terrarium-eco-system

Chemical ecology and RNA-mediated control of DNA loops

DNA Loop-the-Loops

A new full-genome map indicates how DNA is folded within the nuclei of human cells.By Kate Yandell | December 11, 2014

Excerpt: “…many loops were conserved among cell types, and even between mice and humans. But others seemed to drive cell type-specific gene expression patterns.”

My comment to The Scientist Magazine:

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Excerpt: “A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for nutrient acquisition, movement, reproduction, and the diversification of species from microbes to man [via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize protein folding in the DNA of organized genomes].

I think this report on how DNA is folded within the nuclei of human cells makes it obvious that nutrient-dependent pheromone-controlled RNA-mediated amino acid substitutions, protein folding, and feedback loops link the epigenetic landscape to the physical landscape of DNA via what is currently known about the bio-physically constrained chemistry of protein folding and the conserved molecular mechanisms of cell type differentiation.

For cross species examples that include the honeybee model organism, see my 2012 and 2013 reviews, which are based on what we (T.B.) included in the molecular epigenetics section of our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior  and on extension of RNA-mediated cell type differentiation to insects in Organizational and activational effects of hormones on insect behavior and to the life history transitions of honeybees in Honey bees as a model for understanding mechanisms of life history transitions.

Light-induced-conformer-intercoversion-of-hydrogen-bond

Intelligent viruses and cancers?

The Very Intelligent Ebola Virus Takes Front and Center

Excerpt 1) “Ebola doesn’t enter the nucleus. It uses the cell’s machinery of ribosomes and transfer RNA to make proteins from the viral messengerRNA.”
Excerpt 2) “Normally, mechanisms inside the nucleus have complex relations with messenger RNA and the alternative RNA editing process (see RNA alternative editing post). Specific protein complexes help splice the messengerRNA before it is sent from the nucleus to the ribosomes in the cytoplasm to make proteins.”
My comment: Dr. Lieff may be the only one capable of detailing the problem presented by the Ebola viruses in terms of cell type differentiation that other scientists from different disciplines can understand. But first, others must want to understand the complexity that is involved. That requires them to stop thinking that the problem can be attributed to mutations and start thinking in terms of how ecological adaptations occur via nutrient-dependent amino acid substitutions that stabilize the organized DNA in the genomes of non-viral cell types.
See also: Intelligent RNAs in the Brain

Excerpt 1) ‘Viruses and jumping genes changed this dogma into a bidirectional flow of code in and out of the DNA. Alternative splicing added an additional major step with very complex editing of the pre-messenger RNA. In humans as many as 500 different messenger RNAs, and therefore 500 different proteins, can be made from one pre-messenger RNA.”

My comment: No one else seems to recognize the link from pre-messenger RNAs (pre-mRNAs) to the alternative splicings that lead to the production of different messenger RNAs (mRNAs). Alternatively, if they do recognize the link from pre-mRNAs to different mRNAs and cell type differentiation, they may not recognize the fact that the conserved molecular mechanisms of alternative splicings appear to link ecological variation to RNA-mediated amino acid substitutions that determine the virulence of viruses and their ability to manipulate the cell types of different species.
Cross species examples have already been seen in the light of what has happened with other viruses that infected other mammals, but now infect humans. If the molecular mechanisms of cell type differentiation are conserved across species, the amino acid substitutions that determine seasonal variations in the ability to infect humans also reflect that fact that viruses adapt via their ability to use materials found in different cell types of different species to produce new amino acids that allow the viruses to proliferate via subtle changes in their cell types.
See for example: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (with my comment) reported as:Research reveals details of how flu evolves to escape immunity
Excerpt:“…seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution.
My comment: The ability of viruses to change via a single amino acid substitution enables them to escape the immunity of vaccines. This drives the seasonal need to develop new vaccines. Can we expect the same ability to drive changes in the Ebola viruses, which link them to their ability to escape the natural immunity already established in some but clearly not all other animals, including some humans?

See also:

1) The Wall Street Journal (11/3, A8, Marcus, Subscription Publication) reports that researchers have begun to look at the children of individuals who have the rare and fatal genetic disease Niemann-Pick Type C, a disease whose gene may offer protection against the Ebola virus. Institutions whose researchers are investigating such a connection include Albert Einstein College of Medicine, the US Army Medical Research Institute of Infectious Diseases, the Netherlands Cancer Institute and Harvard Medical School.

My comment: Does the gene offer protection or is an amino acid substitution in the DNA of the organized genome the protector against the Ebola virus?

2) Virologists Investigate Ebola’s Connection To Bats. NPR (10/31, Greenfieldboyce) reported in its “Shots” blog and on its “Morning Edition” program on virologists who are focusing on studying Ebola. While “scientists believe the virus circulates in fruit bats…no one knows the details of how bats pass it to humans or other species,” including gorillas, chimpanzees, and antelope, species which have been known to have the virus in the past. A second concern for researchers is the drastic variation in sickness levels among infected humans. Researchers are examining why “some people get very sick, others seem to get less sick, and others may not get sick at all.”

My comment: See my blog post: Are evolutionary theorists ‘nob ends’? “…some researchers seem to think the Ebola viruses mutate and automagically change the biophysically-constrained properties of their chemical bonds. Supposedly, that’s how mutations in viruses enable changes in virulence, which actually arise via amino acid substitutions and changes in hydrogen bonds that link atoms to ecosystems.” Without the link from atoms to ecosystems, even serious scientists are left with only their speculation about how viruses are transmitted across species and why some individuals are more susceptible than others to diseases.

