Behavioral ecology and genomics: new directions, or just a more detailed map?
Excerpt 1): “Transcriptome sequencing, often called RNAseq, both sequences and quantifies the portions of the genome being transcribed under conditions of interest (Wang et al. 2009; De Wit et al. 2012). Such information can be used to identify differentially expressed genes and the mutations underlying variation in gene expression and can lead to the identification of functionally important genes or suites of genes that function together (“modules”) to produce adaptive behaviors.”
Excerpt 2): “1. Having a sequenced genome, or chromosomal region, or a transcriptome, is not necessarily helpful.”
Excerpt 3): “4. New model systems, facilitated by the ease of obtaining genome sequences for a variety of organisms, could be extremely salutary for behavioral ecology (but see #1).”
What else can we expect from evolutionary biologists like Marlene Zuk, who have championed the role of evolution without details of an evolutionary event that links biologically-based cause and effect to increasing organismal complexity in species from microbes to man. See: Paleofantasy: What Evolution Really Tells Us about Sex, Diet, and How We Live
Excerpt: “Armed with a razor-sharp wit and brilliant, eye-opening research, Zuk takes us to the cutting edge of biology to show that evolution can work much faster than was previously realized, meaning that we are not biologically the same as our caveman ancestors.”
My comment: We cannot be biologically different than our ancestors, but Zuk and Balenger would now like others to believe two more things:
1) RNA-directed DNA methylation, which links ecological variation from amino acid substitutions to cell type differentiation and biodiversity in species from microbes to man, may be extremely beneficial in the context of behavioral ecology.
2) Use of RNA/transcription sequencing to explain how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man may not necessarily be helpful.
The reality of Zuk’s claims is best expressed as RNA-mediated events explain how ecological variation leads to ecological adaptations without the pseudoscientific nonsense of mutations. Biologically-based explanations may not benefit evolutionary biologists who would rather tout pseudoscientific nonsensene about the evolution of biodiversity as they continue to misrepresent biologically-based cause and effect.
Indeed, factual representations of RNA-mediated events force evolutionary biologists like Zuk to describe evolutionary events or stop claiming
1) that evolutionary events occur and that
2) they automagically lead to the evolution of biophysically-constrained biodiversity via
3) some unknown biologically plausible mechanism that
4) is not nutrient-dependent and not pheromone-controlled.
See also: (1) An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver and (2) Human pheromones: integrating neuroendocrinology and ethology.
Both reviews link what we detailed about how cell type differentiation occurs in the molecular epigenetics section of our 1996 Hormones and Behavior review: “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”
(1): “…integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.”
(2) It has become obvious that the molecular mechanisms of cell type differentiation, such as alternative splicing techniques of pre-mRNA, are conserved across species and that RNA-mediated events link DNA methylation and transciptome sequencing from ecological variation to ecological adaptations in species from microbes to man. It is equally obvious that health and fitness are determined in the context of nutrient-dependent amino acid substitutions that differentiate cell types via RNA-mediated events, not via evolutionary events.
Others, like Zuk, may continue to believe in their fantasies or to claim that RNA sequencing provides nothing more than a more detailed map of evolutionary events. However, the fact that they have never described a biologically-based evolutionary event precludes use of transciptome sequencing and a detailed map of RNA-mediated events for anything other than a refutation of the pseudoscientific nonsense they have heretofore touted.
See: Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes
Excerpt 1): “The rates of 4 types of elementary evolutionary events (hereinafter Genome Dynamics Events or GDE)…”
Excerpt 2): “Conceivably, genome dynamics is highly sensitive to local ecological factors the exact nature of which remains to be elucidated.’
My comment: Genome Dynamics Events are RNA-mediated by nutrient-uptake and pheromone-controlled physiology of reproduction. We elucidated that in From Fertilization to Adult Sexual Behavior.
What Evolution Really Tells Us about Sex, Diet, and How We Live is nothing. How we live is determined by the nutrient-dependent pheromone-controlled ecological adaptations of our ancestors, and epigenetic effects on our hormone-organized and hormone-activated behaviors. We live in the same context as our ancestors: ecological variation and ecological adaptations. We are not mutating into another species and were not naturally selected to evolve. Mutations perturb protein folding and cause disease and disorders not evolution.
