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Wikipedia refutes theistic evolution

RNA-Directed DNA Methylation

Besides RNA molecules, a plethora of proteins are involved in the establishment of RdDM, like Argonautes, DNA methyltransferases, chromatin remodelling complexes and the plant-specific Polymerase IV and Polymerase V. All these act in concert to add a methyl-group at the 5′ position of cytosines. In contrast to animals, cytosines at all sequence context (CG, CHG, CHH) may get de novo methylated in plants.

There is no such thing as de novo methylation. Methylation is energy-dependent. Virus-driven energy theft prevents methylation and links mutations to all pathology via everything known to young earth creationists, which some of them have been reporting since the late 1990’s. That fact explains why theorists were forced to change RNA-Directed DNA Methylation to RNA interference in a face-saving attempt. Many pseudoscientists have claimed the creationists cannot be scientists and their attacks on young earth creationists have been among the most vicious of all attacks. But now, the young earth creationists have this:

RNA interference (RNAi) RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon.

The so-called unrelated processes linked to RNAi phenomenon were place into the context of what was known about molecular epigenetics in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The alternative splicings are energy-dependent.
See also: Contribution of epigenetic mechanisms to variation in cancer risk among tissues

Because de novo modification appears to take place almost exclusively on CpG islands that are already silenced by polycomb in the normal tissue (8), we suggest that this modification works by preventing these genes from becoming activated, thereby inhibiting normal tissue differentiation, causing clonal selection for cells that may predispose to cancer (31). Indeed, many of these methylation targets have been shown to be “driver” genes in a number of different cell types (Fig. S6).

Virus-driven energy theft prevents what they claim are the de novo modifications and the energy theft links contraint-breaking mutations from viral latency to all pathology. Only biologically uninformed pseudoscientists have continued to portray energy-dependent changes in methylation as if the changes occurred in the context of de novo modification.
See for comparison. These creationists start with energy and link it to experience-dependent cell type differentiation via what is known about sensing and signalling in all living genera.
Multipurpose plant sensors startle scientists

Evolutionary scientists did not predict such elaborate sensory integration in a single protein system.

Sensing and signalling in all living genera is links the physiology of reproduction in soil bacteria to the phyisology of pheromone-controlled reproduction in all livng genera. See for example:
The genome of Chenopodium quinoa

The TSARL1 transcript was alternatively spliced in the sweet progeny of Kurmi and 0654. A SNP in the last position of exon 3 (G2078C) co-segregates with the presence of saponins in the Kurmi × 0654 progeny. The G2078C SNP alters the canonical intron/exon splice boundary (Fig. 4e), probably leading to the alternative splicing at an upstream cryptic splice site in the sweet lines (Fig. 4e). This alternative splicing of TSARL1 results in a premature stop codon…

See also: Start codons in DNA may be more numerous than previously thought

Start codons are important to understand because they mark the beginning of a recipe for translating RNA into specific strings of amino acids (i.e., proteins).

See also: Codon optimality controls differential mRNA translation during amino acid starvation (2016)
They help to make the fact clear that all organisms must eat.
See also:Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016)
They make it clear that the bias between codons or amino acids, and mRNA expression is the link from natural selection for energy as information that links the selection of food to efficient, accurate translation, and folding of  expressed genes.  Simply put, the energy-dependent amino acid optimality code  differentiates between theories of evolution and facts about how ecological variation must be linked to ecological adaptation via the physiology of pheromone-controlled energy-dependent reproduction and supercoiled DNA in all living genera.
Obviously, pseudoscientists who cannot link energy-dependent changes in codon optimality have indirectly been responsible for all virus-driven pathology because they failed to link the viral hecatomb from archaea to the transgenerational epigenetic inheritance of Zika virus-damaged DNA or to all other pathology, including cancer and degenerative diseases.
Thank God, Bill Gates and President Trump are among the billionaires who have decided to help others who have been combating evolutionary theorists to fight disease for several decades.
See also: Combating Evolution to Fight Disease

diseases-disorders

RNA editing refutes theistic evolution

Charge-altering releasable transporters (CARTs) for the delivery and release of mRNA in living animals January 9, 2017
Reported February 19, 2017 as A new way Forward for Gene Therapy

If you want an explanation of how mRNA works within a cell, check out the video above from the Khan Academy.

Unfortunately, the speaker seems to think that sickle-cell disease is caused by a mutation. All serious scientists know that the hemoglobin S variant is a biophysically constrained nutrient energy-dependent ecological adaptation that protects populations from virus-driven genomic entropy due to phages in the class of Sporazoa, which includes the parasite that causes malaria.
See also: HbVar: A Database of Human Hemoglobin Variants and Thalassemias
More than 1200 hemoglobin variants have been reported.
Here is more information on the known variants Dobzhansky (1964) reported that  “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.”
If you want details about how energy-dependent changes in the microRNA/messenger balance link amino acid substitutions in supercoiled DNA to all healthy longevity compared to the fact that virus-driven energy theft is linked from mutations to all pathology, see:
Energy as information and constrained endogenous RNA interference

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

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

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

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

See also: Top-down causation: an integrating theme within and across the sciences?

The papers by Jaeger (microbiology) and Noble (physiology) are strong steps forward in this regard. This is perhaps the area where most needs to be done, across the board in all domains. Areas where striking progress is being made in this regard are epigenetics [22] and social neuroscience [23]. These papers are in fact dealing with top-down causation: the way they provide experimental confirmation of this concept needs to be made more explicit.

