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As Predicted by Intelligent Design, “Junk” Introns Are Actually Functional

As noted earlier in the week, according to two new ground-breaking studies in Nature, introns, perhaps the most famous type of “junk DNA,” have been shown to have important functions. The technical details were already elaborated here. The papers report having uncovered “direct evidence for global functions of introns,” specifically, helping to maintain and regulate cell growth in yeast when nutrients are depleted:

We conclude that introns are specifically required for growth in the stationary phase of the culture when nutrients are depleted. … We conclude that introns have common functions that lead to the repression of genes associated with nutrient depletion and the stationary phase.

Introns are segments of DNA within genes that don’t code for proteins, yet they make up a huge portion of the human genome. As Norman Johnson points out in his Oxford University Press book Darwinian Detectives, “The sum total of intron DNA in humans is 20% of the total DNA, more than ten times the amount that is coding DNA.” (p. 179)

What Introns Do

But what do introns do? Introns are copied into the pre-mRNA transcript during transcription, but they are removed from the “mature” mRNA transcript via splicing, and thus do not directly determine the amino acid sequence of a protein. Because of this, numerous evolutionary molecular biologists over the years have presumed that introns are useless genetic junk. These new papers in Nature say otherwise.

Whenever clear-cut evidence of function is discovered for some type of “junk” DNA, defenders of the standard evolutionary paradigm respond in one of two ways: (a) they deny that they ever called that type of DNA “junk” and claim they anticipated the discovery of function all along, or (b) they attempt to minimize the importance of the studies, claiming they only pertain to that particular genetic element studied and that function cannot be generalized or inferred on a wider scale. 

As for the first tactic (denying that they’ve ever called introns “junk”), consider this admission from an accompanying commentary in Nature: 

In yeast, as in other organisms, introns have been viewed as the dispensable by-product of exon ligation because of their rapid degradation after splicing.

Did you catch that? According to Nature, introns were “viewed as … dispensable” — in other words “junk.”

And Nature is by no means the first to observe that introns have been considered “junk.” Consider this Science Daily article from 2008:

Introns are commonly looked on as sequences of “junk” DNA found in the middle of gene sequences, which after being made in RNA are simply excised in the nucleus before the messenger RNA is transported to the cytoplasm and translated into a protein.

Or consider this from a chapter by W. Ford Doolittle in the book Creative Evolution:

Introns Are Junk

For humans, introns — intervening sequences like that whose characterization very recently led to a new understanding of the origin of life, and soon possibly a reenactment of it — make up most of the junk. (p. 66, emphasis in original)

Here are two last examples (many more could be given): 

“Introns have been regarded for a long time as “junk DNA” and remnants of archaic ancestral genomes.” (Hube and Francastel 2015)

“Biologists tend to call introns ‘junk DNA’ because they have no known function.” (Shane Crotty, Ahead of the Curve: David Baltimore’s Life in Science, p. 93, University of California Press, 2001)

Some of the sources above affirmatively argue that introns are “junk,” but others observe that introns have been called “junk” only to disagree with that assertion. The latter sources would likely dispute those who would claim that these new Nature studies have only found peculiar instances where introns happened to be co-opted for some function. 

“An Important Molecular Guide”

For example, Hube and Francastel (2015) point out that while introns have been viewed as “junk DNA,” they are known to have “fundamental importance in the regulation of mammalian gene expression programs, from transcriptional initiation, termination and stability, through recruitment of the exon-junction complex to recruitment of chromatin remodelers through the spliceosome.” They point out that “high sequence conservation” between the introns of different species indicates function, and that “many studies” have directly determined introns have “a considerable range of biological functions”: 

Being eliminated to allow formation of messenger RNA and inherently non-coding, introns have long been kept in the now famous “junk DNA” drawer. However, and maybe against all odds, high sequence conservation among homologous introns of closely related species suggests functional constraints on intronic sequences throughout evolution. Many studies have now added to the weight of evidence showing that introns can serve a considerable range of biological functions. 

Or consider the first source from Science Daily — discussing a study that found introns serve as “an important molecular guide to making nerve-cell electrical channels.”

An ID Prediction

ID proponents have long predicted that functions would be uncovered for such non-coding DNA. In The Myth of Junk DNA, Jonathan Wells reviews various functions discovered for introns. He points out that introns play vital roles in alternative splicing, where exons of a single gene can be mixed and matched such that one gene can give rise to many different proteins: 

In 2003, Israeli scientists compared alternatively spliced exons in humans and mice and found that over three-quarters of them were flanked by introns with sequences that were 80–88% conserved — suggesting that the introns function in the regulation of alternative splicing. … Sequence conservation suggests function in general, but there is also specific evidence that introns contain codes that regulate alternative splicing. The mammalian thyroid hormone receptor gene produces two variant proteins with opposite effects, and the alternative splicing of those variants is regulated by an intron. An intronic element plays a critical role in the alternative splicing of tissue-specific RNAs in mice, and regulatory elements in introns control the alternative splicing of growth factor receptors in mammalian cells. (p. 41, citations removed)

Wells cites many studies that provide strong evidence that introns are involved in alternative splicing, helping to create diverse proteins required by cells. 

It’s very difficult to argue that functions for introns are just anomalies in a sea of junk. These new Nature papers further confirm that this is the case.

Photo: Saccharomyces cerevisiae, budding yeast, by Mogana Das Murtey and Patchamuthu Ramasamy [CC BY-SA 3.0], via Wikimedia Commons.