2 genes in 2 species (too expensive and too insignificant)

By: James V. Kohl | Published on: March 27, 2015

(click to enlarge)

Characterisation of two Neurogenin genes from the brook lamprey Lampetra planeri and their expression in the lamprey nervous system by Ricardo Lara Ramirez et al.
Abstract excerpt: “Here we report the isolation of two Neurogenin genes, LpNgnA and LpNgnB, from the lamprey Lampetra planeri. Phylogenetic analyses show both genes have orthologues in other lamprey species and in a hagfish.”
My comment: “…the identity of a single functional GPH [glycoprotein hormone] of the hagfish, hagfish GTH, provides critical evidence for the existence of a pituitary-gonadal system in the earliest divergent vertebrate that likely evolved from an ancestral, prevertebrate exclusively neuroendocrine mechanism by gradual emergence of a previously undescribed control level, the pituitary, which is not found in the Protochordates (Uchida et al, 2010)
The authors place what is obviously a nutrient-dependent pheromone-controlled ecological adaptation into the context of evolution via a prevertebrate neuroendocrine mechanism and gradual emergence, which is typical of how evolutionary theorists link pseudoscientific nonsense to biologically-based cause and effect. For example: “Research on GnRH in hagfish provides a rare insight into a primordial neuroendocrine milieu which could approximate what may have been present in animals living more than 300 million years ago.” For comparison, see our 2001 review from the same journal, Human pheromones: integrating neuroendocrinology and ethology, and place what is known about neuroendocrinology and etholgoy into the context of what is known about GnRH in other species, see: Role of olfaction in Octopus vulgaris reproduction.
Excerpt: “Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).”
Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Elekonich and Robinson (2000) is Organizational and activational effects of hormones on insect behavior.
Elekonich and Robinson (2000) linked our 1996 review of RNA-mediated pheromone-controlled hormone-organized and hormone-activated sex differences in morphological and behavioral phenotypes to insects.
Excerpt: “Effects of hormones on brain and behavior occur through three mechanisms: (1) behaviors both organized and activated by hormones, (2) behaviors only organized by hormones, and (3) behaviors only activated by hormones (reviewed in Arnold and Breedlove, 1985; Diamond et al., 1996).” Diamond et al. (1996) is From Fertilization to Adult Sexual Behavior.
See also: Introduction: A Surfeit of Lampreys
Excerpt: “Recently, lampreys have started getting more widespread attention. Research related to lamprey endocrinology (particularly the pivotal hypothalamic-pituitary axis and gonadotropin-releasing hormones), the ecology and conservation of native lampreys, and the use of lampreys in evolutionary developmental (evo-devo) and biomedical studies has raised the profile of this group of ancient fishes.”
My comment: Given the obvious importance of gonadotropin releasing hormone (GnRH), why is it not mentioned in by Ricardo Lara Ramirez et al? Examples of how ecological variation leads to ecological adaptations via conserved molecular mechanisms of the biophysically constrained chemistry of protein folding now link them from light-induced amino acid substitutions in plants and animals to nutrient-dependent pheromone-controlled RNA-mediated amino acid substitutions and cell type differences in all cells of all individuals of all genera via the balance of viral microRNAs and anti-entropic nutrient-dependent microRNAs. See for instance:
1) The phylogenetic utility and functional constraint of microRNA flanking sequences
2) N6-methyladenosine marks primary microRNAs for processing
3) N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
For the role of GnRH in mammals, see also: Feedback loops link odor and pheromone signaling with reproduction
Serious scientists know how RNA-directed DNA-methylation and RNA-mediated amino acid substitutions link cell type differentiation in species from microbes to man. The serious scientists are using what is known in the context of Combating Evolution to Fight Disease. What then can be said for pseudoscientists who seem to understand nothing about the role of vertebrate GnRH?
My experience with Ricardo Lara Ramirez says a lot about the pseudoscientists. I’ve had many encounters with him since he first began to antagonize me on the FB pages of Ulla Mattfolk
Here are my comments from a recent exchange with Ricardo Lara-Ramirez, whose antagonistic comments disappeared when he learned from me that his published work had become available, albeit behind a paywall.
To: Ulla Mattfolk Re: your ongoing rudeness at “Thinking Allowed Original” where you banned me from participation, but are still denigrating my works.
Ricardo Lara Ramirez’ friend Jerome Hui just made the lot of you look like biologically uninformed science idiots. See: The phylogenetic utility and functional constraint of microRNA flanking sequences
Excerpt: “MicroRNAs (miRNAs) have recently risen to prominence as novel factors responsible for post-transcriptional regulation of gene expression. miRNA genes have been posited as highly conserved in the clades in which they exist.”
My comment: From my 2013 review: “…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.”
Ulla Mattfolk You said yourself you would take the discussion to your own group, so let it be so. Don’t misuse my space. My kindness has limits.
James Kohl Your kindness? I will gladly leave you to your ignorance at a time when everything I’ve claimed gains increasing support from experimental evidence. N⁶-methyladenosine marks primary microRNAs for processing
See: Chemical tag marks future microRNAs for processing, study shows
Excerpt: “… these experiments have identified a switch that can be used to ramp up or tamp down microRNA levels, and as a result, alter gene expression”

