to fixation of RNA-mediated amino acid substitutions in organized genomes via DNA repair. The RNA-mediated DNA repair is evidence of how organisms phenotypically adapt.
Food odors and pheromones biophysically constrain ecological adaptations in species from mice to humans. That fact was established via the works of people such as Eugene Daev, who used experimental evidence of biophysical constraints in their refutation of neo-Darwinian pseudoscientific nonsense.
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.

See also: Size matters – the olfactory bulb as a marker for depression (2017)

We assume that reduced neural olfactory input to subsequent limbic and salience processing structures moderates this relation. However, the OB was in an inferior position compared to conventional questionnaires for diagnosis of depression.

Despite two decades of scientific progress, the authors assume that the link between olfaction and emotion processing structures may not be as strong in humans compared to mice. They are either biologically uninformed, or they are lying. In either case, serious scientists do not base their claims on ridiculous assumptions. There may be no serious scientists who have ever worked with Thomas Hummel.
See: Hummel T and microRNA
See for comparison: The tipping point (revisited): 68,000 publications
See also: Feedback loops link odor and pheromone signaling with reproduction (2005) and Olfaction Warps Visual Time Perception (2017)
Attacks on my scientific credibility by Nik Wilmore, who claims these credentials Chemist (Columbia/Harvard), can be linked to this Historical Perspective as the obvious basis for social media attacks by biologically uninformed chemists and other theorists:
A fear of pheromones (1971)

WHAT are we going to do if it turns out that we have pheromones? What on earth would we be doing with such things? With the richness of speech, and all our new devices for communication, why would we want to release odors into the air to convey information about anything? We can send notes, telephone, whisper cryptic invitations, announce the giving of parties, even bounce words off the moon and make them carom around the planets. Why a gas, or droplets of moisture made to be deposited on fenceposts?

Similarly, what are we going to do if it turns out that food odors are the link from quantum physics to quantum souls, and that only pheromones biophysically constrain the virus-driven entropy of organized genomes?
Let food be thy medicine and medicine be thy food.” ― Hippocrates
There are in fact two things, science and opinion; the former begets knowledge, the latter ignorance.” ― Hippocrates
Declare the past, diagnose the present, foretell the future.” ― Hippocrates
Wherever the art of Medicine is loved, there is also a love of Humanity. ” ― Hippocrates
Wherever Money is loved, it is loved more than the Art of Medicine and more than Humanity. ― James V. Kohl
See Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See for comparison: 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

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.

Only if you ignore everything that could be learned about cell biology by playing the game “Cytosis,” could you continue to believe in the ridiculous theories of “Big Bang” cosmologists and neo-Darwinian theorists.

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

Darwin’s “conditions of life” and Kohl’s Laws of Biology attest to the fact that food energy-dependent RNA-mediated DNA repair biophysically constrains viral latency. Changes in the diet lead to ecological variation or from virus-driven energy theft to mutation-driven pathology.
The only recommended use for the term evolution is in the context of the evolution of virus-driven pathology.
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.

See for comparison: Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

We provide a high-resolution cryo-EM structure of a virus-ICAM-1 complex, which revealed critical ICAM-1-binding residues. These data could help identify a possible conserved mode of receptor engagement among ICAM-1-binding enteroviruses and rhinoviruses. Moreover, we identify a single capsid substitution that has been adopted by all pandemic CV-A24v strains and we reveal that this adaptation enhances the capacity of CV-A24v to bind sialic acid. Our data elucidate the CV-A24v receptor repertoire and point to a role of enhanced receptor engagement in the adaptation to the eye, possibly enabling pandemic spread.

The theft of quantized energy as information is linked to the adaptation of the virus. The creation of sunlight an its contract with water typically links the anti-entropic virucidal effects of the sun’s energy from food energy and the pheromone-controlled physiology of reproduction to fixation of amino acid substitutions in the organized genomes of all living genera. If Baggen et al., (2017) Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus was an accurate representation of how viral latency is biophysically constrained, the experimental evidence could help others to maintain their mental health.
See: Avoiding spiritual struggles and existential questions is linked with poorer mental health

Among the study’s findings:

  • An unwillingness to accept spiritual struggle could contribute to major social ills, leading to lost opportunities to engage with people of different faith beliefs and backgrounds and come to view them as threatening.

“This avoidance may lead to the rejection of whole groups of people based on their religious differences or perceived incongruence between, for example, their sexuality or gender-based identity and religious teachings,” Exline said.

  • Mental health providers may find it useful to help clients with spiritual struggles face their difficulties in a more proactive way.

“People seem to be more emotionally healthy if they’re able to accept troubling thoughts,” Exline said. “Looking at spiritual doubts in an objective way seems to help. You may or may not work through them, but at least you can tolerate having them.”

  • Avoidance itself is not a problem; rather, the behavior can become problematic when escaping becomes harmful or contrary to personal goals and sets a rigid pattern of experiencing and responding to the world.

“Regular spiritual avoidance can make it difficult to identify, work toward or experience the qualities that lend a sense of purpose to life,” she said.

  • Using emotional and cognitive energy to push thoughts away will not stop them from continuing to intrude over time.

“Continually being re-visited by these thoughts can create strains on emotional health, especially if a person sees this kind of questioning as morally unacceptable and dangerous,” Exline said.

See for comparison: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone

Dose of TRH is 200 μg and can be given once in a day. In the present study, an attempt has been made to prepare nasal spray of TRH by optimizing its pH, viscosity, osmolality and formulation parameters for use in crisis management.