What don’t pseudoscientists understand about the need to link energy-dependent RNA-mediated protein folding chemistry from metabolism in microbes to their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction before inventing more theories based on definitions and assumptions about interpretations of data?
Each example of RNA editing will continue to link chirality to autophagy and link endogenous RNA interference (RNA editing) to supercoiled DNA via amino acids in supercoiled DNA. If example of virus-driven energy theft are not sufficient to show that it is the cause of all pathology, someone will need to show what causes the mutations that are linked to all pathology.
See also: Genomic Energy Landscapes
Their perspective on the energy landscape theory asks the same old questions about chromosomal inheritance and provides no basis for linking experimental evidence of top-down energy-dependent causation from RNA-mediated protein folding chemistry to all biodiversity via the physiology of pheromone-controlled reproduction. It is another refutation of theistic evolution because it fails to link anything to anything else.
See for comparison: Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection (2014)

Comparing the details of the physical and information theoretic models has already suggested ways of improving the prediction of mutational effects on the stability of protein sequence/structure pairs.

Virus-driven energy theft causes mutations, which link messenger RNA degradation to genomic entropy in hosts because the energy is used for amino acid substitutions that stabilize the organized genomes of viruses. How much evidence of virus-driven energy theft and pathology can be viewed in the context of the fossil record compared to the frozen corpse of “the Tyrolean Iceman?”
See: miRNAs in ancient tissue specimens of the Tyrolean Iceman reported as: Otzi the Iceman: Researchers validate the stability of genetic markers

…microRNAs can remain stable even after 5,300 years.

From the same first author: The missense of smell: functional variability in the human odorant receptor repertoire
The variability of single odorant receptors is clearly linked from energy-dependent changes in base pairs to the microRNA/messenger RNA balance. The balance links SNPs to natural selection for energy-dependent codon optimality.
Codon optimality links single amino acid substitutions from RNA editing to nutrient-dependent pheromone-controlled adaptations. That fact links natural selection from ecological variations to ecological adaptations. The energy-dependent adaptations obviously occur in species from microbes (including viruses) to man. If the adaptations did not occur in all living genera, the microRNAs could not have been linked to genetic markers in the ancient tissue specimens via RNA editing.
See also: Contribution of epigenetic mechanisms to variation in cancer risk among tissues

…the risk of cancer in any given tissue would be correlated with the number of abnormally methylated precancer cells in that cell type. Because de novo modification appears to take place almost exclusively on CpG islands that are already silenced by polycomb in the normal tissue (8), we suggest that this modification works by preventing these genes from becoming activated, thereby inhibiting normal tissue differentiation, causing clonal selection for cells that may predispose to cancer (31). Indeed, many of these methylation targets have been shown to be “driver” genes in a number of different cell types (Fig. S6).

Once again we see that serious scientists know the difference between energy-dependent polycombic ecological adaptations and the virus-driven hecatombic evolution of all pathology, but they clearly do not know how to express what they know in terms that are meaningful to those who know how to link angstroms to ecosystems in all living genera.
 

Alternative splicing of pre-mRNA

George Church refutes theistic evolution

Wednesday Afternoon Lecture Series (WALS) – The future of genetic codes and BRAIN codes

The NIH Director’s Wednesday Afternoon Lecture Series, colloquially known as WALS, is the highest-profile lecture program at the NIH.

The future of genetic codes and BRAIN codes (video)
My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.
Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.
Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
They showed that a single set of light-activated reactions gave rise to most of life’s building blocks simultaneously. Simply put, that fact refutes every aspect of neo-Darwinian nonsense. It also eliminates consideration of any theories proposed by “big bang” cosmologists.
The irony of this is that not one of the young earth creationists I know would fail to link the hydrogen-atom energy-dependent de novo creation of nucleic acid precursors to all biodiversity on Earth via the physiology of biophysically constrained cell type differentiation.
For example, see: Multipurpose Plant Sensors Startle Scientists
Even if a young earth creationist knew nothing about energy-dependent cell type differentiation, he or she would not be likely to link minimal mutational differences, called mutations to the mutation-driven evolution of all biodiversity.
As you can see in the video, George Church has been forced to abide by the rules of serious scientists.
Here is an unavoidable rule: Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.

George Church has, until yesterday, focused his efforts on exogenous RNA interference rather than what is known about endogenous RNA interference, which links supercoiled DNA to the prevention of all virus-driven pathology in all living genera. Most people will not recognize what President Trump has forced the NIH to do before the theistic evolutionist, Francis Collins is replaced. They may read this, but not understand what it means.
Obama Advisers Urge Action Against CRISPR Bioterror Threat

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The likelihood that NIH funding will be used for any studies that do not link prevention from the National Microbiome Initiative to the Precision Medicine Initiative via the microRNAome and energy-dependent microRNA expression can be placed into the context of failed mathematical models, which have not addressed any aspect of energy-dependent biologically-based cause and effect.
Let me help others decipher the content of George Church’s claims in: The future of genetic codes and BRAIN codes
The question (at 54:22) about teratomas is answered with a classic attempt to obfuscate what is known about virus-driven energy theft and all pathology.
How organs assemble in the context of virus-driven energy theft has been placed into the context of energy-dependent viral latency since the time that Sinclair Lewis published “Arrowsmith” in 1925 and Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for his works on chromosomal inheritance.
At 59.00 the question about natural selection for energy-dependent codon optimality leads to another attempt to obfuscate what is known about top-down causation.
At 1:00 he begins to talks about adding a built-in sequencer in your phone.  At this point, you may need some comic relief, which Jon Stewart provided with his question about whether the new technology would be integrated with a camera. See: Jon Stewart interviews Greg Bear.
At 1:04, the question and answer about Alzheimer’s vs cognitive enhancement can be placed into the context of Greg Bear’s works, which were published in 1999 and 2003. They were reviewed by Michael A. Goldman in “Nature.”
Evolution rising from the grave
Living with the Neanderthals
See also: Newly found mechanism for protecting neurons could underlie brain disease

The neurons expel large (4- micron diameter) membrane-bound vesicles (dubbed “exophers”) that are filled with clumped protein and damaged cellular organelles including mitochondria.

