Junk DNA goodbye: the nail in the coffin (Introduction)

by David Turell , Saturday, November 25, 2023, 20:55 (154 days ago) @ David Turell

A new important paper:

https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080

"Abstract
Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information."

From evolution news: https://evolutionnews.org/2023/11/newly-paper-in-bioessays-recognizes-kuhnian-paradigm-...

"This brings us to the article recently published in BioEssays, written by John Mattick, an Australian molecular biologist and Professor of RNA Biology at the University of New South Wales, Sydney. I have no evidence that Mattick has any affinities with intelligent design — but he’s a prime example of a bold scientist who has embraced new theories that challenge the reigning paradigm. Mattick has been indefatigable in following the evidence where it leads regarding evidence of function for “junk DNA.” In part because of his work, biology today has experienced a paradigm shift away from the concept of junk DNA. In fact, Mattick’s new BioEssays article, “A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs,” frames the revolution in thinking over junk DNA precisely in “Kuhnian paradigm shift” terms.

***

" Mattick describes the previously reigning “junk DNA” paradigm in biology as having come from “prevailing assumptions.” The assumptions hold that “‘genes’ encode proteins, that genetic information is transacted and regulated by proteins, and that there is no heritable communication between somatic and germ cells.” This view that genes encode proteins is a key part of the “central dogma” of biology. Of course, no one denies that genes encode proteins — Mattick’s point is that they can do much more than this. They can also encode RNAs and the evidence shows that many non-protein-coding sequences of DNA actually encode RNAs that perform many types of vital functions in the cell."

Comment: the whole concept of junk DNA was a direct result of early concepts, which were wrong. Mattick explains:

"[T]heoretical biologists were integrating Mendelian genetics with Darwinian evolution, leading in 1942 to the so-called Modern Synthesis, which made two primary claims: mutations are random and somatic mutations are not inherited. … In 1968 Kimura proposed the neutral theory of molecular evolution, which posited that “an appreciable fraction” of the genome was evolving independently of natural selection. In 1969, Nei concluded that, given the “high probability of accumulating … lethal mutations in duplicated genomes … it is to be expected that higher organisms carry a considerable number of nonfunctional genes (nonsense DNA) in their genome”, leading Ohno to promote the concept of “junk DNA”, also arguing that “in order not to be burdened with an unbearable mutation load, the necessary increase in the number of regulatory systems had to be compensated by simplification of each regulatory system”. [Emphasis in the original."]

Evolution news: " Against this backdrop — permeated with evolutionary thinking about the origin of the genome — the idea of junk DNA flourished and spread throughout the biology community."

Comment: it is about time.