The optimization of pH is essential in the context of prevention and all treatments that act on the potential of hydrogen. I don’t know of anything in life that does not act on the potential of hydrogen in the context of hydrogen-atom transfer in DNA base pairs in solutuon..
See also: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene

Together, these results provide an in-depth analysis of miRNA dysregulation in glioblastoma and demonstrate the potential utility of these data in the design of miRNA-regulated therapies for the treatment of brain cancers.

Dietary energy substrates reverse early neuronal hyperactivity in a mouse model of Alzheimer’s disease

See also: Lack of sleep boosts levels of Alzheimer’s proteins December 28, 2017
In the study, people who took sleep medication had levels of amyloid beta no lower than people who had slept normally.
See for comparison: microRNA Alzheimer’s 
See also: Blind Loyalty – Why Civil Discourse is Dead October 14, 2017

The more we are tied to something, the stronger our reaction to it. I believe this is the problem with modern politics. We, both sides, have become so tied to our ideals that we cannot have a rational discussion about anything that goes against them.

The politicized practice of medicine prevents recognition of the facts established by serious scientists. For example, the innate antiphage defense system protects all organized genomes from virus-driven entropy via autophagy. That fact was placed into the context of the cell biology game Cytosis.
See also the discussion of Mitochondrial metabolite linked to regulation of neurotransmission

Pat Sweeney I am beginning to think that the genes in the mitochondria that direct the assembly of some of the necessary factors for nerve firing, are in cell types that have not had enough time to evolve or move the genes to the nucleus yet. Other cell types have had enough time to evolve or duplicate the mitochondrial genes into the cell genome and mutate them out of the mitochondrial genome.
Mitochondrial Genes Move to the Nucleus — but it’s not for the sex. The loss of endosymbiont genes can be complete, in which lost genes are absent from the host–endosymbiont complex, a substitution, in which a nuclear allele functions in place of the lost symbiont gene, or a functional transfer of an endosymbiont gene to the nucleus, followed by its loss (Adams and Palmer 2003). Such “functional transfer” involves the relocation of a mitochondrial gene to the nucleus, its acquisition of a promoter, successful targeting to the mitochondria for proper function, and the eventual loss of the gene from the mitochondrial genome altogether. Although this process is probably quite complex and requires numerous evolutionary modifications (Murcha et al. 2005), there is evidence that some mitochondrial genes are preadapted to functional transfer as they contain signals that target them to the mitochondria before functional transfer to the nucleus (Ueda et al. 2008a).
He cited: The Functional Transfer of Genes From the Mitochondria to the Nucleus: The Effects of Selection, Mutation, Population Size and Rate of Self-Fertilization (2009)
and Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade (2013)

My response:

I am beginning to think that some people still do not realize that cell types do not evolve. But now, Pat Sweeney makes claims that differentiate the terms “evolve or duplicate” from phrases such as “mutate them out of the mitochondrial genome” and “evidence that some mitochondrial genes are preadapted.”

The preadaptations are quantized energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction. There is a model for that.

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

There is still no mathematical model of biologically-based cause and effect for comparison, which is why all serious scientists are laughing at the pseudoscientists who still tout “evolution” as an explanation for cell type differentiation in different species that must eat to reproduce.
See for comparison: Impaired mitochondrial β-oxidation in cardiomyocytes: role of the cardiac renin-angiotensin system and miR-208 Wednesday, January 24, 2018
In this webinar we will discuss [facts]:

  • Analysis of mitochondrial function in cardiomyocytes using Agilent Seahorse XF technology
  • Application of mito stress test, glycolysis stress test and palmitate oxidation assays in HL-1 cardiomyocytes
Electron cloud superimposed on the yin yang symbol

The "walking fish" walks straight from quantum physics to quantum souls (3)

The molecular dynamics of the hydrophobic amino acid, valine, link the anti-entropic virucidal energy of sunlight from the Second Law of Thermodynamics to the energy-dependent and temperature-dependent orientational dynamics of the structure of water via methylation and acetylation in the C and N terminus, respectively.
The quantized energy of sunlight must be linked from energy as information to energy-dependent methylation and acetylation to all biodiversity via the effect of the energy on contact with water and the physiology of pheromone-controlled reproduction in the context of changes in base pairs and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all living genera.
Philip Ball inadvertently claims to have missed all the scientific progress during the past 5 decades in: Chiral water in DNA’s hydration shell

I missed previously this nice paper from H. F. M. C. Martiniano and Nuno Galamba in Lisbon on the structure and dynamics of water around a hydrophobic amino acid…

Philip Ball’s admission can be linked to the ignorance of food energy-dependent pheromone-controlled biophysically constrained viral latency in all living genera. Food energy links sunlight on contact with water to hydrophobicity in supercoiled DNA.
From last year: Worms dine on nanoparticles to help test biological force sensor technology

Adding to Goodman’s previous research on how neurons process the sensation of touch, this technique could also enhance our understanding of the forces involved in sensing the world around us. “More detail about how we experience touch could inform the translation of touch into non-biological systems, like prosthetics,” Goodman said.

The spurious link from touch to biological systems and/or non-biological systems makes it seem that — like Philip Ball — they are oblivious to the fact that serious scientists linked 

1) the de novo creation of anti-entropic virucidal light to

2) chirality, which links

3) the speed of light

4) on contact with water from the

5) de novo creation of G protein coupled receptors and

6) all energy-dependent biodiversity via

7) the innate immune system,

8) autophagy,

9) the physiology of reproduction, and

10) supercoiled DNA, which

11) protects all organized genomes from

12) virus-driven energy theft and

13) genomic entropy.