The only mention of exopher in the extant literature indexed on PubMed is in the article published yesterday, C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress.  The authors seem to be trying to make everything known to all serious scientists appear to be new information about the biophysically constrained RNA-mediated transgenerational epigenetic inheritance of morphological and behavioral phenotypes.
This is roughly the equivalent of inventing de Vries 1902 term “mutation,” which was used by theorists to dismiss Darwin’s “conditions of life.”
For comparison, there are now 58,887 indexed articles on PubMed that mention microRNA.  For example, see: MCMDA: Matrix Completion for MiRNA-Disease Association prediction
If you do not object to the level of obfuscation that is required for pseudoscientists to continue touting their ridiculous theories, you may not be allowed to join those who are Combating Evolution to Fight Disease.
What career goals will you pursue after the Trump administration ensures that pseudoscientific nonsense is no longer funded?
Activity-dependent spatially-localized miRNA maturation in neuronal dendrites
Reported as: Bright Spots in Brain Cells

Thanks to Anna Di Cosmo for calling attention to more detailed facts about cell type differentiation that link energy-dependent changes in fluorescence from the weekend resurrection of the bacterial flagellum to endogenous RNA interference and the maturation of brain cells in rats.
Everything known appears to link the conserved molecular mechanisms of nutrient-dependent pheromone-controlled physiology of reproduction in species from archaea to humans.
In any case, no one is challenging the perspective that serious scientists like Anna Di Cosmo have added to what is known about everything that links quantum physics to quantum consciousness via energy-dependent “bright spots in brain cells.”
And there is still no other model for comparison to this model of biologically-based cause and effect. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
A good model predicts, and people who understand the need for a good model of biologically-based cause and effect predictably make the most scientific progress.
In 2013 I wrote:

“…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.”

In 2015, Role of olfaction in Octopus vulgaris reproduction, Anna Di Cosmo’s group concluded:

The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). The knowledge of the nature of the factor released by the optic gland could shed light on the role played by this gland in the reproduction: is it a gonadotropin or a trophic factor? Intriguingly, even though the mechanisms and molecules regulating reproduction are the same in both male and female, O’Dor and Wells (1978) observed mature sperms in young O. vulgaris males independently from optic gland hypertrophy.

 

human-evolution

Fighting for virus-driven pathology

See my series of 5 posts on the tipping point, which was reached when more than 50,000 indexed publications mentioned microRNAs

The tipping point? 50, 000 publications May 16, 2016

See also: MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection

A total of eight viral miRNA were identified, and ten host miRNAs showed significantly different expression upon PRV infection. Among these, five were analyzed by stem-loop RT-qPCR, which confirmed the above data. Interestingly, these viral miRNAs were mainly found in the large latency transcript region of PRV, and predicted to target a variety of genes, forming a complicated regulatory network. Moreover, ten cellular miRNAs were expressed differently upon PRV infection, including nine upregulated and one downregulated miRNAs.

Virus-driven energy theft has been linked to all pathology in species from microbes to humans.
See also: RNA in extracellular vesicles

…we review the classes of RNAs present in EVs, both coding RNAs (messenger RNAs) and noncoding RNAs (long noncoding RNAs, microRNAs, and circular RNAs). The rising attention to EV-resident RNAs as biomarkers stems from the fact that RNAs can be detected at extremely low quantities using a number of methods. To illustrate the interest in EV biology, we discuss EV RNAs in cancer and neurodegeneration, two major age-associated disease processes.

The molecular mechanisms of healthy longevity for comparison to those of virus-driven pathology have been known to all serious scientists since the time of the 1933 Nobel Prizes.
See also: microRNA-binding proteins: specificity and function

This review covers the recent discovery of novel miRBPs, offering a new perspective on the miRNA-mediated gene silencing mechanism.

MicroRNA-mediated gene silencing was linked from nutrient energy-dependent endogenous RNA interference and RNA-directed DNA methylation and cell type stability by amino acid substitutions that differentiate all cell types in all living genera in the context of the physiology of reproduction and supercoiled DNA.
Structural diversity of supercoiled DNA

DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Pseudoscientists do not want anyone to know that they failed to link what organism eat from metabolic networks to genetic networks. They displayed more ignorance than others thought humanly possible by ignoring the fact that all organisms must eat or species do not survive. They placed that fact into the context of mutation-driven evolution and the Trump administration will put a stop to that nonsence.
THE ONE POSITIVE THING ABOUT A TRUMP PRESIDENCY

The lie now is exposed and out in the open. Things aren’t working the way they’re supposed to in America. The majority already sees this.

Ann Stevenson

All of this makes total sense. It appears that our nation is in for some rough times.

No. The people who are fighting to keep disease are in for some rough times. See: Combating Evolution to Fight Disease

Evolution is the lie.
Diane Bottum

What a great little essay you have written here. It certainly has some delicious irony in it, putting pressure on the sore spot as the best way to combat what’s hurting. That’s the trick the physical therapist uses to great advantage, because it works!