My comment: The ‘m6A-switch’ apppears to link ecological variation to nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all genera via the biophysically constrained chemistry of RNA-mediated protein folding.

The link from ecological variation and metabolism of nutrients to species-specific pheromones that control the physiology of reproduction in species from microbes to man, links the viral microRNA/nutrient-dependent microRNA balance to pheromone-controlled fixation of amino acid substitutions at the origins of plant life in the context of light-induced amino acid substitutions in plants and algae and sea-slugs et al.

Dobzhansky (1973) provided an example of an amino acid substitution linked to biodiversity. Like other amino acid substitutions linked to hemoglobin variants in different modern human populations, the variant Dobzhansky mentioned ~41 years ago, is linked to cell type differentiation and to health via increased nutrient-dependent pheromone-controlled genome-wide stability. Evolutionary theorists continue to link amino acid substitutions to physiopathology because they have not learned the difference between an amino acid substitution and a mutation. Most of them probably think the Hemoglobin S variant of sickle cell is a beneficial mutation. Researchers identify red blood cell traits associated with malaria risk in children
We were the first to detail what was known about molecular epigenetics in our 1996 Hormones and Behavior review. This is the latest update to my domain. Epigenetic switch links MicroRNAs to RNA-protein interactions
… if you want to impress me… — Ricardo Lara Ramirez.
James Kohl Why would I want to do that? You are one of the most biologically uninformed antagonists I have ever encountered. Our 1996 review was the basis for extension of the concept of hormone-organized and hormone-activated behavior in insects, which led to the link from molecular epigenetics/pre-mRNAs to life history transitions that your friend Jerome Hui just reported.
Twenty years after my 1995 book publication, which linked crustaceans to insects via the conserved molecular mechanisms we detailed in our 1996 review — and that others have extended across all genera — he also linked crustaceans to insects. See: All in the (bigger) family