The thirteen steps that link sunlight to healthy longevity and the virus-driven theft of quantized energy to all pathology were placed into a context of a section in the news report on worms:

From worm food to human health

The fact that worms and humans must eat to be healthy was not included in the publication on touch in July 2017 as Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces.
The link from nanoparticles to optical sensors via micro-Newton forces preceded retractions of two works that reported on the automagical creation of RNA.
The creation of RNA is food energy-dependent and it was linked from the creation of ATP to all biodiversity in 1964.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

See for comparison: ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

Philip Ball has now linked what he calls Chiral water from the structure and dynamics of water around a hydrophobic amino acid to supercoiled DNA, which links sunlight and food energy to protection of all organized genomes from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA links the theft of quantized energy from mutations to all pathology. Nothing from the claims about optical sensors is pertinent outside the context of the fact that all organisms must find food and reproduce for any species to survive.

That is why I am adding my comments from last year on: Worms dine on nanoparticles to help test biological force sensor technology. Philip Ball must have missed these facts, also.

Two epigenetic traps are required to link hydrogen-atom transfer in DNA base pairs in solution to the energy-dependent physiology of pheromone-controlled reproduction. It is unlikely that the traps automagically emerged and more unlikely that any species has ever evolved from any other species via mutations and natural selection. Instead, the epigenetic traps make it perfectly clear that evolutionary theorists and “big bang” cosmologists know nothing about energy-dependent biophysically constrained RNA-mediated cell type differentiation.

That fact may explain why Vice-President Pence wants the students in public schools to be taught how ecological variation must be linked to ecological adaptation via everything known to physicists, chemists, and biologists. All serious scientists have linked what is known about molecular epigenetics from energy-dependent changes in electrons to to ecosystems in all living genera.

If we raise another generation of students who are biologically uninformed, some human populations in the USA might as well agree to be the naturally selected victims of the forthcoming viral apocalypse. When large populations begin to suffer unnecessarily and die prematurely, the 1918 Spanish flu will be remembered as the harbinger of ignorance that led to the suffering and death of millions, mostly in the cities of the USA. That’s where the panic and riots start.

You’ve read about this in books (Arrowsmith, 1925) and seen the movies. Prepare yourself for the reality of energy-dependent chirality. It’s the First Law of Thermodynamics that everyone must eventually accept. Food energy is biophysically constrained in all cell types until the virus-driven theft of quantized energy links the degradation of messenger RNA from mutations to all pathology.

It would be great if that fact was taught in public schools instead of teaching students to believe in pseudoscientific nonsense. In any case, the sun’s anti-entropic virucidal energy cannot simply be removed from consideration by theorists and/or so called science journalists who have failed to link quantum physics to quantum souls.

See for comparison: Quantum secret sharing for a multipartite system under energy dissipation

… noise is associated with energy dissipation and hence, loss of probability to distinguish and decode the information at the receiving end. Finally, we make this task possible through an optimization algorithm.

In their optimization algorithm, a mathematical model is applied to all forms of life on Earth but the dissipation of energy is not linked to death. Everyone who believes that energy cannot be created or destroyed knows that there is no “quantum secret.” Dissipated energy does not vanish in the context of any model that links the functional structure of supercoiled DNA to the protection of all organized genomes from the virus-driven degradation of messenger RNA.
When theorists tout secrets in the context of quantum physics, the secrets of their mathematical models can be compared to facts. See: Structural diversity of supercoiled DNA
The functional structure and the diversity of supercoiled DNA is energy dependent and biophysically constrained by temperature dependent changes in amino acid substitutions.
See also: Temperature dependence of amino acid hydrophobicities
Reported as: Early Code

“Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,” Carter said in a statement. “This close interaction was likely the key factor in the evolution from building blocks to organisms.”

The pseudoscientific nonsense of the historical perspective on evolution was included in this 2005 claim: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
My comment to The Scientist on the Early Code:

Simultaneous emergence was suggested by Matti Pitkanen who pirated my model of biophysically constrained RNA-mediated cell type differentiation and claimed that “Hens and eggs emerged simultaneously.”

Serious scientists now appear to have discovered the link from the light-induced de novo creation of amino acids to the de novo creation of receptors that link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of genera via the nutrient-dependent chemistry of RNA-mediated protein folding.

The nutrient-dependent physiology of metabolic networks and genetic networks link reproduction to fixation of the amino acid substitutions, which enables all extant biophysically constrained biodiversity, which is exemplified in differences in morphological and behavioral phenotypes.

Claims of simultaneous emergence should be supported by experimental evidence of biologically-based cause and effect, or abandoned along with claims of Mutation-Driven Evolution, like this one: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199)

For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day as Nei’s textbook: June 14, 2013.

Historical perspective from Jon Lieff who is a very confused award-winning blogger: Synchronizing with Brain Clocks

The three previous posts have described new research that each living cell has its own individual clocks based on genetic feedback loops combined with epigenetic loops. The three posts described the discovery of individual clocks, the relation to metabolic cycles in tissues and other cells, and the way immune cell cycles alter responses based on clocks.

The three posts he mentioned fail to include any citations, such as a citation to my published 2013 review, which was a refutation of the neo-Darwinian pseudoscientific nonsense. Jon Lieff has continued to tout his pseudoscietific nonsense after I told him about food energy-dependent Alternative Splicings of RNA on October 27, 2013.
See my comment on his misrepresentations of: Alternative RNA Splicing in Evolution

In our 1996 Hormones and Behavior review, we wrote:”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.”

From Fertilization to Adult Sexual Behavior

The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.