The sore spot is the teaching of pseudoscientific nonsense in the context of neo-Darwinian theory. The theorists removed Darwin’s energy-dependent “conditions of life.” They replaced the energy-dependent pheromone-controlled physiology of reproduction with mutations and natural selection. Subsequently, they were forced to remove natural selection when it became clear that natural selection for energy-dependent codon optimality was the link from endogenous RNA interference to all biodiversity via the physiology of reproduction and supercoiled DNA.
Supercoiled DNA protects all organized genomes from virus driven energy theft and genomic entropy. For instance, the diploid number of chromosomes in chimpanzees is 48 whereas in all healthy humans it is 46. That fact must be placed into the context of what is known about transgenerational epigenetic inheritance.
Chromosomal inheritance is the link from the transgenerational epigenetic inheritance of morphological and behavioral phenotypes to healthy longevity and all biodiversity. Virus-driven energy theft clearly links the loss of energy to an increased number of chromosomes.
See: trisomy.  The virus-driven degradation of messenger RNA links trisomy to the craniofacial morphology of Zika virus-damaged human infants and problematic brain development.  For comparison, nutrient energy-dependent changes linked to endogenous RNA interference link the biodiversity of nematodes to ecologically adapted human populations via the number of different hemoglobin variants. Ecological variation links the number of hemoglobin variants to ecological adaptation in non-human primates and all modern humans. All modern humans are clearly ecologically adapted to the areas on Earth from which their lineages ascended.
This tells us that non-human primates are less well-adapted than modern humans and that archaea are less well-adapted than bacteria. If you help the Trump administration focus their energy on what is known to serious scientists about RNA-mediated cell type differentiation, you will put pressure on the sore “spot” of evolution. Watch how quickly all virus-driven energy theft and all pathology is eliminated by what is currently known about the National Microbiome Initiative, metabolic networks and genetic networks that link endogenous RNA interference to the Precision Medicine Initiative via fixation of amino acid substitutions in the cell types of all individuals of all living genera. Then, watch the economy recover from the astronomical costs of traditional medicine as the Trump administration and its supporters  make America great again.
See also: List of organisms by chromosome count
Try to not link the chromosome count from energy-dependent biophysically constrained endogenous RNA interference to ecological adaptation if you intend to keep touting ridiculous theories about mutation-driven evolution.
See also: The octopus genome and the evolution of cephalopod neural and morphological novelties

…these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise ‘typical’ lophotrochozoan gene complement that contributed to the evolution of cephalopod neural complexity and morphological innovations.

Try not to link the nutrient-energy dependent pheromone-controlled physiology of reproduction in marine bacteria to the nutrient-energy dependent pheromone-controlled physiology of reproduction in all invertebrates and all vertebrates, which is what was done in: 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).

See also: Extracellular vesicles and blood diseases

EVs disseminate various bioactive effectors originating from the parent cells and transfer functional RNA and protein between cells, enabling them to alter vascular function and induce biological responses involved in vascular homeostasis. Although most EVs in human blood originate from platelets, EVs are also released from leukocytes, erythrocytes, endothelial cells, smooth muscle cells, and cancer cells.

Try not to link Dobzhansky’s claims about functional RNA-mediated amino acid substitutions to supercoiled DNA and protection from virus-driven energy theft and all pathology via human hemoglobin variants.

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

Erythrogene: a database for in-depth analysis of the extensive variation in 36 blood group systems in the 1000 Genomes Project

 We also predicted that 36% of the unknown variants alter amino acids in extracellular portions of RBC proteins and hypothesize that some may constitute blood group antigens not yet discovered.

If you are a serious scientist, try to act surprised to find that endogenous RNA interference links amino acid substitutions from energy-dependent protein folding chemistry to all biophysically constrained biologically-based biodiversity.  If you are a pseudoscientist, try to pretend that all serious scientists have known that cell type differentiation is energy-dependent since 1933.

Alternative splicing of pre-mRNA

Mutations: the "driving force" behind human brain complexity?

Evolutionary Psychology Crap in New Scientist

There is a reason why domestic violence is so widespread, says David Buss, an evolutionary biologist at the University of Texas in Austin: it carries a selective advantage, tied with reproductive success.

Larry Moran wrote:

There’s something seriously wrong with evolutionary psychology. And there’s something seriously wrong with respectable science magazines who promote this crap.

Are the science magazines that promote this crap respectable? I lost respect for anyone who still uses de Vries 1902 definition of mutation in attempts to explain how the emergence of life links natural selection from mutations to all extant biodiversity.

Evolutionary psychology Group Description

Evolutionary Psychology is an approach to psychology, in which knowledge and principles from evolutionary biology are put to use in research on the structure and function of the human mind.

Information and vision

Excerpts:

RKS: The retina turn light into visual information which is then processed by specific brain areas dedicated to this task, known as V1 through to V9. 

RKS:
This is established by neuroscience, yet another entire branch of science you dismiss in its entirety in an effort to prove your own feeble points…

RKS:

This involves previous experience, current mood and emotional status, previous behaviour (what you were doing when the visual stimuli occurred) and so on.  In other words there is an entire world of cognitive processing that needs to be consulted before behaviour occurs or is modulated as a result of visual stimuli.

RKS:

Information is also modified in the brain.  Visual information is filtered, in other words the visual information is processed, the colour of scenes is modified to compensate for the changing colour of light through the day (redder in the morning and night, bluer in the middle of the day)…

RKS:
We were discussing information processing with regard to the handling of information gleaned by the senses.  You are discussing in the above the decision making processes which occur in response to sensory stimulation and after that stimulation has been processed.
No supporting argument?  Perhaps you should try reading what I write…
I think it is safe to say that we can group behaviour into three steps:
1) Sensory stimulation;
2) Decision making, Behavioural response;
3) behavioural output.
The information processing being discussed previously concerns the (1) and (3), what happens to sensory stimulation on its way to the decision making process and on its way from the decision making process.  We have not discussed, except for your last statement above, the decision making process per se.

Other discussion groups owned and/or moderated by Robert Karl Stonjek include: Yahoo! Groups
Climate Change Forum
Cognitive NeuroScience
Evolutionary Psychology News Only
Mind and Brain
Physical Sciences
Psychiatry Research

See for comparison: Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

Clarence A. ‘Sonny’ Williams: wrote this to the Neuroscience FB group moderated by Robert Karl Stonjek

Interesting research adding to other evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity. Please note that this research does not identify uniquely human genes, but rather the comparison is between mice and humans. For all we know, the identified genes are present in all primates.

Here, the regulatory region changes found in humans but not mice are involved in activity-dependent synaptic changes (roughly, plasticity).

I responded:

No experimental evidence of biologically-based cause and effect links mutations to anything except pathology. Activity-regulated gene expression is nutrient energy-dependent and controlled by the physiology of reproduction in all living genera.