Excerpt: “…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: Have theorists and their friends been living in the Dark Ages for the past two decades? Do you know anything about the first author of this review From Fertilization to Adult Sexual Behavior or the senior author of this award-winning review? Human Pheromones: “Integrating Neuroendocrinology and Ethology”
…”Anyone can write reviews, all you need is time to read and write.” — Ricardo Lara Ramirez
James Kohl Science fiction novelist Greg Bear integrated everything known about cell type differentiation into two of his science fiction novels because he had the time to read and write. With nothing more that a degree in English he included more details that you or Jerome Hui have learned about about during the past two decades. See: When Genes Go Walkabout Reviewed in “Nature”
See also: NIH grants aim to decipher the language of gene regulation
Millions of dollars continue to be wasted on research done by those, like Ricardo Lara Ramirez, who do not understand RNA-mediated sex differences in cell types, which we detailed in 1996. If you cannot understand the fact that sex differences are linked to cell type differences in all cells of all tissues of all organs of all organism systems in individuals of all species via conserved molecular mechanisms of the biophysically constrained chemistry of protein folding, you are probably among those who have forced serious scientists to continue Combating Evolution to Fight Disease.
Ricardo Lara Ramirez next denigrated my works because I have not published research papers.
James Kohl Why would anyone expect a medical laboratory scientist to publish research papers? That task falls on those who have no experience linking what is known about nutrigenomics and pharmacogenomics via metabolic networks and genetic networks, which is what Greg Bear did based on works by Luis P. Villarreal, which he integrated with works on hormone-organized and hormone-activated behaviors (like our 1996 review). See: Force for ancient and recent life: viral and stem-loop RNA consortia promote life
“… his book Darwin´s Radio is scientifically innacurate, and he also participated on the Halo franchise with really crap ideas on humans being genetically degenerated. LOL” — Ricardo Lara Ramirez
James Kohl You may be the most ignorant researcher I have ever ever encountered. Please ask Jerome Hui about the role of viral microRNAs in degeneracy. If he also knows nothing, ask Ryszard Maleszka, or see: Epigenomics and the concept of degeneracy in biological systems.
See also the review of “Darwin’s Radio.” Review in Nature “He has mustered a cadre of facts, loosely connected and ill understood. There are little happenings at the periphery of Mendelian genetics, at the edge of neo-Darwinian theory, and what used to be beyond the realm of molecular biology. We know that bacteria contain extrachromosomal elements that transmit traits, such as drug resistance, between individuals and between species. We know that elements exist which insert in and excise from the genome, sometimes in response to environmental signals or stresses. Most of us believe that simple, incremental changes in allele frequencies, driven by the forces of genetic drift, mutation, recombination, migration and natural selection, are enough to explain evolution from adaptation to speciation, to the origin of higher taxa. There is no compelling evidence to the contrary, but neither is there compelling evidence in favour of the idea; we simply haven’t observed or catalogued the forces and changes that create new species. Bear fills this void in our understanding with the notion that radical changes in the genome, brought about by mobilization of transposable elements such as human endogenous retroviruses, result in rapid change at the subspecies or species level.”

James Kohl Unlike Ricardo, I was paid to help diagnose and treat patients, not to invent theories based on the assumptions of others about biologically-based cause and effect. Nevertheless, two of my reviews won awards — one for best publication in ethology, one for best publication in social science.
“…one of them last author, WOW, that is laim.” — Ricardo Lara Ramirez
James Kohl Evidently, Ricardo doesn’t realize that the last author is also often the senior author of the work (like his friend, Jerome Hui). The phylogenetic utility and functional constraint of microRNA flanking sequences
Clearly, I’m not trying to get the approval of the biologically uninformed. I’m helping to show others how uninformed people can be. Thanks to Ricardo Lara Ramirez for setting an example

James Kohl What do you think is your most important contribution to the understanding of anything? Tell us about your publications and research.

For example, Characterisation of two Neurogenin genes from the brook lamprey Lampetra planeri and their expression in the lamprey nervous system appears to be an entry-level approach to what Anna Di Cosmo’s group detailed about the role of olfaction and GnRH in the cell type differentiation of octopuses and all vertebrates and invertebrates in Role of olfaction in Octopus vulgaris reproduction. See also Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

I hope that Ricardo intends to pirate what I am telling him about and include it in meaningful attempts to help detail what is currently known about biologically-based cause and effect rather than continue his attempts to meaningfully interpret the pseudoscientific nonsense he has been taught to believe in.

“Phylogenetic analyses show both genes have orthologues in other lamprey species and in a hagfish.” — abstract excerpt from Characterisation of two Neurogenin genes from the brook lamprey Lampetra planeri and their expression in the lamprey nervous system

Ricardo Lara Ramirez should probably consider asking me to read this and comment on what he seems to have missed before he and his co-authors are horribly embarrassed — if it is not too late already. Can others imagine how horrid it would be to have missed everything known about GnRH-modulated gene expression by focusing on downstream effects and characterization of two genes from a single species?

Ricardo Lara Ramirez is crying now because “… the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.” Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

I wonder if Ulla Mattfolk will remove the entirety of this discussion to help Ricardo save face. Hopefully, she will leave it as an example of how someone who is the most biologically uninformed antagonist I have ever encountered backed himself and his institution into a corner of “Dark Ages” ignorance by attacking me. No more funding for Ricardo. How about others? “

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. (p 1014)” Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?