Your focus on the importance of pre-mRNA and alternative splicing is exemplary, especially in the context of neuronal plasticity.

C. elegans is the model organism of neurogenic niche construction that links nutrient-dependent ecological and pheromone-controlled social niche construction to socio-cognitive niche construction in vertebrates and invertebrates. See for review:

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

What you are helping to detail is self-assembly with evidence of olfactory/pheromonal self-organization that is currently missing from evolutionary theory, which attributes speciation to mutation-initiated natural selection even though there is no experimental evidence for that (as I mentioned elsewhere).

See for comparison: Promises and Challenges in Continuous Tracking Utilizing Amino Acids in Skin Secretions for Active Multi-Factor Biometric Authentication for Cybersecurity
In Figure 1., they link the biophysically constrained biocatalytic cascade via two optical detection pathways to the energy-dependent creation of three amino acids. This extends what is known about natural selection for food energy-dependent codon optimality to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
The key to understanding how ecological variation must be linked to ecological adaptations is the role played by fixation of RNA-mediated amino acid substitutions. The measurement of NADH (energy) at 340 nm (ultraviolet), and the conversion of NADH (energy) to a observable yellow color at 580 nm links quantized energy as information from ultraviolet (UV) light to the visible spectrum. That fact is also manifested in results from chemistry testing and other laboratory testing that helps physicians diagnose and effectively treat their sick patients.
Chemists and molecular biologists must know how to link physics to results of diagnostic testing.
See: The Gene Polymorphism of VMAT2 Decrease the Risk of Developing SCZ in Male Han Chinese (link opens pdf)

A GWAS research found an female-specific association with rs7341475 in reelin (RELN ) gene [30]. Most interestingly, in a study show in a same gene, different SNPs conduct different sex-spefic effect: eg, SNPs rs3891636, rs7728773, rs2189663,rs3864283, and rs2526303 of HINT1 gene significant among the female subjects alone, whereas SNP rs7735116 was significant among males alone [31]. These studies indicate there may exit sexspecific genetic risk and protective factors to SCZ.

I placed the failure of all theorists to link energy-dependent changes in base pairs from SNPs to the RNA-mediated amino acid substitutions that differentiate all cell types in all living genera into the context of this invited review of nutritional epigenetics,

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

For comparison to the VMAT2 polymorphism linked to thje decreased risk of schizophrenia, I took a broad-based approach. The ingestion of sago palm-like leaves linked increased endogenous vitamin C from the stablility of the organized genome in mice to the stability of the organized genome in a modern human population via this report: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant.
They linked one a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2 to differences in the morphological and behavioral phenotypes of species from mice to humans. Note: rs3827760 is also known as 1540T/C, 370A or Val370Ala. Nothing known to serious scientists about biophysically constrained biologically-based cause and effect suggest that base pairs and amino acid substitutions evolved to create proteins.
For comparison to Szostak’s retracted claims about RNA, see: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism and compare what is known to serious scientists to the claims of creationists.
Oops! Scientific retraction a major blow to evolution theory

The finding is the latest in a “replication crisis” sweeping the scientific community in which apparent breakthroughs cannot be repeated by other researchers.

Szostak’s study reopens what is perhaps the largest hole in evolutionary theory, as scientists remain unable to explain how the building blocks of life were “spontaneously” created.

Szostak’s comment that his team was “blinded by our belief” is significant. Previously, he condemned “belief systems based on faith” as “inherently dangerous, as they leave the believer susceptible to manipulation when skepticism and inquiry are discouraged.”

My invited review of nutritional epigenetics was returned without review, and no one has commented on the representations in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems that link energy-dependent changes from electrons to ecosystems in all living genera via more than 68,000 published works on microRNAs.
See for instance: Two-Color-Based Nanoflares for Multiplexed MicroRNAs Imaging in Live Cells

…two-color-based nanoflares can simultaneously detect miR-21 and miR-141 expression levels in various live cancer cells successfully. Compared to the traditional single-color-based nanoflares, the two-color-based nanoflares could offer more reliable and practical information for cancer detection, improving the accuracy of early disease diagnosis.

Diagnostics: The changes in the the two-color-based nanoflares will eventually be used to determine the differences in the number of viral microRNAs compared to the number of food energy-dependent microRNAs. The differences will link the weekend resurrection of the bacterial flagellum in P. fluorescens to cell type differentiation in the “walking fish” via dietary differences and biophysically constrained pheromone-controlled reproduction, which requires a source of ingested iodine for the maturation of sex differences in cell types.
Treatment: Exosomes from human umbilical cord blood accelerate cutaneous wound healing through miR-21-3p-mediated promotion of angiogenesis and fibroblast function

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

Energy-dependent physical and biophysical constraints (5)

Summary: Emmy Noethe’s theorems were developed in the early 1900’s. Richard Feynman inadvertently or purposefully alluded to them as examples of human idiocy.
Discover Magazine resurrected the examples of human idiocy in a 2017 article. For comparison, Choi et al., (2017) support the claims that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones.
It is obvious that pheromones biophysically constrain the virus-driven degradation of messenger RNA. That fact links everything currently known about RNA-mediated cell type differentiation to human love in the context of established links from quantum physics to quantum souls. It may surprise some people to know that the virus-driven evolution of love is the antithetical to the food energy-dependent physiology of pheromone-controlled reproduction in all living genera. Indeed, some people may realize that the virus-driven evolution of anything is based upon ridiculous theories that were invented by Emmy Noethe.
See: Energy-dependent physical and biophysical constraints (4)
Natural selection links odors and the food energy from what organisms eat to the de novo creation of microRNAs. The creation of microRNAs is linked to biophysically constrained energy-dependent codon optimality.
Odor and food energy-dependent changes in microRNAs link hydrogen-atom transfer in DNA base pairs in solution from the creation of amino acids to the ability to sense energy and mass in the context of the space-time continuum. The sense of smell in bacteria has been linked to our food energy-dependent visual perception of the space-time continuum.
Publication of Olfaction Warps Visual Time Perception precedes the September 2017 release of the cell biology game Cytosis. The cell biology game links virus-driven energy theft to all pathology.