I added: The Odyssey of Autophagy

Excerpt: “ask a simple question about an interesting phenomenon, pick the right model organism in which that question can be approached genetically and biochemically, and let the grand unity of biology do the rest.”

The question is: Where did the quantized energy in a hydrogen atom come from and where does it go when it is stolen by viruses?

I added: Theorists sell hidden energy

Conclusion: Neo-Darwinian theorists invented ridiculous theories because they did not know where energy came from or where it goes when it no longer sustains life. They sold their theories to the biologically uninformed masses and will continue to sell theories about hidden energy until serious scientists put a stop to the nonsense touted by the evolution industry and the “big bang” cosmology industry.

See also: Structural diversity of supercoiled DNA

Clarence A. ‘Sonny’ Williams (with my emphasis)

Thanks for your contributions, Mr. Kohl, but I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection. Others may want to respond to any comments you make on posts from others, even if they often do not relate to the subject at hand, but this is the last time I will respond to any posts or comments you make.

James Kohl

Thanks for your ongoing antagonism and atheistic nonsense. If not for you and others like you, serious scientists would have nothing to offer to those who want to become biologically informed. See also: http://onlinelibrary.wiley.com/doi/10.1002/bdrc.21146/full Excerpt: “Studies conducted in various animal models have revealed the importance of ncRNAs during gonadal determination and differentiation process. However, the functions of these RNAs in the human sex determination are still not known.”

How much longer will anyone pretend not to know that hydrogen-atom energy in DNA base pairs in solution links nutrient energy-dependent changes in microRNA flanking sequences to all biodiversity via what is known to all serious scientists about autophagy and how the pheromone-controlled physiology of reproduction is linked to supercoiled DNA? When virus-driven energy theft causes malfunctions in receptors, the receptor-mediated events are linked from mutations to pathology, not to the evolution of a new species. I’ve published award-winning review of these facts and other reviews for more than 20 years. And Mr. Williams has come here to plague others with more of his pseudoscientific nonsense.

See for comparison our section on molecular epigenetics from this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

The phylogenetic utility and functional constraint of microRNA flanking sequences

Excerpt: “…miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.”

The de novo assembly of genomes is energy-dependent and biophysically constrained by the physiology of reproduction whether or not you believe in creation. But if you believe that humans evolved via Darwinian natural selection, you should probably learn that Darwin put his energy-dependent “conditions of life” first. He did not seem to believe that anything created itself or any species outside the context of what is now known about autophagy and supercoiled DNA.

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. 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.

I wrote: Robert Karl Stonjek  Attacks on the beliefs of others should not be tolerated, and supposedly, that is why you removed me from your Evolutionary Psychology News FB group.

Please address this attack by Clarence A. ‘Sonny’ Williams, who wrote: “I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.”
 

Robert Karl Stonjek Are you trying to get yourself removed from this group as well??
James Kohl  Thanks for asking. No.
I think this group is a great way to inform others who want to learn what is known to those who have linked energy-dependent changes in angstroms to ecosystems via autophagy and supercoiled DNA, as represented in this parody. https://www.youtube.com/watch?v=gwy2lD1reos&feature=youtu.be
James Kohl See also: https://www.youtube.com/watch?v=iM_I6rtIgn0
The alternative may be to remove anyone from this group who has already linked 2016 Nobel Laureate, Ben Feringa’s works to 2016 Nobel Laureate Yoshinori Ohsumi’s works. See for example: Dynamic control of chirality and self-assembly of double-stranded helicates with light

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

See also the section on Regulation of autophagy by amino acids in: Autophagy in the liver: functions in health and disease

James Kohl They make it perfectly clear that autophagy is the only obvious link from the fixation of RNA-mediated amino acid substitutions in the cell types of all living genera to their morphological and to their behavioral diversity. In the same article, they help to show that virus-driven energy theft is the link to all pathology. See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna+autophagy (534 published works link energy-dependent changes in microRNAs to autophagy.

See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna 56723 published works link nutrient energy-dependent microRNAs to all cell type differentiation in all living genera and they also link virus-driven energy theft to all pathology.

Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt: “Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.” — Kalevi Kull

Clarence A. ‘Sonny’ Williams is still touting “…evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity.”

He has ignored all the experimental evidence of biologically-based cause and effect during the past twenty years. I don’t know what else to do besides cite Kull’s comment and point out that Clarence A. ‘Sonny’ Williams is not even trying to move forward with “cutting edge” knowledge about RNA-mediated cell type differentiation. He is stuck trying to sell hidden energy — as if he were even less informed than most theorists.

See for comparison: Cultural differences may leave their mark on DNA

This is a big advancement of our understanding of race and ethnicity,” Burchard said. “There’s this whole debate about whether race is fundamentally genetic or is just a social construct. To our knowledge this is the first time anyone has attempted to quantify the molecular signature of the non-genetic components of race and ethnicity. It demonstrates in a whole new way that race combines both genetics and environment.
Alternative splicing of pre-mRNA

Mutations: the "driving force" behind human brain complexity?

Evolutionary Psychology Crap in New Scientist

There is a reason why domestic violence is so widespread, says David Buss, an evolutionary biologist at the University of Texas in Austin: it carries a selective advantage, tied with reproductive success.

Larry Moran wrote:

There’s something seriously wrong with evolutionary psychology. And there’s something seriously wrong with respectable science magazines who promote this crap.

Are the science magazines that promote this crap respectable? I lost respect for anyone who still uses de Vries 1902 definition of mutation in attempts to explain how the emergence of life links natural selection from mutations to all extant biodiversity.

Evolutionary psychology Group Description

Evolutionary Psychology is an approach to psychology, in which knowledge and principles from evolutionary biology are put to use in research on the structure and function of the human mind.

Information and vision

Excerpts:

RKS: The retina turn light into visual information which is then processed by specific brain areas dedicated to this task, known as V1 through to V9. 

RKS:
This is established by neuroscience, yet another entire branch of science you dismiss in its entirety in an effort to prove your own feeble points…

RKS:

This involves previous experience, current mood and emotional status, previous behaviour (what you were doing when the visual stimuli occurred) and so on.  In other words there is an entire world of cognitive processing that needs to be consulted before behaviour occurs or is modulated as a result of visual stimuli.

RKS:

Information is also modified in the brain.  Visual information is filtered, in other words the visual information is processed, the colour of scenes is modified to compensate for the changing colour of light through the day (redder in the morning and night, bluer in the middle of the day)…

RKS:
We were discussing information processing with regard to the handling of information gleaned by the senses.  You are discussing in the above the decision making processes which occur in response to sensory stimulation and after that stimulation has been processed.
No supporting argument?  Perhaps you should try reading what I write…
I think it is safe to say that we can group behaviour into three steps:
1) Sensory stimulation;
2) Decision making, Behavioural response;
3) behavioural output.
The information processing being discussed previously concerns the (1) and (3), what happens to sensory stimulation on its way to the decision making process and on its way from the decision making process.  We have not discussed, except for your last statement above, the decision making process per se.

Other discussion groups owned and/or moderated by Robert Karl Stonjek include: Yahoo! Groups
Climate Change Forum
Cognitive NeuroScience
Evolutionary Psychology News Only
Mind and Brain
Physical Sciences
Psychiatry Research

See for comparison: Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

Clarence A. ‘Sonny’ Williams: wrote this to the Neuroscience FB group moderated by Robert Karl Stonjek

Interesting research adding to other evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity. Please note that this research does not identify uniquely human genes, but rather the comparison is between mice and humans. For all we know, the identified genes are present in all primates.

Here, the regulatory region changes found in humans but not mice are involved in activity-dependent synaptic changes (roughly, plasticity).

I responded:

No experimental evidence of biologically-based cause and effect links mutations to anything except pathology. Activity-regulated gene expression is nutrient energy-dependent and controlled by the physiology of reproduction in all living genera.

I added: The Odyssey of Autophagy

Excerpt: “ask a simple question about an interesting phenomenon, pick the right model organism in which that question can be approached genetically and biochemically, and let the grand unity of biology do the rest.”

The question is: Where did the quantized energy in a hydrogen atom come from and where does it go when it is stolen by viruses?

I added: Theorists sell hidden energy

Conclusion: Neo-Darwinian theorists invented ridiculous theories because they did not know where energy came from or where it goes when it no longer sustains life. They sold their theories to the biologically uninformed masses and will continue to sell theories about hidden energy until serious scientists put a stop to the nonsense touted by the evolution industry and the “big bang” cosmology industry.

See also: Structural diversity of supercoiled DNA

Clarence A. ‘Sonny’ Williams (with my emphasis)

Thanks for your contributions, Mr. Kohl, but I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection. Others may want to respond to any comments you make on posts from others, even if they often do not relate to the subject at hand, but this is the last time I will respond to any posts or comments you make.

James Kohl

Thanks for your ongoing antagonism and atheistic nonsense. If not for you and others like you, serious scientists would have nothing to offer to those who want to become biologically informed. See also: http://onlinelibrary.wiley.com/doi/10.1002/bdrc.21146/full Excerpt: “Studies conducted in various animal models have revealed the importance of ncRNAs during gonadal determination and differentiation process. However, the functions of these RNAs in the human sex determination are still not known.”

How much longer will anyone pretend not to know that hydrogen-atom energy in DNA base pairs in solution links nutrient energy-dependent changes in microRNA flanking sequences to all biodiversity via what is known to all serious scientists about autophagy and how the pheromone-controlled physiology of reproduction is linked to supercoiled DNA? When virus-driven energy theft causes malfunctions in receptors, the receptor-mediated events are linked from mutations to pathology, not to the evolution of a new species. I’ve published award-winning review of these facts and other reviews for more than 20 years. And Mr. Williams has come here to plague others with more of his pseudoscientific nonsense.

See for comparison our section on molecular epigenetics from this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

The phylogenetic utility and functional constraint of microRNA flanking sequences

Excerpt: “…miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.”

The de novo assembly of genomes is energy-dependent and biophysically constrained by the physiology of reproduction whether or not you believe in creation. But if you believe that humans evolved via Darwinian natural selection, you should probably learn that Darwin put his energy-dependent “conditions of life” first. He did not seem to believe that anything created itself or any species outside the context of what is now known about autophagy and supercoiled DNA.

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. 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.

I wrote: Robert Karl Stonjek  Attacks on the beliefs of others should not be tolerated, and supposedly, that is why you removed me from your Evolutionary Psychology News FB group.

Please address this attack by Clarence A. ‘Sonny’ Williams, who wrote: “I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.”
 

Robert Karl Stonjek Are you trying to get yourself removed from this group as well??
James Kohl  Thanks for asking. No.
I think this group is a great way to inform others who want to learn what is known to those who have linked energy-dependent changes in angstroms to ecosystems via autophagy and supercoiled DNA, as represented in this parody. https://www.youtube.com/watch?v=gwy2lD1reos&feature=youtu.be
James Kohl See also: https://www.youtube.com/watch?v=iM_I6rtIgn0
The alternative may be to remove anyone from this group who has already linked 2016 Nobel Laureate, Ben Feringa’s works to 2016 Nobel Laureate Yoshinori Ohsumi’s works. See for example: Dynamic control of chirality and self-assembly of double-stranded helicates with light

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

See also the section on Regulation of autophagy by amino acids in: Autophagy in the liver: functions in health and disease

James Kohl They make it perfectly clear that autophagy is the only obvious link from the fixation of RNA-mediated amino acid substitutions in the cell types of all living genera to their morphological and to their behavioral diversity. In the same article, they help to show that virus-driven energy theft is the link to all pathology. See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna+autophagy (534 published works link energy-dependent changes in microRNAs to autophagy.