Ricardo Lara Ramirez thanked me for telling him his paper was published.

James Kohl You’re welcome. Please send a pdf reprint to jvkohl@RNA-mediated.com and watch for my review. I’m tempted to comment only on the abstract.

Ricardo Lara Ramirez laughed at me and noted that I could not get the paper because it was behind a paywall, and that he would not send a reprint.

James Kohl That’s why I requested the reprint (because it was behind a paywall). An author’s copy would be fine. All of my published works are distributed for free.

“…your knowledge on evolution is really crap.” — Ricardo Lara Ramirez

James Kohl Agreed. My focus is on an atoms to ecosystems model of how ecological variation leads to ecological adaptations via nutrient-dependent RNA-mediated amino acid substitutions.

…more of his ridiculous antagonism — Ricardo Lara Ramirez

James Kohl Ricardo Lara Ramírez = JERK! (Waiting to hear from Denis Noble and many others who may review his most recent published work because it reflects poorly on institutions like Harvard and Oxford). Based on this excerpt from Role of olfaction in Octopus vulgaris reproduction: “…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).,” Ricardo Lara Ramirez appears to have published a career-breaking paper, which is typical of what biologically uninformed researchers do. That’s why serious scientists are “Combating Evolution to Fight Disease.”

See also: Vitamin D vital for gene expression in developing brains The study investigated the gene expression of four neurotrophic genes responsible for the production of proteins which relate to the survival, development and function of neurons (nerve cells).

James Kohl Was it Ricardo or you Ulla Mattfolk who just removed all his antagonistist posts? No response: I added support for my model.

Electrical synapses connect a network of gonadotropin releasing hormone neurons in a cichlid fish

Anesthetics Act in Quantum Channels in Brain Microtubules to Prevent Consciousness

Reported as: Anesthesia points to deeper level ‘quantum channels’ as origins of consciousness
Excerpt: “Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.”
See for additional comments on quantum consciousness:

The quantum / classical RNA-mediated ‘tipping point’

All comments from Ricardo Lara Ramirez have also been removed here. Only the disrespectful taunts of Ulla Mattfolk remain. Has anyone else encountered such ignorance from anyone who thinks they are biologically informed but has not learned anything about biologically-based cause and effect in the past 20 years?

Ulla Mattfolk Aaaah, how did I not think of that? But, tell me, how exactly does the cosmic strings interfere to create the RNA-mediated, light-induced, top-down causation?

March 22 at 5:29pm ·
Ulla Mattfolk You see, I am such a pre-scholar biologist – physicist, with a fancy for theoretical thinking….

March 22 at 5:30pm ·
Ulla Mattfolk Dark strings interfere only gravitationally, which is a big problem here, because causation is mostly em-induced, as in the light-induced top-down causation. I don’t quite get the reasoning of yours… and even how pheromones are linked here, as they require sensors of some sort….

March 22 at 5:43pm ·
Ulla Mattfolk Even if we talk anti-entropy the situation is difficult.

March 22 at 5:44pm ·
Ulla Mattfolk Ok, this was hilarious, my friend…

March 22 at 5:46pm ·
Ulla Mattfolk But we are actually talking nonsense…

March 22 at 5:47pm ·
Ulla Mattfolk Poor James…

March 22 at 5:47pm ·
Ulla Mattfolk My life was prolonged a bit at least…

March 22 at 5:49pm ·
Ulla Mattfolk This all is directed towards James Kohl, that spam our walls with his links on RNA-mediated xaxaxa.

March 22 at 5:50pm ·
Ulla Mattfolk I am tolerant mostly, and I should maybe learn to totally ignore these situations.

March 22 at 5:55pm ·
Ulla Mattfolk I tried hard to discuss with him, but it is impossible, unfortunately.

March 22 at 6:05pm ·
Ulla Mattfolk My impression is that he does not want to discuss, he wants to give his links only…

March 22 at 6:07pm ·

Ulla Mattfolk And over and over again the same links… it is too much for me.

March 22 at 6:10pm ·

Ulla Mattfolk The problem is that I removed him from this group and he cannot answer, so this is rudely done, a bit. But he is so rude himself. March 22 at 6:16pm ·

See also: Olfaction, ecology, and intelligence