3) Reuters (11/2, Hirschler) also reported bats to be the prime suspect for spreading Ebola to humans, although bats themselves do not get sick with the virus. Additionally, bats are known to carry several other viruses which can include rabies and severe acute respiratory syndrome (SARS). Researchers are investigating bats’ ability to carry such disease without becoming sick and learn the mechanisms by which they do so.

My comment: The most likely reason that frugivorous (fruit) bats carry — but do not succumb to such viruses, is that levels of ingested vitamin C stabilize their organized genomes via nutrient-dependent amino acid substitutions associated with the complexity of  DNA repair mechanisms. The most likely mode of transmission to humans during their preparations to eat the bats (categorized as bush-meat). Food preparation is the suspected mode of transmission that supposedly enabled the change from SIV in other primates to HIV in humans. However, even if no one ever killed, cooked, and ate a bat, transmission might still occur as was represented in the recent science fiction movie “Contagion.”
Excerpt: “The fictional virus reaches humans through a series of animal encounters: a bat eats some fruit then drops it in a pig pen, the pig eats it, then is butchered and handled by a chef who comes in contact with Gwenyth Paltrow.”
My comment: I am reminded of how Greg Bear linked human endogenous retroviruses to the evolution of human biodiversity in his science-fiction novels, ‘Darwin’s Radio’ and ‘Darwin’s Children’. However, the changes caused by the viruses were beneficial, not deadly.
4) US Hospitals Prepare For Ebola. The Wall Street Journal (10/31, Armour, Subscription Publication) explored the debate about treatment for Ebola patients in US hospitals. An ethical dilemma exists because physicians may want to pursue aggressive treatments for Ebola patients, though some of those treatments increase the risk of exposure of the disease to hospital staff. Stephen Cantrill, the American College of Emergency Physicians’ Ebola panel chairman, explained that the issue of defining “futile care […] with modern Western medicine […] is going to be very tough.” The Journal reported on several hospitals who said they may not provide CPR to an Ebola patient.
My comment: What if the most effective preventative treatment was supplementation with vitamin C. It could facilitate DNA repair to prevent the damage in infected humans from the cytokine storms associated with the ability of the virus to adapt to different mammalian hosts — perhaps via a single amino acid substitution? Alternatively, what if the thermodynamic cycles of protein folding in the viruses could not occur at body temperatures above 104 degrees? Could a steaming hot bath or sauna cure before the virus killed?
Will someone like Jon Lieff or Brian Cox comment, or will we all be killed by the pseudoscientific nonsense about evolution touted by people like Neil deGrasse Tyson in the series Cosmos? See his comments on Episode#2 . Note the difference between serious scientists and creative pseudoscientists, like Tyson, reported here: “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. 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…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.”
May God help us all if the pseudoscientists do not quit touting their nonsense about “emergent truths” while trying to teach others to believe in the magic of Mutation-Driven Evolution as if “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.”
For comparison, see Nutrient-dependent/pheromone-controlled adaptive evolution: a model, with its examples of how ecological variation leads to ecological adaptations. The conserved molecular mechanisms of RNA-mediated cell type differentiation via amino acid substitutions in species from microbes to man seem to be consistent with what Jon Lieff suggests is a very intelligent virus.
Its level of intelligence can be compared to the intelligence of evolutionary theorists who think that viruses mutate and evolve or that bacteria evolved into humans. Why don’t they know that viruses ecologically adapt to ecological variation that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of every living species on this planet? Do they not understand how the physics, chemistry, and conserved molecular mechanisms are manifested in species from microbes to man? It’s beginning to look like some people are not intelligent enough to think about anything except what they were taught to believe in.
See also: A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats
Excerpt: “We found shifts associated with frugivory across the entire OR subgenome. Particular shifts in diversity within functional genes and pseudogenes, rather than the simple pseudogenization of a large number of ORs, suggests adaptive changes linked to ecological specialization in the highly derived frugivorous phyllostomids.
My comment: Ecological specialization links the nutrient-dependent pheromone-controlled physiology of reproduction to the highly successful radiation of bats via the experience-dependent de novo creation of olfactory receptor genes. De novo creation of genes has been touted as if it were the holy grail of evolutionary biology. However, it appears to be the holy grail of creationists like Dobzhansky since it is linked from RNA-mediated events to the amino acid substitutions that differentiate cell types in species from microbes to man. Dobzhansky he noted what occurred among primates: “…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.” see: Nothing in Biology Makes Any Sense Except in the Light of Evolution
It appears that nothing about evolution makes sense, unless it is placed back into the context of the light of creation via the de novo creation of olfactory receptor genes. Experience-dependent de novo creation of receptors can be linked from light-induced amino acid substitutions to nutrient-induced receptor-mediated RNA-mediated amino acid substitutions in animals via quaternary and ternary switches. The complexity of these switches is linked directly to cell type differentiation in health and disease via the conserved molecular mechanisms manifested in the morphological and behavioral phenotypes of species from microbes to man.

Time for a sermon or common sense?

The thing that hath been, it is that which shall be; and that which is done is that which shall be done: and there is no new thing under the sun. — Ecclesiastes 1:9
In the light of the sun, we can now revisit what JBS Haldane wrote in 1963 about “The four stages of acceptance:
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.” — Review of The Truth About Death, in: Journal of Genetics 1963, Vol. 58, (p.464)”
I learned of this approach to acceptance many years ago, and found a source for it. The source attests to the fact that acceptance of biological facts has always lagged behind the acceptance of the theory of evolution, which JBS Haldane helped to invent and define in terms of population genetics. See for examples: Science, Pseudoscience, and The Three Stages of Truth — cited in The Truth in Small Doses: Why We’re Losing the War on Cancer-and How to Win It.
See also:
Arguments against new ideas generally pass through three distinct stages, from `It’s not true’, to `Well, it may be true, but it’s not important’, to `It’s true and it’s important, but it’s not new — we knew it all along. (p. 1) — John D. Barrow. The Artful Universe. Oxford University Press, 1995.
We now can put what has been known all along about the link between light-induced amino acid substitutions into the context of “…no new thing under the sun” — Ecclesiastes 1:9, and what Dobzhansky (1964) wrote, presumably about people like JBS Haldane:
“…the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!”
In the same article, Dobzhansky noted — 50 years ago — 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.”
In 1973, he then placed that fact into this context “…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” into the context of Nothing in Biology Makes Any Sense Except in the Light of Evolution. He also linked his creationist beliefs to evolution via mutations and amino acid substitutions.
1) “It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist.”
2) “Most mutations involve substitutions of single nucleotides somewhere in the DNA chain coding for a given protein. Therefore, one can calculate the minimum numbers of single mutations needed to change the cytochrome C of one organism into that of another.”
Calculations were used that made it appear that mutations accumulated over eons and led to the evolution of biodiversity.
We now know that single nucleotide substitutions link amino acid substitutions to cell type differentiation via nutrient-dependent RNA-mediated events, which occur quickly and do not occur due to mutations. Simply put, it has become clearer that mutations do not change the cytochrome C or any other aspect of metabolism in one organism into that of another species.
Mutations cause perturbed protein folding that cannot lead to from one species to the evolution of another species. Mutations lead to pathology. The sooner theories about the evolution of biodiversity are removed from the facts about cell type differentiation, the sooner progress will be made towards understanding and treating cancer and the ecological adaptations manifested in the Ebola viruses and other viruses.
But wait, how did I get from the Ebola viruses to cancer and back? I did it with the explanatory power of  nutrient-dependent pheromone-controlled cell type differentiation. How would an evolutionary theorist do that? See also: From HIV to cancer, IL-37 regulates immune system for additional information that appears to link cell type differentiation in viruses to uncontrolled cell type proliferation in cancers via conserved molecular mechanisms.
What I’ve recently seen is attempts to link ‘protein isoforms’ and alternative splicings of pre-mRNA as if both were representations of biologically-based cause and effect. See this Wikipedia entry with my emphasis:
Excerpt: “A protein isoform is any of several different forms of the same protein. Different forms of a protein may be produced from very closely related gene duplicates—as ‘same protein’ or ‘a protein’ makes no sense for highly diverged paralogs that arose from a single ancestral gene that duplicated billions of years ago and subsequently diverged greatly in sequence, structure and functionality—or may arise from the same gene by alternative splicing. In older literature one can also encounter the use of the term isoform to describe alleles of the same gene, but currently the terms refers mostly to paralogous and alternatively spliced proteins, not alleles.”
Apparently, the theorists think they can get away with more misrepresentations of how nutrient-dependent cell type differentiation occurs within a few generations as recently shown in lizards. If they can continue to convince others that RNA-directed DNA methylation and RNA-mediated events that link cell type differentiation to a single ancestral gene and evolutionary events across billions of years, most of us may be dead by the time the rest of us realize we were tricked into believing in a ridiculous theory instead of biologically-based facts.

achiral-glycine

De novo DNA methylation?

Epigenomics and the control of fate, form and function in social insects

Excerpt: “De novo DNA methylation is critical for developmental divergence of female larvae towards the honeybee worker caste and is progressive [49,51].”

de novo is a Latin expression meaning “from the beginning

DNA methylation does not automagically occur. From the beginning, it has been nutrient-dependent and RNA-directed. Nutrient-dependent RNA-directed DNA methylation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. If de novo DNA methylation automagically occurred, there would be no link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.
In the honeybee model organism and other model organisms, RNA-directed DNA methylation links nutrient-dependent amino acid substitutions to cell type differentiation in all cells via conserved molecular mechanisms. The metabolism of nutrients to pheromones controls the differentiation of cell types that result in the morphological and behavioral phenotypes of every bee in the hive.
The article that suggests de novo DNA methylation automagically occurs appears to place nutrient-dependent RNA-directed DNA methylation and RNA-mediated cell type differentiation by amino acid substitutions into the context of the evolution of biodiversity. First, the authors link the automagical evolution of biodiversity manifested in the morphological and behavioral phenotypes of species from microbes to man to de novo methylation. Then, the authors add “… nutrition may have a significant and direct role in directing patterns of epigenomic control during developmental caste determination.’
See for comparison: Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation
“Epigenetic modifications include chromatin remodeling, histone tail modifications, DNA methylation and, more recently, have expanded to include non-coding RNA and microRNA gene regulation [3].
DNA methylation is the most widely studied form of epigenetic modification and occurs within the one-carbon metabolism pathway, which is dependent upon several enzymes in the presence of dietary micronutrients as cofactors, including the availability of folate, choline and betaine through the diet (Fig. 1). Through an ATP-driven reaction, methionine is converted into S-adenosylmethionine (SAM), the universal cellular methyl donor [4]. DNA methyltransferases (DNMTs) covalently attach methyl groups from SAM to the carbon-5 position of cytosine bases, generating 5-methylcytosine thus methylating DNA.”
Here are some differences between de novo DNA methylation and nutrient-dependent DNA methylation in the context of the evolution of biodiversity.
1) There is no such thing as de novo DNA methylation. That means there is no such thing as de novo RNA-mediated cell type differentiation by amino acid substitutions, which differentiate the cell types of all individuals of all species.
2) Nutrient-dependent RNA-directed DNA methylation links RNA-mediated cell type differentiation by amino acid substitutions to the differentiation of cell types in all individuals of all species.
Summary, cell type differentiation that occurs via nutrient-dependent amino acid substitutions is controlled by the metabolism of nutrients to species-specific pheromones. The pheromones control the physiology of nutrient-dependent reproduction, which links it from RNA-directed DNA methylation to pheromone-controlled fixation of the amino acid substitutions that differentiate all cell types via conserved molecular mechanisms in species from microbes to man.
For examples, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.  Also see, Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB  for the most recent publication on nutrient-dependent amino acid substitutions that differentiate the cell types of bacteria in the context of antibiotic resistance previously reported to be driven by mutations that somehow caused bacteria and other species to evolve.

See also: Jack A, Connelly J. J, Morris J. P. DNA methylation of the oxytocin receptor gene predicts neural response to ambiguous social stimuli. Frontiers in Human Neuroscience. 2012;6:280.
Also see:

Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.

poster-from-jesse

Pharmacogenomics

“The gene, cell, tissue, organ, organ-system pathway is a neuroscientifically established link between sensory input and behavior. Marts and Resnick (2007) stress the importance of this pathway in the context of a systems biology approach to pharmacogenomics.” (Kohl, 2012)

“Naftolin (1981) stressed its importance to the understanding of sex differences. This pathway is sensitive to conditioning. Sensory input from an organism’s environment activates and reactivates the pathway and causes changes in hormone secretion that condition hormone-driven behavior.” (Kohl, 2012)

See the full tutorial on Pharmacogenomics here
Nutrient-dependent RNA-directed DNA methylation links altenative splicings of pre-mRNA from ecological variation to ecological adaptations in species from microbes to man via conserved molecular mechanisms. See Diamond, Binstock, and Kohl (1996), especially our section on Molecular epigenetics. Our focus was on the gonadotropin releasing hormone (GnRH) neuronal system of mammals because it links what is known about sex differences in cell type differentiation from yeasts to primates. However, the molecular epigenetics of cell type differentiation link genetic networks and metabolic networks to all cell type differences in all individuals of all organisms.
See also: Prenatal Ethanol Exposure Disrupts Intraneocortical Circuitry, Cortical Gene Expression, and Behavior in a Mouse Model of FASD
“Changes in gene expression reported in this study may be caused by altered DNA methylation, an epigenetic modification that cells use to mediate gene expression (Moore et al., 2013), cell differentiation, and embryonic development (Monk et al., 1987; Feng and Fan, 2009)…. Methyltransferase activity can be modified by exposure to ethanol; chronic exposure to ethanol is associated with reduced DNMT3B mRNA expression and hypermethylation in adults (Bönsch et al., 2006). Embryonic exposure to ethanol has been shown to alter DNA methylation patterns at neurulation, with increased methylation of genes on chromosome 10 and X correlating with an increase in neural tube defects (Liu et al., 2009). Furthermore, ethanol exposure impacts methyl donors (Mason and Choi, 2005), highlighting a possible mechanism by which ethanol, through methylation, can drive downstream epigenetic modifications and alter gene expression, as we have seen in this study (Haycock, 2009).”
Epigenetic effects of food odors and social odors called pheromones link the alpha mating pheromone of yeasts to the human response to ethanol exposure. The yeasts produce ethanol and ethanol alters the GnRH-directed luteinizing hormone (LH) response to in adult humans. The GnRH-directed LH response also links epigenetic effects of food odors and human pheromones on GnRH and its downstream effects on other hormones that affect behavior during its development. For example, a single nutrient-dependent amino acid substitution associated with exposure to food odors links the systems complexity of behavioral development to differences in adolescent and adult human behavior via cell type differentiation. See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults.
The link from food odors and nutrient uptake to an amino acid substitution and life history transitions in humans can now be compared to the life history transitions during the development of honeybees. The transitions effectively link epigenetic effects on all other model organism to humans, which means they can be considered in the context of amino acid substitutions linked to morphological and behavioral phenotypes via genetic networks and metabolic networks. Genetic and metabolic networks drive all biological processes. You can think of them as bridges between the organism and the individual molecules – proteins and genes – that form all living cells.
The extent of these bridges in other organisms was detailed in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.The availabilty of genetic testing that links genetic networks and metabolic networks via RNA-mediated events and amino acid substitutions that differentiate cell types heralds the next generation of personalized medicine in which practitioners can learn more about how to prevent reactions to medications and how to ensure the right dose is presecribed on the basis of individual differences in cell types that are manifested in links between genes, metabolism, and behavior.

human-evolution

Sexual differentiation of cell types in plants

Antheridiogen determines sex in ferns via a spatiotemporally split gibberellin synthesis pathway
Excerpt: “Homosporous ferns have evolved a mechanism to favor cross-fertilization by controlling the sex ratio among individuals or prothalli within the population with the aid of antheridiogens. Antheridiogens are pheromones…”
Reported as:

Researchers find ferns communicate with one another to decide gender

Excerpt: “The intercommunication abilities demonstrated by the ferns is an example of a growing field in botany that some have taken to calling plant neurobiology—when plants exhibit behavior that resembles activities of animals.”
My comment to Science Magazine
Biologically-based cause and effect in these ferns appears to parallel what is known about biophysically-constrained thermodynamic cycles of nutrient-dependent protein biosynthesis and degradation in other genera, which is controlled by the metabolism of nutrients to species-specific pheromones.
From an atoms to ecosystems perspective this links nutrient uptake to RNA-directed DNA methylation; RNA-mediated amino acid substitutions; and to pheromone-controlled chromosomal rearrangements associated with ecological speciation but not necessarily associated with mutations, natural selection, and the evolution of biodiversity.
Have homosporous ferns somehow evolved a mechanism that appears to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man? To me it seems more likely that ecological variation led to RNA-mediated ecological adaptations like those that are manifested in the morphological and behavioral phenotypes of other living organisms with cell types that are differentiated by amino acid substitutions.
For examples, see: Signaling Crosstalk: Integrating Nutrient Availability and Sex “The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.”
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932994/
See also: Feedback loops link odor and pheromone signaling with reproduction “Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.” http://www.ncbi.nlm.nih.gov/pubmed/16290036
The link from microbes (yeasts) to mammals seems to be nutrient-dependent amino acid substitutions, like those Dobzhansky (1973) reported in Nothing in Biology Makes Any Sense Except in the Light of Evolution “…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.” http://www.jstor.org/stable/4444260
If what others are reporting in the context of mutations in the Ebola viruses are ecological adaptations, our response to the threat may need to be reconsidered in the context of reports like this one: Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry. http://www.sciencedirect.com/science/article/pii/S0168170206001882
My comment to the phys.org site:

“…plants exhibit behavior that resembles activities of animals.”

That suggests conserved molecular mechanisms of the nutrient-dependent pheromone-controlled physiology of reproduction extend across all genera, as does everything else currently known about the physics, chemistry, and molecular

biology of biophysically-constrained protein biosynthesis and degradation. Indeed, it would be incredibly odd if these “…ferns have evolved an antheridiogen-mediated communication system“The communication system clearly exemplifies how ecological variation leads to ecological adaptations via RNA-directed DNA methylation and amino acid substitutions that differentiate cell types, which are manifested in the morphological and behavioral phenotypes and ecological speciation in all other genera.
If ferns somehow evolved that level of organism-level complexity, their evolution would seem like a miracle that could be compared to their ability to ecologically adapt.
poster-from-jesse

Are evolutionary theorists 'nob ends'?

Interview – Prof Brian Cox and Robin Ince

Robin Ince “Am I wrong to sometimes be scared of science idiots?”

Brian Cox  “…my favoured response would be: ‘you bunch of utter nob ends’.

 See also:  “The problem with today’s world is that everyone believes they have the right to express their opinion AND have others listen to it. The correct statement of individual rights is that everyone has the right to an opinion, but crucially, that opinion can be roundly ignored and even made fun of, particularly if it is demonstrably nonsense!”– Brian Cox

James Kohl shared The Skeptics’ Guide to the Universe‘s photo.

“[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. 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…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.”
That’s nonsense! See for comparison:
1) Whole-exome sequencing identifies a de novo TUBA1A mutation in a patient with sporadic malformations of cortical development: a case report “We successfully identified a causative TUBA1A mutation in a patient with sporadic MCD associated with a simplified gyral pattern by using whole-exome sequencing. The identified novel mutation (E27Q) was located in the N-terminal region of the amino acid sequence. Rapid and comprehensive mutation analysis by using whole-exome sequencing may be useful for genetic counseling in sporadic cases of human disorders derived from multiple candidate genes.” My comment: Mutations cause diseases.
2) Exome sequencing and subsequent association studies identify five amino acid-altering variants influencing human height. Excerpt: “This study demonstrated the utility of next-generation sequencing in identifying genetic variants and loci associated with complex traits.” My comment: Increasing organismal complexity arises via amino acid substitutions that stabilize the organized genome.
3) Exome RNA sequencing reveals rare and novel alternative transcripts Excerpt: “…we propose that ExomeRNAseq may be an excellent approach for cross-species comparisons. It was recently shown that exome capture on DNA can efficiently be used to map variation across primates (24,25), and it should work equally well for RNA based capture. Since we show that we can find a large number of coding variants in the data, exome enrichment at the level of RNA can be used both for annotation of gene models and identification of variation.” My comment: ExomeRNAseq reveals the involvement of RNA-mediated events that link amino acid substitutions to increasing organismal complexity. See also: “…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.” Dobzhansky (1973)

4) Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations Excerpt: “RNA sequencing (RNA-Seq) is a powerful method for the measurement of global gene expression (1, 2). As a discovery tool, the method has dramatically increased our knowledge of the transcriptome, providing new insights into transcript diversity, including the discovery of new structural variants such as alternative splicing, gene fusions or rearrangements, and low-expressed molecules.” My comment:  “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to…” — from the ‘molecular epigenetics’ section of our 1996 review.

5) Genetic mutation Excerpt: ” …mutations provide the “raw material” upon which the mechanisms of natural selection can act.” My comment: I cannot imagine a more ridiculous statement of cause and effect. But remember: “…everyone has the right to an opinion, but crucially, that opinion can be roundly ignored and even made fun of, particularly if it is demonstrably nonsense!”– Brian Cox

6) For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Excerpt: “This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology.”
My comment: My model links what is currently known about physics, chemistry, and conserved molecular mechanisms, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. I include aspects of RNA-directed DNA methylation in model organisms and provide examples of RNA-mediated events that link amino acid substitutions to cell type differentiation in all cells of all individuals and all tissues in all organs of all organ systems in all organisms that exemplify increasing organismal complexity.
For comparison, evolutionary theorists seem to believe in the pseudoscientific nonsense about mutation-driven evolution. “In other words, genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.” (p. 199)

Teleological argument A teleological or physico-theological argument, also known as an argument from design, is an argument for the existence of God or, more generally, for an intelligent creator “based on perceived evidence of deliberate design in the natural or physical world”.[1]

Please join me and others as we ignore and even made fun of the demonstrable nonsense touted by evolutionary theorists. It’s time for serious scientists to move forward by linking the present to the past via what is known about amino acid substitutions that differentiate the cell types of all cells in all individuals of all species from microbes to man. Thus, the question also arises: Are human ethologists ‘nob ends’? See for example, Jay R. Feierman who is the moderator of the human ethology yahoo group.  He wrote:

On 11/1/12: “Random mutations are the substrates upon which directional natural selection acts.
On 2/16/13 : “Random gene mutation is the variance generator upon which natural selection operates.
On 2/23/13: “…random genetic mutations generate the substrate upon which natural selection can act. Random genetic mutations create structural variations in protein enzymes…

 I wonder if Brian Cox also thinks Feierman is a ‘nob end.’ Similarly, is Robin Ince wrong to be scared of science idiots, like Feierman.

Others should begin to fear all science idiots and/or each ‘nob end’ who is currently attempting to manage an RNA-mediated crisis. For example, some researchers seem to think the Ebola viruses mutate and automagically change the biophysically-constrained properties of their chemical bonds. Supposedly, that’s how mutations in viruses enable changes in virulence, which actually arise via amino acid substitutions and changes in hydrogen bonds that link atoms to ecosystems. As people interact among the ecosystems of remote areas in West Africa, they will encounter more viruses that have adapted to their ecosystems. When people cannot adapt to the new viruses as quickly as the viruses adapt to the ecosystems of vitamin-deficient or undernourished people, the recipe for world-wide disaster has been established in the context of what viruses do best. They adapt! Viruses do not mutate and evolve. No species on this planet has ever done that. All have adapted to ecological variation or become extinct. Thus, across all creation of all species, viruses may both predict and be responsible for the fate of all cell types including our nutrient-dependent cell types that have differentiated, not evolved, via our pheromone-controlled physiology of reproduction. Simply put, if our Creator does not intervene, evolutionary theory may lead to the physical death of us all, which will link the present to the past as yet another testament of who is in control of all outcomes.

The concept that viruses might play a fundamental role in the evolution of the complexity of cellular life, as here proposed, may seem novel to many, especially to evolutionary biologists.” There’s a reason for that.  If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based.

Physics

No excuses: Creation and the meaning of organismal complexity

E.O. Wilson On ‘The Meaning Of Human Existence’

Excerpt: “We’re one species — glorious though we are — we are just one species out of an estimated eight million,” Wilson said. “At the present time, we only know almost exactly two million species — enough to give them a scientific name. Six million species are out there, maintaining the planet for us as an autonomous ecosystem and stabilization system.

Book Excerpt: ‘The Meaning of Human Existence’

“Six million species are out there, maintaining the planet for us as an autonomous ecosystem and stabilization system. With our own eyes we can see through the dark glass, fulfilling Paul’s prophecy, “Now I know in part; then I shall know fully, even as I am fully known.” Our place and meaning, however, are not being revealed as Paul expected—not at all. Let’s talk about that, let us reason together.”
My comment: Our place and meaning continue to be revealed as Paul expected. The revelations come precisely as stated by Paul in Romans 1:20 “For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and deity; so that they are without excuse:

The invisible things that occur link atoms to ecosystems via what is currently known about physics, chemistry, and molecular epigenetics. There is no excuse for E.O. Wilson’s philosophical approach to biophysically-constrained ecological adaptations in species from microbes to man. He simply ignores what has been learned by serious scientists about nutrient-dependent RNA-directed DNA methylation.  What’s been learned attests to Paul’s reasonable claims each time something new is revealed about increasing organismal complexity. For example, it has become perfectly clear that RNA-mediated events link ecological variation to ecological adaptations via amino acid substitutions that differentiate all cell types in all individuals of all species. There is nothing random about that. Those who claim that the amino acid substitutions are involve mutations ignore the fact that nothing except food is naturally selected.
In Arrival of the Fittest: Solving Evolution’s Greatest Puzzle, Andreas Wagner credits Nature and natural selection for evolution via metabolism and nutrient-dependent amino acid substitutions, which obviously differentiate cell types in all cells of all individuals of all species. However, he also repeatedly cites statistical analyses that show increasing organismal complexity does not evolve. Morphological and behavioral phenotypes are manifestations of nutrient-dependent ecological adaptations. See the reviews of his book, which include: “Andreas Wagner is one of those rare scientists with the courage and intellect to see the real nature of evolution.’ — Frank Vertosick, author of When the Air Hits Your Brain ” Add mine: “Creationists will jump for joy as evolutionary theorists cry in their beers. Wagner links nutrient-dependent metabolism to cell type differentiation from brewer’s yeasts to mammals via the concerved molecular mechanisms of amino acid substitutions that differentiate cell types in all living species.” James V. Kohl (perfumingthemind.com) co-author of The Scent of Eros: Mysteries of Odor in Human Sexuality.
As E.O. Wilson did in The Social Conquest of Earth, Andreas Wagner ignores the fact that all ecological adaptations are nutrient-dependent and pheromone-controlled. Wilson wrote: “In contrast, human beings, along with monkeys, apes, and birds are among the rare life forms that are primarily audiovisual, and correspondingly weak in taste and smell. We are idiots compared with rattlesnakes and bloodhounds. Our poor ability to smell and taste is reflected in the small size of our chemosensory vocabularies…” (p. 269) Minimally, Wagner advance a more scientific perspective that attests to the fact that amino acid substitutions link the de novo creation of olfactory receptor genes to experience-dependent changes in enzymes that link cell type metabolism to chemical communication among cells and also among the individuals of different species.
E.O. Wilson, and Andreas Wagner might benefit from revisiting Dobzhansky (1972) to again learn that “Reproductive isolation evidently can arise with little or no morphological differentiation.” (p. 665) The idea that birds or any other life forms are primarily audiovisual has never been supported by experimental evidence of biologically-based cause and effect. For contrast, what’s been learned about olfaction in birds extends their nutrient-dependent pheromone-controlled physiology of reproduction to the conserved molecular mechanisms of amino acid substitutions and chromosomal rearrangements, which lead to the species diversity manifested in the morphological and behavioral phenotypes of birds. See for example: New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis.
Did Wilson’s acclaimed historical perspective influence Wagner’s current perspectives on nutrient-dependent hormone-organized and hormone-activated behaviors? Clearly, one need only start by ignoring the pheromone-controlled physiology of insects to continue with claims that miss the link from nutrient uptake to the metabolism of nutrients and pheromone-controlled social behaviors in species from microbes to man. But first, perhaps these theorists need to stop claiming that mutations and or natural selection lead to the evolution of biodiversity. By starting over, they can learn what was intuitively obvious to Dobzhansky, and begin to read the current literature that accurately represents how ecological variation leads to ecological adaptations via the metabolism of nutrients to sex differences in species-specific pheromones in invertebrates and vertebrates.
See for example: Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment
Excerpt 1) “In comparison to D. melanogaster, the house fly genome has a larger number of genes associated with immune response, detoxification and chemosensation.”
Excerpt 2) As the obvious comparison for the M. domestica repertoire, D. melanogaster has 52 genes encoding OBPs [86], 60 genes encoding 62 ORs and 60 genes encoding 68 GRs via alternative splicing of some loci [87], and 65 genes encoding IRs [85].
The link from alternative splicings of pre-mRNA to cell type differentiation via amino acid substitutions is not likely to become clearer than it is in the above excerpts. And null hypothesis testing is not likely to reveal that alternative splicings of pre-mRNA arise in the context of mutations and natural selection that supposedly lead to increasing organismal complexity via molecular mechanisms of perturbed protein folding that invariably lead to diseases and disorders, which are also caused by septic environments and global vectors of diseases that encourage ecological adaptations via extinction of species that do not adapt to ecological variation. However, I must point out the fact that (Z)-9-Tricosene is a sex pheromone produced by female house flies (Musca domestica) to attract males. In bees, it is one of the communication pheromones released during the waggle dance.[3] The article authors portray the link from chemoreceptors to gustation as if it were more important than the link from the nutrient-dependent de novo creation of odor receptors to the pheromone-controlled physiology of reproduction in species from microbes to man.
For example, serious scientists recently reported that Humans Can Discriminate More than 1 Trillion Olfactory Stimuli. Our discriminatory abilties exemplify the link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species.
From Kohl (2012): “Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”
From Kohl (2013) “…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”
What model of biologically-based cause and effect is E.O. Wilson offering us? What can he tell us about RNA-directed DNA methylation and cell type differentiation in ants for comparison to what is known in honeybees? See for example: Epigenomics and the concept of degeneracy in biological systems. It extends what is known about RNA-mediated events from ecological variation to ecological adaptations in primates.
Excerpt: “Deacon [27] gives the example of endogenous ascorbic acid synthesis (vitamin C) existent among some primate lineages and missing in others. All prosimians except Tarsiers synthesize ascorbic acid endogenously but anthropoid primates have lost this function. A shift in diet among anthropoid ancestors has led to a reliance on acquiring ascorbic acid from dietary sources such as fruit. Once food sources containing ascorbic acid were available in reliable and plentiful quantities, the gene responsible for endogenous ascorbic acid synthesis was no longer needed, became selectively neutral, and was free to accumulate mutations without deleterious outcomes for the organism. Mutational variants were no longer eliminated because exogenous ascorbic acid became regularly available. Selection began to operate not simply on genes for ascorbic acid synthesis but also across a distributed network of sensory biases, behavioural inclinations and digestive-metabolic mechanisms that increased the probability of obtaining ascorbic acid from the environment.”
Why hasn’t Wilson or Wagner linked nutrient-dependent pheromone-controlled cell type differentitation via amino acid substitutions to species diversity? Is it reasonable for Wilson or for Wagner to continue touting the pseudoscientific nonsense of theories that link mutations and natural selection to the evolution of biodiversity when serious scientists know that biodiversity is nutrient-dependent and pheromone-controlled via conserved molecular mechanisms of RNA-mediated amino acid substitutions in species from microbes to man, including ants?
Is is reasonable for Wilson to cite Scripture outside its Biblical context, or for Wagner to ignore it (e.g., when he mentions creation), as a means to advance a philosophical approach? Is it reasonable for anyone to ignore the Islamic creationist’s book: The Miracles Of Smell And Taste and claim that Paul was also wrong about his revelations in the context of our place and meaning? Is it reasonable to ignore Dobzhansky’s creationist claim that “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” ?
Evolutionary theorists seem unable to grasp the fact that they continue to pit their nonsense against accurate representation of biologically-based cause and effect that epigenetically link one generation after another in species from microbes to man via conserved molecular mechanisms, which was indirectly addressed in the following passage from Jeremiah 31:29.
“In those days they shall say no more, The fathers have eaten a sour grape, and the children’s teeth are set on edge.” If the link to transgenerational epigenetic inheritance across species is not clear, perhaps this quote will help. “Every human is born into meanings that pervade the social sphere and his parents’ house even before his birth.” (p. 85)
Nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance attests to the power of hormone organization and activation across generations of invertebrates and vertebrates. But the examples from others species are equally clear. See: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans
See also, the article and my comments on: The Nose Knows

The human nose can differentiate more than a trillion odors, a study finds.