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

Taken together, the facts about olfaction link the sense of smell in bacteria from quorum sensing to our visual perception of mass and energy in the context of the space-time continuum. It is no trouble for a serious scientist to consistently link quantum physics from food energy to the creation of quantum souls via changes in the microRNA/messenger RNA balance and the pheromone-controlled physiology of reproduction.
Richard Feynman inadvertently did that when he claimed that the different measures for units of energy used by other theoretical physicists were examples of human idiocy.

See for comparison: The Universe According to Emmy Noethe (Discover Magazine, 2017)

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large. That was one of two theorems she proved that year in Göttingen, Germany. The other theorem, which would ultimately have a far greater impact, uncovered an intimate link between conservation laws (such as the conservation of energy) and the symmetries of nature, a connection that physicists have exploited ever since. Today, our current grasp of the physical world, from subatomic particles to black holes, draws heavily upon this theorem, now known simply as Noether’s theorem.

Emmy Noethe’s so-called theorems, which she developed in the early 1900’s, attempted to explain how the concept of entropy might not appear to defy everything known to serious scientists about the biophysically constrained energy-dependent physiology of pheromone-controlled reproduction, which links feedback loops from odors and pheromones to the creation of all energy-dependent biodiversity on Earth.
Simply put, more than 100 years ago Emmy Noethe’s theorems suggested that all representations of energy-dependent biologically-based cause and effect are wrong. For a current representation of what is known, see: Feedback loops link odor and pheromone signaling with reproduction.
The physiology of pheromone-controlled reproduction links what organisms eat to all energy-dependent biodiversity via the de novo creation of genes and gene activation that is biophysically constrained by the metabolism of food to pheromones which control the physiology of reproduction in all living genera.
See also: AMP-enabled FLT3-ITD detection

Independent and bidirectional probes are specifically optimized to detect internal tandem duplications (ITDs) of all sizes. The reads originating from these probes are bioinformatically assembled by Archer Analysis using a de novo assembler to form longer consensus sequences that span the ITD. These longer sequences are then aligned to the reference genome to identify the presence of even very large ITDs (> 250bp).a
a Only available on Illumina® instruments

Use of a so-called “de novo assembler” eliminates any consideration of energy as information that must be used in the context of bioinformatics and the identify of reference genomes that are used to identify pathological gene variants that arise in the context of energy-dependent de novo gene creation.  The link from Emmy Noethe’s theorems to the pseudoscientific nonsense about the  “de novo assembler” may not be clear without examination of facts about the physiology of reproduction.
For example, see: Physiology is rocking the foundations of evolutionary biology

Perhaps the elegant mathematics and the extraordinary reputation of the scientists involved blinded us to what now seems obvious: the organism should never have been relegated to the role of mere carrier of its genes.

For information on Emmy Noethe’s reputation and her elegant mathematics, see:

The Mighty Mathematician You’ve Never Heard Of (2012)

She invented a theorem that united with magisterial concision two conceptual pillars of physics: symmetry in nature and the universal laws of conservation.

Noether’s brilliance was obvious to all who worked with her, and her male mentors repeatedly took up her cause…

A Fight for the Soul of Science (2015)

Silk accused these theorists of “moving the goalposts” of science and blurring the line between physics and pseudoscience. “The imprimatur of science should be awarded only to a theory that is testable,” Ellis and Silk wrote, thereby disqualifying most of the leading theories of the past 40 years. “Only then can we defend science from attack.”

See for comparison:

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems April by James V Kohl

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.

From my publications alert: What’s new for ‘microRNA’ in PubMed on July 26, 2017
Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA

MicroRNAs are small non-coding RNAs that bind to the 3′-untranslated region of target mRNAs and have transcriptional or translational inhibitory function in eukaryotes. Before microRNAs were widely known, bacterial non-coding small RNAs around 50-200 nt in length were discovered whose mechanism of action resembled that of microRNAs. Recently, RNAs that are of similar size to or smaller than microRNAs have been discovered in bacteria and indeed, this class of small RNAs have been found throughout all domains of life. Moreover, recent findings suggest that these tiny RNAs can be released via extracellular vesicles (such as exosomes in eukaryotes and outer membrane vesicles in bacteria), which in turn heralds a new field of research, interkingdom communication. This review discusses two similar classes of small RNAs in evolutionarily distinct eukaryotes and bacteria. In addition to their biogenesis and regulation, we discuss small RNA vehicles and their secretion. Impact statement The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

See also:Impact statement

The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

As indicated in my 2014 invited review of nutritional epigenetics, which was returned without review, endogenous functions of regulatory RNAs such as small RNAs in bacteria and microRNAs in eukaryotes have been extensively detailed in the context of biophysically constrained biologically-based cause and effect. These authors attest to the fact that the structure and function of bacterial small RNAs and eukaryotic microRNAs are not limited to their food energy-dependent de novo creation in their cells of origin.
The fact that small RNA and micro-RNA-mediated cell type differentiation occurs in the context of hydrogen-atom transfer in DNA base pairs in solution links the information in this review to claims that small RNAs in seawater solutions and microRNAs in blood link “common molecule” status to “… the function of small RNAs in intercellular and even interkingdom communication.”  The fact that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones that biophysically constrain the virus-driven degradation of messenger RNA, links everything currently known about cell type differentiation from quantum physics to quantum souls via the food energy-dependent physiology of reproduction in all living genera.
See also: Choi JW[Author] microRNA
For example: MicroRNA profiling in the mouse hypothalamus reveals oxytocin-regulating microRNA
For comparison: @36:18 Larry Young explains the virus-driven evolution of love as if serious scientists had learned nothing about receptor-mediated behaviors.

