I looked into this question, and wrote up an essay with my findings. This essay got longer and longer, as I added a tutorial (for readers who are not biologists) on the human genome, and included some global musings on the Intelligent Design effort. The full essay is posted at the top of this blog window as Junk_DNA_Design, or just click here.
Below is the Summary of this essay:
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The researchers of ENCODE Project, the successor to the Human Genome Project, have been working to identify regions of functionality throughout the human DNA. Medical benefits are expected from this increased understanding. The ENCODE results to date were released in early September in the coordinated publication of 30 academic papers, accompanied by news conferences and press releases. ENCODE spokesmen claimed they had found “biochemical functionality” in some 80% of the genome; this was presented as a shocking discovery which overturned the alleged consensus that nearly all DNA (outside of the 1-2% that was known to code for proteins) was functionless “junk.” Intelligent Design proponents immediately hailed these results as support for design, and as evidence for the failure of “Darwinism”.
The reality is:
(1) The type of “biochemical functionality” used here for the 80% figure does not at all translate to having any real effect on the organism. ENCODE researchers did identify some regions of genuine genetic functionality, but these amounted to only 8% of the genome, not 80%.
(2) The term “junk DNA” has been thrown around a lot, but with widely differing shades of meaning. This can cause confusion. Genetics researchers have been aware for decades of the functionality of non-coding DNA. The reason that the huge ENCODE project was conceived and funded was because everyone already believed that there was lots of function there to be discovered. So it was no surprise when they found the function that they were looking for.
(3) No one can tell in advance which DNA an inscrutable Intelligent Designer would choose to place into a genome, so no scientific finding here can ever count for or against Intelligent Design. The naturalistic alternative (that the human genome developed from earlier primates) fits the physical evidence just fine.
Below we cover in some detail the facts of the human genome and of the ENCODE accomplishments, the hype from ENCODE spokesmen, and the spin by Intelligent Design proponents. By not thinking carefully about its presuppositions, the Intelligent Design movement has condemned itself to a fruitless and (in practice) deceitful policy of trying to undermine evolution. We suggest an alternative approach which engages the valid concerns of believers in Intelligent Design, while stepping away from the god-of-the-gaps abyss.
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Letters to Creationists 
– “No one can tell in advance which DNA an inscrutable Intelligent Designer would choose to place into a genome, so no scientific finding here can ever count for or against Intelligent Design.” –
Nicely said. This is a point that gets lost too easily in these debates. Since theory interprets data, and since there is no theory of intelligent design, there can be no evidence for intelligent design. Without a theory, no data can be said to be consistent with theory, and no evidence can emerge from inquiry. If ID were really science this issue would have been addressed a long time ago but they know they can’t build a theory of intelligent design so they fake it. And that’s why ID is just a series of arguments against evolution instead of a series of positive arguments in favor of ID.
https://evolutionnews.org/2019/01/as-predicted-by-intelligent-design-junk-introns-are-actually-functional/
Evidence for function of introns. Introns make up about 20% of DNA.
Still think introns are “junk” Scott?
As usual, Don, you misrepresent what I actually wrote, which here was “…Genetics researchers have been aware for decades of the functionality of non-coding DNA. The reason that the huge ENCODE project was conceived and funded [and completed in 2012] was because everyone already believed that there was lots of function there to be discovered.”
So no, I never stated or considered that intron sequences were non-functional “junk”.
While Intelligent Design authors in that Evolution News article can quote-mine away and find various instances where some biologists injudiciously used the word “junk” or “non-functional”, it has been known in the biology community for decades that some non-coding DNA can have function. This goes back to at least David Comings’ paper in 1972.
Specifically on introns, a 10-second search turned up this 2012 paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325483/ which states,
“…In this review, we show that introns in contemporary species fulfill a broad spectrum of functions, and are involved in virtually every step of mRNA processing…”
I.e., by 2012 (and earlier, per the references in this paper), we already knew there is plenty of function in introns, and so it is reasonable to expect that even more function will be discovered as science progresses. So (although some authors like to hype their results on introns as being revolutionary or whatever) there is nothing remarkable in the latest results, and nothing to threaten the theory of evolution, despite your insinuations.
Quinodoz et al., RNA promotes the formation of spatial compartments in the nucleus. Cell, 4 Nov 2021, https://doi.org/10.1016/j.cell.2021.10.014.
Interesting paper on noncoding RNA.
“…Genetics researchers have been aware for decades of the functionality of non-coding DNA.”
Yes I know your reply. But interesting paper nontheless.