terrarium-eco-system

Genes, orchid odors, and pheromones from blonds

by with No Comment AdaptationsAlternative SplicingsDiseases & DisordersEcologyHuman BrainHuman PheromonesModel OrganismsNeuronal PlasticityNutrigenomicsPharmacogenomicsPhysicsRNA DirectedRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariations

1) The Genetics of Blond Hair (2014) and

2) Orchids give off human ‘body odor’ to attract mosquitoes (2016)

Both articles link RNA-mediated cell type differentiation in all invertebrates and all vertebrates to every aspect of cell type differentiation in plants.

  1. …studies of genetic variation in thousands of people have linked at least eight DNA regions to blondness based on the fact that a certain DNA letter, or base, was found in people with that hair color but not in people with other hair colors. Some of those base changes, or single-nucleotide polymorphisms (SNPs), were in genes involved in the production of pigments, such as melanin.
  2. Along with components common to many flowers, P. obtusata gives off some chemicals found in human body odor, the researchers reported here today at the annual meeting of the Society for Integrative and Comparative Biology. Although the orchid’s “body odor” is barely detectable by humans, it does set off electrical activity in the mosquito’s antennae, indicating it may very well attract the insects.

My comment: Unfortunately, the nutrient energy-dependent base changes are not linked from the SNPs to the amino acid substitutions that differentiate all cell types. Most people do not know the amino acid substitutions are required to stabilize the organized genomes of all plants and all animals. Thus, blond hair is not linked to anything important to survival. Instead the odor of the orchid is linked from the magic of gene-centric cause to the evolution of blonds.
The report on SICB 2016 by Pennisi is disappointing. See for contrast: Bipolar drug turns foraging ants into scouts

On 1/8/16 I wrote:

See also:
“Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity”
Reported elsewhere as: “Newly discovered windows of brain plasticity may help with treatment of stress-related disorders”
Ms. Pennisi is one of few journalists that may link the BDNF Val66Met to the COMT Val158Met variant and life history transitions from the honeybee model organism to humans via what is known about molecular epigenetics and what is currently being presented during SICB 2016.

My comment: After I posted that comment, I found her report on the SICB 2016 presentation.  For comparison, in her 2015 SICB conference report, she linked all invertebrates to all vertebrates via a presentation on microRNAs. This year, instead of moving forward, she stopped short by not connecting energy-dependent base changes to the microRNA/messenger RNA balance and SNPs to differences in odors of plants and humans.  She could have linked those differences from plants to invertebrates and all vertebrates via microRNAs, adhesion proteins, and what is now known about supercoiled DNA.
See: All in the (bigger) family
Excerpt:

…researchers have learned that production of both hormones depends on the same rate-limiting enzymes. And Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes.

My comment: The microRNAs and the hair color rs12821256 polymorphism link nutrient-dependent changes in tissue-specific enhancers to localized changes in morphological phenotypes in particular body regions and to the odors associated with the morphological phenotypes. Blond hair is a morphological phenotype.
See for other examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

The 2016 SICB presentation links attraction of mosquitoes to RNA-mediated amino acid substitutions in orchids, which link flower odors to the pheromones of people. That transfer of information across species and kingdoms could be used by other researchers in attempts to prevent disease transmission by mosquitoes.
See: Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex
Excerpt:

  1. The Or expressed in an OSN determines the sensitivity and specificity of the OSN [5], which in turn governs innate and learned olfactory behaviors, such as attraction to food and pheromones and avoidance of repellents [6].
  2.  …the Or-Orco complex has two important characteristics. First, the biophysical properties of the channel vary according to subunit composition, even with highly similar proteins such as BmOr-1-Orco and BmOr-3-Orco. Second, because ligand-selective Or sequences within and between insect species are extremely divergent, the primary amino acid sequence of the ion-conducting pore is likely to differ according to the subunit composition of the Or-Orco complex.

Feedback loops link odor and pheromone signaling with reproduction in all invertebrates and vertebrates via the conserved molecular mechanisms of RNA-mediated cell type differentiation. The de novo creation of an olfactory receptor (Or) expressed in an OSN is the link that “…governs innate and learned olfactory behaviors, such as attraction to food and pheromones…” Thus, the avoidance of repellents  is linked to the conserved molecular mechanisms of RNA-mediated amino acid substitutions and cell type differentiation across species.
Three questions arise:

  1. Could plant odors be used to trap disease carrying mosquitoes?
  2. If so, is there any need to cause mutations in mosquitoes and see if the mutations can be transmitted across generations?
  3. Should works like these be funded?

