Newly Published Paper in BioEssays Recognizes
Kuhnian “Paradigm Shift” Against Junk DNA
November 22, 2023, 7:44 AM
September, I wrote about
prolific functions discovered for short tandem repeats (STRs), formerly
considered a type of “junk DNA.” Now a newly published paper in BioEssays has
strongly rebuffed the idea of junk DNA — using the language of Kuhnian paradigm
shifts. Before we go any further, let’s review just what a Kuhnian paradigm
shift is.
The phrase comes from the work of a famous Harvard University historian
and philosopher of science, Thomas Kuhn. In his
influential book The Structure of
Scientific Revolutions, he documented how new ideas in science
typically take hold through what are called “paradigm shifts,” where the
leading framework within a field (the “paradigm”) starts to accrue evidential
problems (goes into “crisis”) until it finally gives way to a new idea that
challenges the status quo. Kuhn further showed that most scientists spend most
of their time doing “normal science” — basically solving scientific puzzles
within the framework of the dominant paradigm. He observed that the scientists
of the old guard paradigm are “often intolerant” of “new theories” that are
being proposed by new scientists proposing ideas that challenge the reigning
paradigm. A new theory “emerges first in the mind of one or a few individuals”
but then it spreads because the field faces “crisis-provoking problems,”
especially among scientists who are “so young or so new to the crisis-ridden
field that practice has committed them less deeply than most of their
contemporaries to the world view and rules determined by the old paradigm.”
A Junk DNA Paradigm Shift
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. The paper has a nice video abstract, but here’s
what it says in written form:
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.
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.
Junk DNA and Evolution
So the central dogma of molecular biology is part of what is
perpetuating the idea that if a stretch of DNA doesn’t encode a protein then it
isn’t doing anything and is “junk.” But there’s another major driver of the
failing junk DNA paradigm in biology — and it stems directly from evolutionary
thinking. 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.]
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.
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