See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna 56723 published works link nutrient energy-dependent microRNAs to all cell type differentiation in all living genera and they also link virus-driven energy theft to all pathology.

Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt: “Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.” — Kalevi Kull

Clarence A. ‘Sonny’ Williams is still touting “…evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity.”

He has ignored all the experimental evidence of biologically-based cause and effect during the past twenty years. I don’t know what else to do besides cite Kull’s comment and point out that Clarence A. ‘Sonny’ Williams is not even trying to move forward with “cutting edge” knowledge about RNA-mediated cell type differentiation. He is stuck trying to sell hidden energy — as if he were even less informed than most theorists.

See for comparison: Cultural differences may leave their mark on DNA

This is a big advancement of our understanding of race and ethnicity,” Burchard said. “There’s this whole debate about whether race is fundamentally genetic or is just a social construct. To our knowledge this is the first time anyone has attempted to quantify the molecular signature of the non-genetic components of race and ethnicity. It demonstrates in a whole new way that race combines both genetics and environment.
rp_levels-of-organization.jpg

Energy-dependent chirality (2)

See Energy-dependent chirality
2013 MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination
See also E. Ben-Jacob
Ben-Jacob et al., have linked everything currently known about natural information processing from natural selection for energy-dependent codon optimality to healthy longevity and from virus-driven energy theft to mutations that cause cancer.
See for comparison: LH Tsai
Tsai laboratory

Our primary goal is to elucidate the mechanisms underlying neurological disorders affecting learning & memory. The major research areas include age disorders, autism, and Alzheimer’s disease.

2012 MicroRNAs in learning, memory, and neurological diseases

Recent advances in methods of next-generation sequencing, such as RNA-seq, offer the means to quantitatively evaluate the functions of miRNAs in a genome-wide manner in large cohorts of samples. These new technologies have already yielded valuable information and are expanding our understanding of miRNA-based mechanisms in higher-order brain processing, including learning and memory and cognition, as well as in neuropsychiatric disorders.

2015 Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

The exposure to a new sensory experience, for instance, profoundly alters the morphology and connectivity of neural circuits, and these changes are thought to be instrumental in the formation of long-lasting memories and adaptive responses (Goelet et al., 1986).

They linked ecological variation to experience-dependent changes in the connectome and ecological adaptations.
2016 Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior
They linked the ecological adaptation to social behavior.
Reported as: Researchers identify genome-modifying enzyme linked to Rett Syndrome

To understand how the HDAC3 protein regulates the genes, the researchers then analysed them further. In particular, they hoped to identify any motifs, or patterns of DNA sequence, to which regulatory proteins, known as transcription factors, could bind. Transcription factors are proteins that control which genes are turned on or off within the genome.

They linked ecological variation to gene regulation via energy-dependent transcription
2016 Gamma frequency entrainment attenuates amyloid load and modifies microglia
Abstract conclusion:

Our findings uncover a previously unappreciated function of gamma rhythms in recruiting both neuronal and glial responses to attenuate Alzheimer’s-disease-associated pathology.

They linked light-induced changes in gamma oscillations (20-50 Hz) to pathology via levels of amyloid-beta (Abeta)1-40 and Abeta 1-42 isoforms in the context of energy-dependent changes in the onset of plaque formation and cognitive decline in the mouse model of Alzheimer’s disease.
isoform: any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence.
Tsai et al., have linked everything currently known about natural information processing from natural selection for energy-dependent codon optimality to RNA-mediated amino acid substitutions and healthy longevity and from virus-driven energy theft to mutations that cause neurodegenerative diseases. They place what is known about amino acid substitutions into the context of isoforms.
See also: 2017 In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory
Everything known about natural selection for energy-dependent codon optimality and healthy longevity for comparison to virus-driven energy theft and the mutations linked to all pathology is placed into this context:

“… neuronal activity induces relocalization of gene loci to ‘transcription factories’, and specific enhancer–promoter looping contacts allow for precise transcriptional regulation.

Learning and memory appear to depend on specific enhancer–promoter looping instead of energy-dependent changes that link microRNAs from amino acid substitutions to healthy longevity and virus-driven energy theft to cancer via the works of Eshel Ben-Jacob et al.

Enhancer–promoter looping interactions are an important event in transcriptional initiation, but looping is not always sufficient to drive expression per se. This is exemplified by the finding that many looping contacts are established prior to gene activation [66].

Claims about enhancer–promoter looping interactions obfuscate facts about energy-dependent transcription, which is established in the context of energy-dependent changes in the microRNA/messenger RNA balance. The works of LH Tsai et al., go a long way towards obfuscating the facts serious scientists have learned form the works of the late Eshel Ben-Jacob et al.
See also: Language and Communication as Universal Requirements for Life (link opens pdf)

If stem-loop consortia build complex consortia, they initiate social interactions not present in a pure chemical world, that is, biological selection emerges. This designates the crucial step from inanimate world to life (Figure 16.8).