human-evolution

Do not miss the misrepresentations

January 25, 2016 Reported as 1) “… they hypothesise short bursts of rapid species diversification, such as after the famous mass extinction event…”

January 11, 2016 Reported as 2) “…a newly identified protein, Wuho (WH), regulates the activity of FEN1 when around a replication fork, ensuring it does more good acting as a flap endonuclease than damage as a gap endonuclease.”

January 7, 2016 Reported as 3) “Exosomes Protect and Perpetuate Chemical Attractants”

February 12, 2016 Reported as 4) “…three sources of variation that have driven the radiation of this group. These are post-speciation hybridization, where distinct species interbreed; de novo mutation, where random mutations arise during DNA replication; and ancestral variation, where variants are carried through from the ancestral population.”

February 22, 2016 Reported as 5) “…neurons anticipate the quick, automatic eye movements know as saccades, and compensate accordingly.”

My comment: In one month, reports on 5 different research groups collectively linked energy-dependent chemotaxis and phototaxis from soil bacteria to the construction of the eye in primates via energy-dependent changes in exosomes. The exosomes link nutrient-dependent microRNA flanking sequences and hydrogen-atom transfer in DNA base pairs in solution from RNA-mediated cell type differentiation in all living genera to supercoiled DNA, which protects all organized genomes from virus-driven entropy.

The five research groups reportedly linked sources of innate variation to hybridization, random mutations, and transgenerational epigenetic inheritance of nutrient-dependent pheromone-controlled variants. The variants link the morphology and behavior of yeasts to humans via the nutrient-dependent RNA-mediated immune system and amino acid substitutions in the context of the pheromone-controlled physiology of reproduction.

If Einstein (molecular mechanics), Schrodinger (anti-entropy), or Dobzhansky (amino acid substitutions) were not still dead, they would be rolling on the floor laughing about the ignorance displayed by neo-Darwinian evolutionists — or crying. Are you laughing, or crying? In either case, it is time to join others who are Combating Evolution to Fight Disease. If you don’t, the diseases that neo-Darwinists link to evolution will probably kill you, too.

Clearly, you and your loved ones will not evolve into a new species. No species ever has, except in theory.

[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.

See also: PLOS Biology ICYMI: Festive Five for honorable mention of the fact that Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses
Excerpt:

Our findings suggest that viruses have evolved to inhibit RTL1 activity, ultimately resulting in successful viral infection

My comment: [Sarcasm alert] Where on Earth do the viruses get the energy to do that? Did Einstein, Schrodinger, Dobzhansky, or anyone else ever tell us about left-over energy that could be used by viruses for their evolution?

amino acid homeostasis

Exosomes and the RNA-mediated future of medicine (3)

September 11, 2015

Case Western Reserve scientists discover long-sought genetic mechanism for cancer progression

Excerpt:

Action of a key lncRNA different in colon cancer versus normal colon tissue

My comment: In yet another ridiculous misrepresentation of all that is currently known about how the epigenetic landscape is linked to the physical landscape of DNA in all cell types of all individuals of all living genera, these researchers are reporting epigenetic links between metabolic networks and genetic networks as if the origins of the networks arose in genes.

See for comparison: A genetic mechanism for cancer progression
Excerpt:

Methylation is a process where a methyl group is added into critical points along our DNA.
DNA methylation can help prevent cancer by maintaining a healthy level of gene expression, which in turn controls the extent of cell growth in the body.

My comment: Their diagram indicates that de novo methylation automagically occurs. Anyone who asks how methylation occurs will find that it is nutrient-dependent and RNA-mediated during thermodynamic cycles of protein biosynthesis and degradation that typically protect DNA from damage. The DNA damage is due to virus-perturbed protein folding, which links exosomes to microRNA-mediated events.
Simply put, pathology results from the accumulation of viral microRNAs when viruses steal the nutrient-dependent energy that cells require for proper differentiation of cell types. See also:
MicroRNA-627 Mediates the Epigenetic Mechanisms of Vitamin D to Suppress Proliferation of Human Colorectal Cancer Cells and Growth of Xenograft Tumors in Mice
Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
Claims about de novo methylation are obvious attempts to obfuscate what has been known to serious scientists about the biophysically constrained chemistry of RNA-directed DNA methylation and nutrient-dependent protein folding linked to healthy longevity by the nutrient-dependent microRNA-mediated suppression of viral microRNAs. Not only vitamin D suppresses the proliferation of cancer cells. All nutrients help to suppress DNA damage via RNA-directed DNA methylation.
Case Western Reserve scientists may not be willing to admit to discovering what Darwin claimed about his “conditions of life.” Many others have since put mutations and/or natural selection first to fit into the context of their ridiculous theories about evolution.
Claims about de novo methylation can be compared to claims about de novo genes in the context of the de novo creation of olfactory receptor genes that link the epigenetic landscape to the physical landscape of DNA in organized genomes via RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all genera.
See also: rna-directed dna methylation and my blog posts rna-directed dna methylation

amino acid homeostasis

Exosomes and the RNA-mediated future of medicine (2)

GDNF-Transfected Macrophages Produce Potent Neuroprotective Effects in Parkinson’s Disease Mouse Model
Excerpt:

…genetically-modified macrophages released exosomes with incorporated GDNF that may facilitate GDNF transport into the target cells and preserve it against degradation.

published 9/17/14 and reported on 9/11/15 as:

Smart cells teach neurons damaged by Parkinson’s to heal themselves

Excerpt:

In addition to delivering GDNF, the engineered macrophages can “teach” neurons to make the protein for themselves by delivering both the tools and the instructions needed: DNA, messenger RNA and transcription factor.