By Rina Shaikh-Lesko | March 25, 2014

Excerpt: Clear attestations to the plasticity of our olfactory system, which links ecological variation to ecological adaptations, now suggest that “adaptive evolution” should be called ecological adaptation. In the presence of food odors and nutrients that are metabolized to species-specific pheromones, which control the physiology of reproduction, ecological adaptation is what’s expected to occur.
My additional comment: Paul’s prophecy attests to the fact that we have learned what human existence means. It means there is no excuse for not being a creationist because everything currently known about physics, chemistry, and molecular biology attests to the invisible aspects of God’s creation. Wilson claims that humanity “…arose entirely on its own through an accumulated series of events during evolution.” It is not reasonable to believe such ridiculous claims in the absence of experimental evidence of biologically-based cause and effect, which is exemplified in the context of RNA-mediated amino acid substitutions (see Wagner, 2014) and cell type differentiation in species from microbes to man.
Those who remain unwilling to accept the fact that ecology must be their theology may continue to contribute what they think are meaningful diatribes, which may be accepted by uncritical reviewers. But others have learned how ecological variation leads to ecological adaptations and that fact makes claims about mutations, natural selection, and the evolution of biodiversity meaningless. See also: Ecology is my theology

Physics

RNA-mediated genetic engineering (Part 3)

RCas9: A programmable RNA editing tool

Excerpt: “The researchers envision a wide range of potential applications for RCas9. For example, an RCas9 tethered to a protein translation initiation factor and targeted to a specific mRNA could essentially act as a designer translation factor to “up-” or “down-” regulate protein synthesis from that mRNA.”
My comment: This “up-” or “down-” regulation of protein synthesis from mRNA occurs naturally in the context of RNA-mediated genetic engineering. Nutrient uptake alters the microRNA/messenger RNA balance and thermodynamic cycles of DNA methylation, protein biosynthesis, and degradation. Protein biosynthesis and degradation are stabilized by nutrient-dependent amino acid substitutions that differentiate all cell types of all individuals of all species.
It is important to again note that RNA molecules function as the central conduit of information transfer in biology. Moving forward, that fact will limit the pseudoscientific nonsense that evoltionary theorists have continued to tout. Clearly, DNA is not the central conduit of information transfer in biology, and information transfer is essential to ecological adaptations. If information about the epigenetic landscape does not lead to accurate representations of cause and effect via RNA-mediated changes to the physical landscape of DNA in organized genomes, ecological variation cannot lead to ecological adaptations manifested in the morphological and behavioral phenotypes of species from microbes to man. Instead, DNA mutations would lead to the evolution of biodiversity and no known molecular mechanisms allow that to happen.

neuronal-plasticity

Ecologically linked adapted ants and brains

Ants Swarm Like Brains Think

A neuroscientist studies ant colonies to understand feedback in the brain.
By Carrie Arnold April 24, 2014
Excerpt: “The behavior of each individual in the group is set by the rate at which it meets other ants and a set of basic rules. Its behavior alters that of its neighbors, which in turn affects the original ant, in a classic example of feedback. The result is astonishing, complex behavior.”
My comment: The molecular mechanisms of nutrient-dependent intracellular, intercellular, and extracellular signaling appear to be conserved in species from microbes to man. In ants, the mechanisms are pheromone-controlled. If no other organism on this planet supports representations that mutations are somehow responsible for evolution, what could explain the lack of acceptance for the scientific truth?
Ecologically linked variation results in nutrient-dependent pheromone-controlled ecological adaptations via conserved molecular mechanisms.  Ecologically linked changes in nutrient-dependent morphology and pheromone-controlled species-specific behaviors does not seem like a difficult concept to grasp. That means it is time for those who cannot seem to grasp it to explain why they think mutations, or anything else, might be responsible for the behavior of any organism.
Odor memories regulate olfactory receptor expression in the sensory periphery of honeybees. It is unlikely that any other regulatory mechanisms cause differences in morphology and behavior in other model organisms, especially ants. Thus, the fact that “…olfactory receptor expression is experience-dependent and modulated by scent conditioning…” is one that should be considered in the context of the mechanism that appears to underlie the plasticity of signaling that involves nutrient-dependent pheromone-controlled changes in the microRNA/messenger RNA balance, DNA methlylation, and RNA-mediated amino acid substitutions that differentiate the cell types of individuals in species from microbes to man.
If others consider the possibility that mutations somehow cause controlled changes in morphology or behavior in any organism, they should provide reasons for such considerations so that their reasoning can be compared to what is known about biological facts that link ecological variation to ecological adaptation in all species.
Signaling Crosstalk: Integrating Nutrient Availability and Sex (microbes)
Feedback loops link odor and pheromone signaling with reproduction (vertebrates)
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (viruses to whales and humans)