• Perspective

RNA Function

Excerpt: “While the mechanism for how lncRNAs establish these domains is not fully understood, it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization.”

My comment to Science Magazine:

Title:
RNA and dynamic nuclear organization

Received:
Fri, 12 Sep 2014 03:12:03 -0400

Your Comment:
The authors seem to link RNA-mediated events to evolutionary events that have not been described. Also, a brief look at their other works suggests there is now enough experimental evidence to support the claim that RNA-mediated events link ecological variation to nutrient-dependent ecological adaptations outside the context of evolutionary theory.

If so, Rosenberg and Queitsch (2014) may have predicted the paradigm shift in “Combating Evolution to Fight Disease.” They hinted at the likelihood that evolutionary biology might be eliminated by what has become increasingly more obvious to molecular biologists, since Dobzhansky (1973). Therefore, I repeat part of an earlier comment:

“Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.”

Moving forward, if RNA-mediated events organize the cell nucleus, mutations manifested in perturbed protein folding are not likely to lead to natural selection and the evolution of biodiversity. The requirement for DNA to be found in organized genomes is biophysically constrained via the conserved molecular mechanisms of protein biosynthesis and degradation in species from microbes to man.

Instead, nutrient-dependent RNA-mediated events that appear to differentiate all cell types in all individuals of all species via amino acid substitutions link the de novo creation of new proteins to the increasing organismal complexity manifested in the morphological and behavioral phenotypes of species from microbes to man.

We can again look back on Dobzhansky (1973) and his claim that “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” Unless mutations also lead to cell type differentiation in different species, it’s time for all biologists to abandon evolutionary theories and accept biologically-based facts in attempts to eliminate the diseases and disorders of perturbed protein folding.

Addendum: Evolutionary theorists set the stage for misunderstanding and confusion by failing to explain how any mechanism might support their ideas about mutations and natural selection, which somehow supposedly led to the evolution of biodiversity. No evolutionary events were ever detailed in the context of biologically-based cause and effect.

Now, as co-author on this perspective, John Rinn seems to understand much more about the importance of RNA-mediated events than he did in Janurary, 2013. Back then, with co-authors he wrote: “As natural selection can only act on mutations that drive phenotypic variation…” The portrayal of the base pair change and nutrient-dependent RNA-mediated amino acid substitution in the context of some unknown evolutionary event failed to link it to the evolution of biodiversity. The result was somewhat comical. See the story-telling video. Note the confusion. What are they calling an adaptation, adaptive mutation, variant, coding mutation, and an amino acid substitution? How is it linked to evolution of the mouse or human genome via the amino acid substitution associated with the morphological differences?

The amino acid substitutions is not linked to the evolution of anything! The amino acid substitution links the epigenetic landscape to the physical landscape of DNA in the organized genomes of mice and man via RNA-mediated events, not mutations, not natural selection, and not evolutionary events.

There is no such thing as an evolutionary event! Ecological variation is epigenetically linked to ecological adaptations via nutrient-dependent pheromone-controlled cell type differentiation, which depends on RNA-mediated events and removes the pseudoscientific nonsense of mutations, natural selection, and the evolution of biodiversity from any further consideration whatsoever — unless you are a theorist. Theorists can continue their story-telling about mutations, natural selection, and the evolution of biodiversity. But if you are a serious scientist, you should laugh about those stories. I hope that John Rinn can now look back and laugh at the video, now that Genome Biology Volume 15 Issue 1 has been published. See his co-authored review:

‘Oming in on RNA–protein interactions

Excerpt: “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].”

Does that sound familiar? In our 1996 Hormones and Behavior review we (TB) wrote: “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.” Is anyone surprised by the likelihood that sex differences in cell types and all other cell type differentiation appears to occur via the conserved molecular mechanisms we detailed in our section on molecular epigenetics and in the rest of the review?