No matter how much obfuscation of facts about energy-dependent chromatin remodeling is introduced via use of different terms, such as chromatin topology, stem-loop and enhancer–promoter looping, the word play can always be viewed in the context of funding attempts that are the primary concern of politicized science.

fruit-dove

Theories vs facts about polycombic adaptation

See: Demoncrats fight polycombic ecological adaptation

Exosomes as miRNA Carriers: Formation–Function–Future

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

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

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

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

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

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

Conclusion:

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

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

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

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

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

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

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

rp_levels-of-organization.jpg

Happy biophysically constrained Thanksgiving (in the USA)

Is there any other holiday in the world that celebrates biophysically constrained cell type differentiation in all living genera?
The availability of amino acids and proteins in new genes is nutrient energy-dependent. The de novo creation of genes is biophysically constrained by the innate immune system and the physiology of reproduction. That fact was detailed for a general audience in Biblical Genesis.
Today, all of us can be thankful that the pseudoscientific nonsense of neo-Darwinian theory was replaced earlier in the month with experimental evidence of how new genes are created in the context of energy-dependent hydrogen-atom transfer in DNA base pairs in solution, single nucleotide polymorphisms, microRNA flanking sequences and RNA-mediated amino acid substitutions that stabilize the naturally fluorescent supercoiled DNA in all organized genomes.
We had this: “…insight coming from re-analyses of translated transcripts in yeast that suggested that de novo gene evolution could even be more prevalent than gene duplication-divergence processes [13]
The energy-dependent de novo creation of genes in the context of duplication and divergence was accurately portrayed like this: “…the exact network of interactions between the nuclear lamina and the genome depends on the protein components of the nuclear envelope, the epigenetic state of the genome, and the availability of specific proteins that interpret these epigenetic signals and mediate interactions with the nuclear lamina.
Naturally occurring DNA fluorescence in bacteria and dinosaur osteocytes proves that the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution is the basis for the creation of all biodiversity on Earth.

Simply put, God started with the creation of energy contained in hydrogen atoms as information, which is exactly what the Holy Bible says about His Word and the Light (the quantized anti-entropic virucidal energy of sunlight).Schrodinger (1944) linked it to the works that led to the Nobel Prize in Physiology or Medicine (1933) awarded to Thomas Hunt Morgan for linking inheritance to chromosomal rearrangements. Schrodinger and Dirac shared the prize in Physics that year.

If you remember how your sheets smelled after they had been hung out to dry in the sun, you have already experienced an example of purifying selection for energy-dependent codon optimality, which can be placed into the context of the Nobel Prize-winning works from 1933, or not. You can tell atheists and agnostics about the energy-dependent purifying selection before asking them where they think the energy in a hydrogen atom came from, or not.

When a friend asked me about that, I was forced to learn more about subatomic particles, but what I learned does not matter as much now that the energy has been linked to the creation of new genes. The de novo creation of genes is referred to as the “holy grail” of biology.

However, the energy-dependent protection of the new genes from virus-driven energy theft is also important. If energy-dependent protein folding chemistry is not biophysically constrained and protected from energy theft, life on Earth could not exist.

Thank God, for the anti-entropic virucidal effects of ultraviolet (UV) light, which links femotosecond blasts of UV light to energy-dependent RNA-mediated DNA repair outside the context of claims about emergence and evolution. For comparison, see:

Evolution: Dynamics of De Novo Gene Emergence

Conclusion (with my emphasis):

It has been suggested that the seemingly finite amount of stable protein folds observed across all domains of life is indicative of an early origin of all folds [16–18], possibly under different conditions and functions than the ones today [17]. However, entirely new folds have been shown to arise de novo in viruses [19] and new domains are present in recently acquired regions of old genes, as well as in young genes [20]. Until now, de novo evolved genes are largely underrepresented in structural analyses, and it seems that resolving their structure is a challenge that will provide us precious information about the origin of stable folds, molecular functions and the interaction between genome and environment.

Resolving the issues of virus-driven energy theft, which have been underrepresented in claims about the structure of functional DNA requires all serious scientists to include the role of virus-driven energy theft in the context of protein folding chemistry. There has never been a suggestion made by any serious scientist that the de novo creation of genes could occur outside the context of biophysically constrained protein folding chemistry. That’s why all serious scientists have linked energy-dependent changes from angstroms to ecosystems via the creation of genes and the virus-driven energy theft that links mutations to loss of function manifested in all pathology.

See also: Although sequence-specific association of co-regulated genomic loci is appealing, random interactions between loci with shared chromatin properties might be an equally effective way of modulating transcription levels.

Pseudoscientists who make claims like this have never supported them with experimental evidence of biologically-based cause and effect. Why would anyone include such a claim in the same article that proved the de novo creation of genes was energy-dependent and biophysically constrained via supercoiled DNA, which protects all organized genomes from virus-driven energy theft?

Alternative splicing of pre-mRNA

Energy-dependent purifying selection / autophagy (4)

Energy-dependent purifying selection / autophagy (3)

My question: What is an abiotic environment?

See:

abiotic factors found in aquatic systems may be things like water depth, pH, sunlight, turbidity (amount of water cloudiness), salinity (salt concentration), available nutrients (nitrogen, phosphorous, etc.), and dissolved oxygen (amount of oxygen dissolved in the water). Abiotic variables found in terrestrial ecosystems can include things like rain, wind, temperature, altitude, soil, pollution, nutrients, pH, types of soil, and sunlight.

My question: When did Schrodinger’s negative entropy of sunlight become an abiotic factor/variable?

See: What is Life? (1944)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

Erwin Schrödinger (1887–1961) is best known as a co-recipient of the 1933 Nobel Prize in Physics, which is the same year that Thomas Hunt Morgan won the Nobel Prize in Physiology or Medicine for discoveries elucidating the role that the chromosome plays in heredity. Simply put, between two 1933 Nobel Laureates from different disciplines, we learned why the concept of the environment must include everything from energy-dependent changes in angstroms to ecosystems in all living genera.

See for instance:

The concept of the environment used for our discussion is very broad; it incorporates considerations of both the molar and the molecular levels.(1996)

See also, the alternative:  One crank dies, another rises to take his place

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.

The unprovoked attack on my accurate representation of biologically-based cause and effect can only be compared to the attacks of PZ Myers on the accurate representations of others. For comparison, Roger Penrose may become best known for leading the way with his support of Schrodinger’s claims in this concise statement:

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

—  Roger Penrose 8 August 1991)

I hope that PZ Myers will become well known for ignoring all the claims that have ever been made by serious scientists and for touting only the claims made by other pseudoscientists and their idiot minions.

See: Energy-dependent purifying selection / autophagy (5)