MedicalXpress.com suddenly seems interested in reporting on the role of exosomes in RNA-mediated cell type differentiation, which is what I did yesterday in this blog post. Exosomes and the RNA-mediated future of medicine
See also: UNC smart cells teach neurons damaged by Parkinson’s to heal themselves
Excerpt: “By teaching immune system cells to make this protective protein, we harness the natural systems of the body to combat degenerative conditions like Parkinson’s disease,” Batrakova said.
See also: RNA-binding protein influences key mediator of cellular inflammation and stress responses

terrarium-eco-system

Exosomes and the RNA-mediated future of medicine

The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins

Reported as:

The exosome regulates the processing, degradation, and surveillance of a plethora of RNA species.

Excerpt:

…the exosome employs a general mechanism of recruitment to defined substrates and that this process is regulated through adaptor proteins.

Journal article excerpt: (subscription required)

The nuclear exosome processes precursors of numerous stable RNA species (Allmang et al., 1999) (rRNA, snoRNA, and snRNA) and degrades by-products of RNA processing reactions. Additionally, it targets for surveillance numerous cryptic unstable transcripts (CUTs) (Wyers et al., 2005) and aberrant RNAs. In the cytoplasm the exosome degrades aberrant mRNAs identified by the NMD (nonsense-mediated decay) (Takahashi et al., 2003) and NGD (no-go decay) (Doma and Parker, 2006) pathways.

My comment: Attempts to place the general molecular mechanisms of biophysically constrained nutrient-dependent substrates’ RNA-mediated amino acid substitutions and protein folding chemistry that determines cell types in all individuals of all genera into the context of neo-Darwinian theories have continued to become increasingly more foolish.
See for example: Steven Tucker: The man who found the Homo Naledi fossils
When will students in your country be taught what is known about cell type differentiation instead of being taught to believe in ridiculous theories? See, for example:

Scientists home in on origin of human, chimpanzee facial differences

Excerpt:

The key lies in how genes involved in facial development and human facial diversity are regulated—how much, when and where the genes are expressed— rather than dissimilarities among the genes themselves.
My comment: The key to gene regulation has always been nutrient-dependent and RNA-mediated via gene duplication and RNA-mediated amino acid substitutions that are fixed in the organized genomes of species from microbes to humans via the biophysically constrained chemistry of protein folding and successful nutrient-dependent reproduction.
If you let pseudoscientists ignore that fact when they report results from fossil evidence, the evolutionary theorists will make monkeys of us all.

See instead:
International Society for Extracellular Vesicles (ISHE) exclusive video collection
includes the panel discussion: Exosomes Role in the Future of Medicine
See also: Context-specific microRNA function in developmental complexity
Excerpt:

When also considering the large number of primate-specific miRNAs expressed in the brain (Berezikov et al., 2006) and that a single pyramidal neuron in the cortex may form up to 10000 synapses with other cells, it is tantalizing to hypothesize a role for miRNA as key regulatory molecules in the development of the exquisitely complex programmes of gene expression and the decentralized modifications of individual synaptodendritic connections that are required for the cortical complexity observed in the human brain.

My comment: Do not be the last serious scientist in the world to learn how cell type differentiation occurs in all cells of all individuals of all living genera. Other serious scientists will think you have always been a biologically uninformed theorist.
See also: The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors
Excerpt:

…among the human proteins identified, 59 have a yeast homolog that has not been examined for a role in ribosome synthesis. Significantly, these include putative methyltransferases, protein modification enzymes, and structural cellular components, as well as gene products
involved in translation, pre-mRNA splicing, or DNA replication. These are all cellular processes recently shown to share highly specific trans-acting factors with ribosome synthesis.

My comment: It should be obvious that mutations, which perturb thermodynamic cycles of RNA-mediated protein biosynthesis and degradation cannot be linked to the evolution of biodiversity, which is nutrient-dependent and controlled by the physiology of reproduction in all living genera.
See also: Viral and Cellular Genomes Activate Distinct DNA Damage Responses
and Loss of lamin A function increases chromatin dynamics in the nuclear interior, which was reported as: Preventing chromosomal chaos: Protein-based genome-stabilizing mechanism discovered
Excerpt:

According to Garini, this protein-mediated mechanism is fundamental to the stability of life as we know it.

The stability of life is nutrient-dependent, receptor-mediated and the stability of species is controlled by the physiology of reproduction in the context of chromosomal rearrangements, not mutations or natural selection or evolution.
See also:  Exosomes and the RNA-mediated future of medicine (2)
For a ridiculous misrepresentation of biologically-based cause and effect, see: One crank dies, another rises to take his place PZ Myers attacks anyone who does not support his ridiculous opinions.
Excerpt:
Behold James Vaughn Kohl. (my comment from Jan 3, 2014 may not appear unless you set the post rating to 1.0)

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.

See also: I repeat: Octopuses are NOT aliens

Excerpt:

The problem for atheists becomes bigger almost every day.
Where is PZ Myers, when we need to learn more about cell type differentiation via mutations, now that all serious scientists have abandoned that pseudoscientific nonsense because they have learned about biologically-based cause and effect?
See for example: DNA methylation pathways and their crosstalk with histone methylation http://dx.doi.org/10.1038/nrm4043
Why isn’t little PeeZee slamming down the creationists now that they reported the link from virus-driven entropic elasticity to genomic entropy?
Also:

August 25, 2015
The best way to refute pseudoscientific nonsense linked to evolutionary theories invented by neo-Darwinists is with facts about cell type differentiation in the context of climate change and the physiology of reproduction, which links ecological variation to ecological adaptations via the microRNA/messenger RNA balance. The balance is linked to biodiversity via chromosomal rearrangements, not by virus-driven mutations that cause gene loss.See: Mayo Clinic Researchers Find New Code That Makes Reprogramming of Cancer Cells Possible https://www.youtube.com/watch?v=yGYTLOGZ40U
Also:

August 23, 2015
See also: http://freethoughtblogs.com/pharyngula/2014/01/06/one-crank-dies-another-rises-to-take-his-place/“…he was actually a biologist, had a Ph.D. in zoology, and taught at the University of Vermont. He had a “scientific” theory, which was his, which he thought explained all that evolutionary change while refuting those silly scientists who believed that mutations occurred. No! Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species…”Mutations perturb protein folding, which is why they cannot be linked to evolution.The differences in alleles are nutrient dependent and they link RNA-mediated events to the biophysically constrained chemistry of protein folding and the physiology of reproduction in all genera via amino acid substitutions and chromosomal rearrangements, which is what the octopus genome sequencing just showed.
Also:

August 21, 2015
Re: I just know this nonsense is going to be propagated by creationists everywhere, and I’m going to have to slam it down repeatedly.Thanks for acknowledging the fact you will be forced to address what is known to serious scientists about the link from microRNAs to biodiversity that refutes all claims of theorists about beneficial mutations.Jerome Hui and others linked all crustaceans to all insects via nutrient-dependent changes in the microRNA/messenger RNA balance. There is no reason to believe that anything else links marine invertebrates to primates.Besides, octopuses are referred to as the “primates of the sea.” The sequencing of the octopus genome links the conserved molecular mechanisms of biophysically constrained nutrient-dependent protein folding to RNA-mediated events and chromosomal rearrangements, which are clearly linked to all extant biodiversity without the nonsense about beneficial mutations and evolution.
Also:

August 27, 2015
The Octopus Genome: Not “Alien” but Still a Big Problem for Darwinism http://www.evolutionnews.org/2015/08/the_octopus_gen098681.html
Excerpt:
Whenever you see “de novo” origin of a gene invoked, you know that evolutionary biologists lack any explanation for how that gene arose.”
Slam ’em down, PZ. Alternatively, encourage your anonymous idiot minions to try.
terrarium-eco-system

Multi-omic analysis features (SNPs, miRNA)


See also: Viral and Cellular Genomes Activate Distinct DNA Damage Responses
Excerpt:

Central to life is the faithful replication, inheritance, and maintenance of genomic DNA. The MRE11/RAD50/NBS1 (MRN) complex andATMplay a critical role in this biological mandate (Ciccia and Elledge, 2010). Cellular double-strand breaks (DSBs) are sensed by MRN and trigger the assembly of DNA damage response (DDR) foci that amplify global ATM signaling to induce cell-cycle arrest and DNA repair (Polo and Jackson, 2011). DNA viruses are an ancient and persistent threat to both cellular genome integrity and viability.

You can lean more about RNA-mediated correction factors here.

Excerpt:

Innovative multi-omic analysis features (SNPs, miRNA).

My comment: Typically, RNA-mediated events control virus-driven DNA damage. How could any serious scientist not consider the effects of viral microRNAs on cell type differentiation? All effects must be compared to the epigenetic effects of nutrient-dependent microRNAs on DNA repair, which links ecological variation to ecological adaptation via the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein biosynthesis and degradation.
See also: RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II’s rules
Abstract excerpt: 

Noncoding RNAs regulate gene expression at both the transcriptional and post-transcriptional levels, and play critical roles in development, imprinting and the maintenance of genome integrity in eukaryotic organisms [1,2,3]. Therefore, it is important to understand how the production of such RNAs are controlled.

My comment: Biologically uninformed researchers cannot understand how the production of potentially beneficial noncoding RNAs is controlled by nutrient energy and how cell type differentiation is perturbed by viruses that steal the nutrient energy that is required for fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera.
See also: Combating Evolution to Fight Disease
Excerpt:

An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans.
The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.
See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.
RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events.

My comment: Any article that mentions the evolution of anything without consideration of Darwin’s ‘conditions of life’ is an article that bastardized his theory. Darwin clearly linked ecological variation to ecological adaptation before cause and effect was linked via nutrient-dependent RNA-mediated chromosomal rearrangements in white-throated sparrows and all other living genera.
See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
Excerpt:

Estrogen receptor-mediated differences in parental feeding behavior appear to contribute to sex differences and species differences in morphology and in overt social behavior.

My comment:   “the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6
See also: Armed Forces in the Cell Keep DNA Healthy
Excerpt:

We aren’t surprised to notice that these articles say nothing about evolution.

See also: Ready to Return and Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation.
For comparison of what is known to serious scientists about ecological variation and ecological adaptation in the context of an atoms to ecosystems model, see this video representation of my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See also: Scientists map genes at work in human embryos’ earliest days