The holy grail of evolutionary biology is Creation via adaptations without mutation-initiated natural selection.
Rare event of histone demethylation can initiate singular gene expression of olfactory receptors [Published online before print December 16, 2013]
Significance: In mammals, the sense of odors relies on the peculiar expression pattern of olfactory receptors (ORs). Each single neuron chooses one, and only one, from all ~1,400 OR genes that are present in a mouse genome. In neurobiology, a long-standing mystery is how such singularity can be achieved. We show theoretically that a simple kinetic scheme of OR activation followed by feedback can be solely responsible for the observed singularity, as long as the two timescales—slow activation by epigenetic modification and fast feedback by transcriptional regulation—are well separated. Our work provides the theoretical underpinning behind the choice of ORs, and demonstrates how the nervous system utilizes the kinetics of epigenetic changes to direct neurogenesis.
Article excerpt: “… the only missing piece in OR singularity is the activation step responsible for the required kinetic bottleneck. It is even possible that both the H3K9me3 and H3K9me2 demethylases are downregulated by the feedback, which may enhance the sensitivity and robustness of the feedback.”
My comment: Ecological variation is the activation step responsible for the required kinetic bottleneck in my model. Nutrient availability enables the de novo creation of OR genes. The creation of new olfactory receptors (ORs), enables the receptor-mediated entry of nutrients into cells. The entry of nutrients into the cell via de novo creation of the OR genes facilitates the nutrient-dependent differentiation of cell types in different individuals of different species. Thus, the ecological variable of nutrient availability and the epigenetic effect of nutrients on the de novo creation of ORs biophysically constrains the diversity of cell types during adaptations. The ecological adaptations can then be linked directly from the de novo creation of ORs to ecological, social, neurogenic, and socio-cognitive niche construction. That is how nutrient uptake and the de novo creation of ORs is directly linked to increasing organismal complexity in species from microbes to man. Increased organismal complexity also exemplifies de novo Creation of new cell types, which is made possible by the availability of food and the epigenetic effects of food “odors”.
“Deciphering the genetic mechanisms that operated during the past 650 Myr of animal evolution to create the seemingly infinite variety of animals that populate our planet has been one of the holy grails in biology.”
Acknowledging that the holy grail of evolutionary biology has been found will lead to recognition that ecological, social, neurogenic and socio-cognitive niche construction is non-random and not the result of mutation-driven evolution. Moving forward, after first dispensing with the nonsense of mutation-initiated natural selection, we can already see that a new Holy Grail has replaced the one sought after by evolutionary biologists.
Abstract except: “The construction of a comprehensive structural, and importantly functional map of the network of elements and connections forming the brain represents the Holy Grail for research groups working in disparate disciplines.”
We can now also dispense with the caveat Simon LeVay added after first noting the benefits of my model.
Benefits: “This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions.”
Caveat: “Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another.”
Article excerpt: ” While the association between pheromones, olfaction and courtship may seem obvious, an intriguing relationship has been identified between food-olfaction and male courtship .”
The obvious association between food odors, pheromones, olfaction and courtship has been the topic of everything I have published during the past two decades. During that time, the few people who have acknowledged that fact that my model makes sense have been horribly outnumbered by theorists who think that mutation-initiated natural selection makes sense. Thus, we have reached a turning point, which can be simply addressed with this question:
Is the de novo creation of ORs the holy grail of evolutionary biology?
Creationist/Theorist: PAY ATTENTION TO WHAT I TOLD YOU 4-5 DECADES AGO
Dobzhansky (1973): “Nothing in Biology Makes Any Sense Except in the Light of Evolution” excerpt: “It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.”
Dobzhansky (1964) “…the process of adaptation to the environment is the main propellant of evolutionary change. Evidence is rapidly accumulating which, in my opinion, substantiates the hypothesis. It remains, however, not only to convince the doubters but, what is more important, to discover just how the challenges of the environment are translated into evolutionary changes.”
Clearly, Dobzhansky was right, and everything we have since learned attests to the obvious fact that: Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4]. However, we can now frame evolutionary divergence in its proper context. It’s not what theorists have thought about in terms of mutation-driven evolution. Ecological variation drives divergence via the de novo Creation of olfactory receptor genes that enable organisms to adapt to their ever-changing environments with observable increases in organismal complexity. Organismal complexity is not due to mutations. Organismal complexity requires Creation (i.e., the holy grail of evolutionary biology).
For contrast, in the current literature we read:
The effects of olfactory/pheromonal input on intercellular signaling and the de novo creation of olfactory receptor genes links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Thus, any theorist who does not agree that the de novo creation of olfactory receptor genes is the holy grail of evolutionary biology, is someone who fails to recognize “…how the challenges of the environment are translated into evolutionary changes.” The translation of the environment to organized changes occurs via adaptations that clearly involve the de novo creation of genes, not mutation-initiated natural selection. Thus, theorists who believe in mutation-driven evolution can be compared to bird watchers and butterfly collectors in the same light of adaptations to the environment that Dobzhansky (1964) portrayed them in: “… 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!”
Thank God that serious scientists have finally discovered that the holy grail of evolutionary theory is Creation. Theorists may now abandon their theories and join serious scientists in the pursuit of more scientific facts.
On 12/17/12, I asked: Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?
The response from Lomvardas indicated his confusion about cause and effect, so I wrote :
“Thank you. In my model, the bottom-up epigenetic effects on stochastic gene expression are largely dependent on adaptively evolved glucose uptake and the top-down epigenetic effects on stochastic gene expression come from the metabolism of nutrient chemicals to species specific pheromones. The honeybee model organism best exemplifies this epigenetic tweaking of immense gene networks and how the epigenetic effects of food odors and pheromones on the glucose-dependent secretion of mammalian gonadotropin releasing hormone also links genes to behavior and back. The additional information about the histone core and fine-tuning of the required plasticity appear to attest to the control of chromatin remodeling by the microRNA / messenger RNA balance. It would interest me to learn if others agree with that proposal given the extreme technicalities of the issues addressed by Santoro and Dulac.”
On 1/18/13, Editor: Andy Collings, refused to post the comment: “…we have decided against posting your latest comment (below) because the discussion deviates away from the article in question.”
On 6/14/13 I published Nutrient-dependent/pheromone-controlled adaptive evolution: a model and detailed the fact that food odors epigenetically effect the conserved molecular mechanisms that enable ecological adaptations in species from microbes to man. I included examples that extend the model across species.
See also: Kohl (2012) A gene that codes for the mammalian olfactory receptor, OR7D4, links food odors to human hunger, dietary restraint, and adiposity (Choquette et al., 2012). OR7D4 exemplifies a direct link1 from human social odors to their perception (Keller, Zhuang, Chi, Vosshall, & Matsunami, 2007) and to unconscious affects2 on human behavior associated with human olfactory-visual integration (Zhou, Hou, Zhou, & Chen, 2011); human brain activation associated with sexual preferences (Savic, Heden-Blomqvist, & Berglund, 2009), human learned odor hedonics; and motor function (Boulkroune, Wang, March, Walker, & Jacob, 2007). Insect species exemplify one starting point along an evolutionary continuum from microbes to humans that epigenetically links food odors and social odors to multisensory integration and behavior.
 To avoid the confusion of using different terms for chemical signals that epigenetically effect the de novo creation of genes, I refer to the chemical signals as odors. Most people intuitively understand what food odors are and what social odors are. They may also understand that the difference between food odors and social odors are species-specific, which is why they commonly referred to as pheromones