See also: orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET
My comment: Mutagenesis experiments clearly showed how loss of an Or in an OSN could be linked from amino acid substitutions to differences in morphological and behavioral phenotypes in mosquitoes and in flies.
See also: Targeted mutagenesis of Ae. aegypti orco

Excerpt

a, Snake plot of Ae. aegypti Orco with amino acids colour-coded to indicate conservation with Drosophila melanogaster. The amino acids encoded by the DNA bound by the orco ZFN (blue) and the epitope of the Drosophila anti-Orco antibody (green) are indicated.

My comment: Reporters who fail to link what is currently known about RNA-mediated cell type differentiation across species from microbes to man are not to be blamed for the diseases and suffering that neo-Darwinian evolutionary theorists have caused by their failure to understand any aspect of cell type differentiation. Researchers who continue to report their results from mutagenesis experiments in the context of ridiculous theories, or without adding the context known to serious scientists who link atoms to ecosystems, can be blamed.
If researchers do not ask their primary investigators to explain how atoms are linked to ecosystems so that they can design experiments and report results in the context of what is known to serious scientist, we will have many more years of SICB conferences that amount to little more than expensive social gatherings paid for with government funding.
For example see: Vandewege, MW, S Mangum, T Gabaldon, TA Castoe, DA Ray, FG Hoffmann (Under revision) Contrasting patterns of evolutionary diversification in the olfactory repertoires of reptile and bird genomes.  Genome Biology and Evolution.
My comment: There is no pattern of evolutionary diversification in vertebrates or invertebrates. There is only experimental evidence of how ecological variation is linked to ecological adaptation via the de novo creation of olfactory receptors in olfactory sensory neurons.
Researchers who have failed to link genes, orchid odors, and human pheromones prevent paradigm shifts. Paradigm shift preventers contribute to disease and suffering, while serious scientist are Combating Evolution to Fight Disease .

 
 

achiral-glycine

Anti-entropic solar energy

by with No Comment AdaptationsEcologyLight EnergyModel OrganismsNutrigenomicsPharmacogenomicsPhysicsRNA Directed

“We have a group trying to model the mitochondrion” — Ulla Mattfolk

Trash pickup problem

Excerpt: “The PGAM5 protein would be regulated by an allosteric mechanism, in which its biological function would switch from activation of the PINK1/PARKIN pathway for removal of damaged mitochondria to the FUNDC1 pathway for removal of damaged mitochondria,” according to Hannink. “Peptides behave like drug molecules; any time you can identify a biological process that is regulated by a peptide, that peptide becomes a leading candidate in the search for small, drug-like molecules that will act the same way.”

My comment: Antagonist Ricardo Lara Ramirez mentioned that “You could call DNA´s arrangement high-dimensional if you consider the entire chromosome. This is how DNA is packed to form chromosomes.”

His comment and misplaced focus on DNA caused me to wrongly think the discussion might benefit from including RNA-mediated events in the context of atoms to ecosystems. But Ricardo Lara Ramirez and other theorists don’t seem to like my attempts to discuss RNA. I think that’s because nutrient-dependent pheromone-controlled feedback loops link RNA-mediated amino acid substitutions to chromatin loops and protein folding.

The differences in protein folding are the link to chromosomal rearrangements and biodiversity in my model. My model takes their ridiculous theories about “emergence” and places them into the context of biologically-based cause and effect.  See, for example:

All in the (bigger) family

Excerpt: “Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes.”

My comment: Antagonist Ricardo Lara Ramirez is familiar with the works by Jerome Hui. But they don’t seem to know that the anti-entropic energy of the sun links nutrient-dependent microRNAs  and viral microRNAs from entropic elasticity to cell type differentiation via RNA-mediated amino acid substitutions. If they knew that, they might be able to link the pathway from nutrigenomics to pharmacogenomics, which I have detailed, and what is known about cell type differentiation of all cells in all individuals of all genera via the physiology of their nutrient-dependent reproduction.

Instead, Ulla Mattfolk claims my works and blog posts like this one are mere inferences. See: Quantum physics, quantum biology, and quantum consciousness

If not for Joseph Kover, I would have nothing to do with theorists, like Ulla Mattfolk and Ricardo Lara Ramirez. They are two of the most biologically uniformed antagonists I have ever encountered. Only Matti Pitkanen is worse. He placed everything I’ve detailed in the context of RNA-mediated cell type differentiation into the context of his ridulous theory about the simultaneous emergence of hens and eggs.

Was ribosome the first self-replicator? “

Excerpt: Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.”

My comment: Among the other discussants I first encountered via Ulla Mattfolk, only Joseph Kover has been helpful. I think he directed my attention to Near-Infrared Laser-Induced Structural Changes of Glycine·Water Complexes in an Ar Matrix, which among other things, helps with Untangling the quantum entanglement behind photosynthesis.  Now, Joseph Kover claims he is planning to write something and discuss details that he has not mentioned in Facebook discussions.

Great. That’s what I did when I published Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors (2012) and Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013).  I’ve spent more than $2000 in the past two years to establish the domains PerfumingtheMind.com and RNA-Mediated.com, where I have continued to encourage discussion.

Ricardo Lara Ramirez has on several occasions chided me because both domains are “deserted” and I have been banned from discussion groups, like Ulla Mattfolk’s — and several others, like the Society for Integrative and Comparative Biology (SICB) group.  If not for the fact that one of the SICB 2015 presenters, who went to school with Ricardo Lara Ramirez just confirmed what I claimed in my 2014 invited review on nutritional epigenetics, I would think that telling the truth about biologically-based cause and effect was of no use to theorists.

In my 2013 review, I wrote: “The small non-coding RNA molecules are called microRNAs (miRNAs). MiRNAs alter intercellular signaling by changing the balance between miRNAs and messenger RNA (mRNA) . The changes are linked to health and to pathology (Mori et al., 2014).” Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
Sorry, I used intercellular when I meant intracellular. Hopefully, the context makes that clear. Intercellular means “between the cells” and intracellular means “inside the cells”.

In January 2015, Jerome Hui reported that the same enzymes in both insects and crustaceans were linked by the same set of microRNAs , which control expression of the genes for those enzymes.

On March 17, 2015, I read this report: ‘Junk DNA’ Used To Sort Species
Excerpt: Non-coding RNAs such as microRNAs (miRNA) are now recognized as important regulators of gene expression. Now, a team of researchers led by Professor Jerome Hui from the Chinese University of Hong Kong has found another use for miRNA—to understand the evolutionary relationship between different species. They first compared non-coding sequences between human, chimpanzee, gorilla, orangutan, and macaque, and successfully recovered the evolutionary history of human and our close relative, showing that chimpanzees share the closest common ancestor with human, followed by gorilla, orangutan, and then macaque being the more distant relatives.
My comment: In the journal article, they claim “This study establishes a new approach for resolving animal species relationships, building markedly on ideas first noted in Field et al. [9], and suggests that the flanking sequences of miRNAs are under strong functional constraint after speciation events.”
Dobzhansky (1973) was the first to note that “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).
In our 1996 Hormones and Behavior review, we placed the differences in the cell types of primates and other species into the context of RNA-mediated pheromone-controlled species-specific cell type differentiation, which is functional constrained after speciation by nutrient-dependent species-specific pheromones.
In my 2013 review, I noted that “…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 claim that their findings build “…markedly on ideas first noted in Field et al. [9]…” (2014) suggests they are 18-41 years behind the extant literature on RNA-mediated amino acid substitutions and cell type differentiation in all cells of all individuals of all genera, which occurs in the context of their biophysically constrained chemistry of nutrient-dependent protein folding.
The context of my attempt to discuss RNA-mediated cell type differentiation is this report: NASA Is Amazed By A Huge, Unknown, Energy Field. See also: Correctly modeling biological energy I doubt the ability of theorists to understand anything about biologically-based cause and effect until they learn that solar energy is the energy that fuels the nutient-dependent physiology of reproduction on this planet.
 
 

human-evolution

Sneaking up from behind

by with One Comment AdaptationsEcologyPhysics

I’ve been busy following the current research and attempting to discuss it, which led me to not finish this blog post. I started writing it last week. Since then, as I had anticipated, others have tried to sneak up from behind and stake their claims to links from physics to cell type differentiation that I have already detailed. Before moving forward with explanations on the role of light-induced amino acid substitutions in a follow-up blog post, I’ll post this now with a caution to those who try to pirate my works. Don’t do it unless you first understand enough about systems biology to avoid claims like the one Matti Pitkanen made.

He claimed that light-induced RNA-mediated changes somehow led to the simultaneous emergence of chickens and their eggs. See for instance: Was ribosome the first self-replicator? It may be best to download the PDF, since he may remove his blog post due to his embarrassment. (I have a copy of the PDF that I downloaded).

He wrote (emphasis mine): “Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.“

————————————————————-Last week I wrote:

The invited review of nutritional epigenetics linked below was returned was returned without review. My questions to physicists about aspects of quantum biology remain unanswered, which makes it clear that researchers from yet another discipline intend to try to sneak up from behind me and claim that they already knew everything I have detailed during 20 years of published works.

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

Abstract excerpt: 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.
Physicists won’t admit that light-induced amino acids substitutions link the sun’s biological energy from quantum mechanics to biogenesis via light energy changes caused by the earth’s atmosphere, which enable the formation of achiral glycine. From its de novo creation difference in hydrogen energies can be linked to carbon based life via the creation of chiral amino acids and proteins that differentiate all cell types of all individuals of all species. Before I move forward and explain more about physics, here’s a brief review of what others are now claiming. They are still a few years behind the available information on biologically-based cause and effect, but they are sneaking up fact — and not citing my published works as they proceed to make many related claims.

The Gut Microbiome and the Brain

This open access article was published on November 17, 2014 reported on January 22, 2015 as:

You are what you eat: How gut bacteria affect brain health

Excerpt: “In “The Gut Microbiome and the Brain”, Leo Galland, Foundation for Integrated Medicine (New York, NY), presents the most up-to-date understanding of the relationship between the proteins produced by intestinal bacteria and the human central nervous system. The author explores the various mechanisms through which the microbiome can influence the brain: by stimulating and over-stimulating the immune system, producing neurotoxic agents, releasing hormones or neurotransmitters identical to those made by the human body, or through direct neuronal stimulation that sends signals to the brain.”
My comment: The Foundation for Integrated Medicine threw information into the face of the Society for Integrative and Comparative Biology (SICB) members who were left to wonder about biologically based cause and effect that links species from microbes to man — even after their presentations earlier this month linked all crustaceans to all insects.
See: All in the (bigger) family reported January 16, 2015
Excerpt 1) “A flurry of other presentations compared different classes of molecules—respiratory proteins, microRNAs, and the heat shock proteins produced in response to stress—in insects and standard crustaceans.”
Excerpt 2) “In insects, falling levels of so-called juvenile hormone stimulate the transition to adulthood; the analogous hormone in crustaceans is methyl farnesoate, which spurs growth and molting. Juvenile hormone is thought to be specific to insects, whereas methyl farnesoate is inactive in that group. But researchers have learned that production of both hormones depends on the same rate-limiting enzymes. And Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes.”
My comment: Animal models link nutrient-dependent metabolism of food by gut microbes to changes in the microRNA/messenger RNA balance that link the de novo creation of enzymes from  RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all species. For examples, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Introduction: “Members of the Society for Integrative and Comparative Biology (SICB) recently organized and held an ecological epigenetics symposium (January, 2013). Clearly, a new generation is familiar with the concept of ecologically driven epigenetic effects, which can be caused by sensory input that effects hormones, which affect behavior.”
In All in the (bigger) family, we read “Insects and crustaceans “are the most divergent organisms on the Earth, and as biologists we’d really like to understand how that came to be,” says Jonathon Stillman, a marine environmental physiologist at San Francisco State University’s environmental research center in Tiburon.”
How could anyone not understand that all organisms are what they eat because what they eat changes the microRNA/messenger RNA balance, which underlies the differences in RNA-mediated amino acids that determine the cell type differences that link morphological and behavioral phenotypes during the development of species from microbes to man?
What’s next:
1) Review: influenza virus in pigs.
2) The pig as a large animal model for characterization of host-pathogen interactions
Excerpt: “…we were able to perform highly controlled experimental infections and to study changes of symptoms, viral titer, and expression of microRNAs/mRNAs as the influenza infection progressed in time…”