Where do genes come from? – Carl Zimmer

The pseudoscientific nonsense touted in this video has been refuted by decades of experimental evidence. The experimental evidence links RNA-directed DNA methylation from nutrient-dependent amino acid substitutions to the de novo Creation of olfactory receptor genes and fixation of amino acid substitutions in the DNA of organized genomes. Fixation occurs via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man.

Evolution: Dynamics of De Novo Gene Emergence

“…it was an insight coming from re-analyses of translated transcripts in yeast that suggested that de novo gene evolution could even be more prevalent than gene duplication-divergence processes [13].”

In our 1996 review we linked RNA-mediated events to nutrient-dependent pheromone-controlled cell type differentiation via conserved molecular mechanisms in species from microbes to man, starting with sex differences in cell types of yeasts. Nothing about the molecular epigenetics of nutrient-dependent de novo Creation of genes has changed since the beginning of time. Every aspect of de novo gene Creation refutes the pseudoscientific nonsense touted by Zimmer, other science journalists and most science popularizers, like Neil de Grasse Tyson.

I’ve included several links to published works that support my claim that exposure to chemicals associated with nutrients (e.g., food odors) is responsible for de novo Creation of olfactory receptor genes and the downstream effects of their Creation on the Creation of other genes through RNA-mediated events and amino acid substitutions that differentiate all cells of all individuals of all species. At least 50 other articles from my database of references attest to the fact that new genes do not come from evolution, and that mutations cause pathology not increased organismal complexity. See for examples:

See: A universal trend of amino acid gain and loss in protein evolution “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”

Re: Fixation of “…amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments.”

It’s nutrient-dependent, RNA-mediated, and pheromone-controlled. No experimental evidence of biologically-based cause and effect links mutations to the Creation of functional genes.

 “…this gene emerged fully functional out of non-coding genetic material, previously termed “junk DNA,” in a startlingly brief interval of evolutionary time.

Epigenetics is an inheritable phenomenon that affects gene expression without base pair changes. Epigenetic phenomena include DNA methylation, histone modifications, and chromatin remodeling.

“…we demonstrate OSN-specific and differentiation-dependent intra- and interchromosomal aggregation of silent ORs. Our analysis provides evidence for an instructive role of nuclear architecture in monogenic olfactory receptor expression.”  (monogenic olfactory receptor expression = nutrient-dependent de novo gene creation)

1) “Male-specific repression of FMO3, a key biosynthetic enzyme, arose de novo in Mus” 2) “Synchronized changes in odor biosynthesis pathways and odor-evoked behaviors could ensure species-appropriate social interactions.” (Odor biosynthesis pathways are nutrient-dependent.)

Examinations of the function of de novo origin and the function of noncoding RNA genes should become more frequent and appreciated in the future studies.Claims that link RNA-directed DNA methylation to RNA-mediated events that determine cell type differentiation via amino acid substitutions in species from microbes to man were exemplified in my most recent published review. Claims that link evolution to the creation of new genes continue to be made in the absence of any experimental evidence that links any evolutionary event to the Creation of anything. Zimmer, other journalists, and those who some people think are popularizing science, continue to make pseudoscientific nonsense more popular than biological facts that link ecological variation to ecological adaptations via conserved molecular mechanisms in species from microbes to man.

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

In Kondrashov’s “Gene duplication as a mechanism of genomic adaptation to a changing environment,” olfactory receptor proteins are one of the main duplicated gene families. This suggests duplication leads to an increase in sensitivity to a particular odor, which may be adaptive under certain conditions. For example, duplication of an olfactory receptor that enables increased glucose uptake in starving yeasts is adaptive. However, in well-nourished yeasts, control of de novo olfactory receptor gene creation by the metabolism of nutrients to species specific pheromones helps to ensure the organisms do not out-reproduce their food supply. Thus, the first example of nutrient-dependent pheromone-controlled adaptive evolution is apparent in Schmidt (2013) “Signaling Crosstalk: Integrating Nutrient Availability and Sex.”

This signaling crosstalk is also exemplified in the conserved molecular mechanisms of nutrient-dependent amino acid substitutions in nematodes, insects, other mammals, and humans. The substitutions link species-specific morphogenesis and the metabolism of nutrients associated with other sensory input to the species-specific pheromone-controlled physiology of reproduction.

For contrast, no experimental evidence links mutations and population-wide fixation of new alleles. Thus, it becomes clear that adaptive evolution is nutrient-dependent and pheromone-controlled sans mutations.

This leaves some evolutionary theorists waiting for other theoretical models to automagically appear. For example, Chelo et al (2013) conclude: “But our results show that further empirical work and more theoretical models are required to accurately predict the fate of that allele over long time spans.”

Meanwhile, experimental evidence of conserved molecular mechanisms that link the epigenetic ‘landscape’ to the physical landscape of DNA in the organized genomes of species from microbes to man has shown that fixation of new alleles is nutrient-dependent and pheromone-controlled. This brings up the question of why anyone would wait for theoretical models to explain what is already known about evolution. It’s nutrient-dependent and pheromone-controlled, which is consistent with Darwin’s ‘conditions of life’ but not with Haldane’s or any other theory of mutation-driven evolution.

Instead, the rapid expression dynamics that we uncovered in individual cells are consistent with models of transcriptional bursting (24). In each cell, independent bursts of transcription occur from both alleles over time, but RNA from only one allele is often present at any given time. Because stochastic losses of RNA substantially inflates naive estimates of allelic expressions, stringent controls such as split-cells and dilution series are of critical importance for accurate allelic expression analyses in single cells. It is likely that stochastic transcription of heterozygous alleles contributes to variable expressivity—phenotypic variation among cells and individuals of identical genotypes—which may have fundamental implications for variable disease penetrance and severity (25–28).RNA that is present from only one allele at any given time can be linked from RNA-directed DNA methlyation to de novo gene Creation in my model.

Levine et al., who described the first examples of de novo originated genes in Drosophila melanogaster, already noted that non-coding RNAs expressed at low levels could contribute to the birth of novel protein coding genes (Levine et al., 2006). 

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