poster-from-jesse

How to find a "holy grail" under your nose

Proteomics provides new leads into nerve regeneration

Excerpt:

“…the “holy grail” of regenerating a nerve enough for it to resume its function has been largely elusive.”

My comment:  Theorists who are looking for the “holy grail” of nerve cell regeneration don’t realize that it is literally ‘right under their nose.’
The sense of smell links the anti-entropic epigenetic effects of the sun’s biological energy to nutrient-dependent DNA repair via the light-induced de novo creation of amino acids and the amino acid substitutions that differentiate all cell types in all individuals of all species. The amino acid substitutions are linked from the origins of nerve cells in C. elegans to brain development in other organisms via viruses and the entropic elasticity attributed to viral microRNAs.
If nutrient-dependent microRNAs fail to prevent the genetic entropy caused by the accumulation of viruses, deficits in DNA repair and nerve cell regeneration lead to neurodegenerative diseases, like Alzheimer’s.
Human pheromones have been linked to the pathway from food odors and pheromones to successful reproduction via brain development in all invertebrates and vertebrates. That fact seems to have escaped the notice of theorists. Evidence of interest in proteomics is a good sign that some theorists may still have a chance to contribute to scientific progress. However, their failure to recognize the fact that proteins cannot self-assemble and that nerve cells and brains cannot simply emerge via a series of beneficial mutations will probably keep their contributions to the bare minimum. Their minimal contributions differentiate the value of pseudoscientific nonsense compared to biological facts.
Scientific progress has consistently been made by those who link odors and pheromones from the anti-entropic epigenetic effects of nutrient energy to the de novo creation of olfactory receptor genes and the biodiversity of nutrient-dependent morphological and behavioral phenotypes. Biodiversity is enabled by the fixation of amino acid substitutions via the pheromone-controlled physiology of reproduction in species from microbes to man.
Welcome to the world of proteomics that’s been hiding right under your nose.
See:
Feedback loops link odor and pheromone signaling with reproduction http://www.sciencedirect.com/science/article/pii/S0092867405009815
Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis http://www.freshpatents.com/-dt20110721ptan20110178009.php
Reproduction: A New Venue for Studying Function of Adult Neurogenesis? http://www.ncbi.nlm.nih.gov/pubmed/20887675
and Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14345.html

See also: Team follows zinc to uncover pathway that fine-tunes brain signaling

Excerpt:

“…used specially developed technologies to “follow the zinc” have uncovered a previously unknown pathway the brain uses to fine-tune neural signaling—and that may play a role in Alzheimer’s and other diseases.”

My comment: What they refer to as a previously unknown pathway was linked from inhalation of a naturopathic zinc-containing anti-viral remedy to loss of olfactory acuity and specificity in people who failed to follow the instructions for use of the product. If the pathway were unknown, the instructions for use probably would not have clearly tried to prevent people from inhaling the product. The problems might have been prevented if serious scientists had examined the literature on RNA-medicated cell type differentiation, which includes our 1996 review: From Fertilization to Adult Sexual Behavior
 
Excerpt:

“Another example of biological sex differences which are neither gonadal nor hormonal, however, is provided by the homologous but dimorphic zinc finger proteins ZFX and ZFY encoded on the X and Y chromosomes (North et al.,1991). An early study of human expression of ZFX and ZFY reported different transcript sizes from the two genes and this difference was even apparent in somatic tissues (Page, Disteche, Simpson, De La Chapelle, Andersson, Alitalo, Brown, Green, and Akots, 1990). ZFX and ZFY are described as “DNA-binding proteins” and via their binding of sexually dimorphic proteins, chromatin structure and transcription could be modulated in sexually dimorphic ways as a result of females having only ZFX binding events, whereas males would have a mixture of both ZFX and ZFY binding events (Fiddler, Abdel-Rahman, Rappolee, and Pergament, 1995; Lau and Chan, 1989; Zwingman, Erickson, Boyer, and Ao, 1995).”

 
 

poster-from-jesse

What about birds?

A sex researcher who typically fails to respond to my comments and questions recently noted that: “New species are only supposed to arise when a population separates into two.”
She asked: “So what’s going on with the birds on tiny Santa Cruz Island?”
I would have been happy to tell her — if ever she had responded to my past comments. Instead, her question makes good cannon fodder for this blog.
See: This Jay Is Evolving in a Very, Very Weird Way
Excerpt (with my emphasis): “…may not appear to be something you’d consider a “revelation,” but it really is—if you believe in evolution. Ever since Darwin and his famous finches, biologists have thought that in order for a species to diverge into two new species, the two populations had to be physically isolated. Those finches, for instance, each live on a different Galapagos island, where their special circumstances have resulted in specialized bill shapes. Yet the two varieties of island scrub jay (they haven’t technically speciated—yet) live on the same tiny island.”
My comment: I was reminded of a comment made in 1995 by Jay R. Feierman after I presented my detailed model of the gonadotropin releasing hormone-driven pheromone-controlled physiology of reproduction in all vertebrates. He asked: What about birds?  Feierman claims to believe that “Random mutations are the substrates upon which directional natural selection acts.” I suspect that many sex researchers also believe in that pseudoscientific nonsense, which explains why they, too, might ask “What about birds?” If you believe in evolution, you may also believe that they evolved from dinosaurs.
Serious scientists with questions about ecological variation and ecological adaptations in birds would simply refer to our 1996 Hormones and Behavior review article on the RNA-mediated sexual differentiation of cell types. Our model has since been linked via the biophysically constrained chemistry of nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions to the differentiation of all cell types in all individuals of all species.
The answer to the question “What about birds?” has not changed during the past two decades. Social scientists will prefer the comments made by PZ Myers and other biologically uninformed participants on his blog at: One crank dies, another rises to take his place.
Alternatively, on January 16, 2013 I wrote:

http://gbe.oxfordjournals.org/content/3/812.abstract
“…population geneticists such as Wright (1941) showed that the probability of fixation of these chromosomal rearrangements is so low that they would not be easily established in the population unless population size is very small (say less than 10). For this reason, the idea that new species are formed by chromosomal rearrangements was almost abandoned.”
Almost abandoned? PZ Myers called Davison a “crank” for encouraging discussion of that idea, which has since been fully supported by experimental evidence. Why does an atheistic biology teacher want others to think that someone else is a crank because that person doesn’t agree with the ridiculous idea of mutation-driven evolution?
http://www.pnas.org/content/early/2014/01/08/1317165111.abstract
“The evolution of behavior relies on changes at the level of the genome; yet the ability to attribute a behavioral change to a specific, naturally occurring genetic change is rare in vertebrates. In the white-throated sparrow (Zonotrichia albicollis), a chromosomal polymorphism (ZAL2/2m) is known to segregate with a behavioral phenotype. Individuals with the ZAL2m haplotype engage in more territorial aggression and less parental behavior than individuals without it. These behaviors are thought to be mediated by sensitivity to sex steroids, and the chromosomal rearrangement underlying the polymorphism has captured a prime candidate gene: estrogen receptor 1 (ESR1), which encodes estrogen receptor α (ERα). We therefore hypothesized that the behavioral effects of the ZAL2m rearrangement are mediated by polymorphism in ESR1. We report here that (i) the ESR1 promoter region contains fixed polymorphisms distinguishing the ZAL2m and ZAL2 alleles; (ii); those polymorphisms regulate transcription efficiency in vitro and therefore potentially do the same in vivo (iii); the local expression of ERα in the brain depends strongly on genotype in a free-living population; and (iv) ERα expression in the medial amygdala and medial preoptic area may fully mediate the effects of genotype on territorial aggression and parenting, respectively. Thus, our study provides a rare glimpse of how a chromosomal polymorphism has affected the brain and social behavior in a vertebrate. Our results suggest that in this species, differentiation of ESR1 has played a causal role in the evolution of phenotypes with alternative life-history strategies.”
A few hours later, I was banned from participation. PZ Myers claimed I was a homophobe.
Obviously, he did not want to address the experimental evidence that supported my claims about the role of chromosomal rearrangements. They are nutrient-dependent and pheromone-controlled in all animal species. That fact is a refutation of theories about mutations, natural selection, and the evolution of biodiversity, and it is becoming increasingly more difficult to ignore the biologically-based facts that we detailed in the molecular epigenetics section of our 1996 review.
Excerpt: The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning…
Excerpt: Molecular distance. As measured in centimorgans, human and other species’ male and female chromosomes, including the autosomes, tend to have different lengths in various segments. To some extent, this suggests a correlation with physical distance but instead the differing lengths are based upon rates of recombination; although sections of most female chromosomes are longer than their homologous counterparts in male chromosomes, in some segments of various chromosomes opposite length-difference occurs, with males having larger centimorgan values than females in those regions (Lawrence, Collins, Keats, Hulten, and Morton, 1993; Murray, Buetow, Weber, Ludwigsen, Scherpbier-Heddema, Manion, Quillen, Sheffield, Sunden, and Duyk, 1994; Straub, Speer, Luo, Rojas, Overhauser, Ott, and Gilliam, 1993).
Excerpt: Molecular epigenetics. It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes.
All that social scientists and other pseudoscientists can do is ban people like me, who continue to supply accurate representations about biologically-based cause and effect and ask “What about birds?” They really don’t want to know that cell type differentiation is nutrient-dependent and pheromone-controlled in all animal species.  If they did, they would have learned that sometime during the past twenty years — like serious scientists have.
See also:
Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
Evolution of Darwin/’s finches and their beaks revealed by genome sequencing
Every inch a finch: a commentary on Grant (1993) ‘Hybridization of Darwin’s finches on Isla Daphne Major, Galapagos’
Excerpt (with my emphasis): “…ecological speciation and sexual speciation have in this case acted in concert; and in consequence this lineage had proceeded some distance down the path that eventually leads to distinctive ecological specialization and complete sexual isolation [22,34] (figure 6).
My comment: That appears to answer the question about these birds. “So what’s going on with the birds on tiny Santa Cruz Island?” I suspect that ecological speciation and sexual speciation occur via the conserved molecular mechanisms we detailed in 1996 because there is no other model for that. This is the model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. With few exceptions pseudoscientists and social scientists continue to ignore that fact that this model explains all questions about links between metabolic networks and genetic networks in all species, because the epigenetic links are RNA-direceted by DNA methylation and RNA-mediated amino acid substitutions.
See also: New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis