Art Hunt, from the archives of Uncommon Descent June 14, 2010:
As far as the functional vs. non-functional business, there is one key fact that IDists ignore in all of this. I refer, of course, to the fact that intronic RNA is made and then thrown away. We don’t call it “junk” because we don’t know if it does anything, we call it so because it is discarded.
Arthur Hunt
Sternberg Plasters Matheson, Comment #357009
So Art says something is labeled junk because it is eventually discarded. How much of an organism is eventually discarded? If humans discard most of the molecules that constitute their bodies over the years, then by that standard everything is junk! The fact that something is eventually discarded is not evidence it was always junk. Consider the stages of a rocket ship or the Space Shuttle’s boosters, etc. By Art’s standard, rocket boosters are junk…
But now almost two years later, from the pages of the prestigious scientific journal Nature June 3, 2012, we have evidence overturning Art’s claim that intronic RNA is junk:
These findings reveal the role of intronic RNAs in fine-tuning gene expression regulation at the level of transcriptional control.
….
Intronic sequences contain a number of ncRNAs (conservative estimates suggest that 65% of noncoding transcripts map to intergenic regions and 35% to intronic regions38), including many well-characterized regulatory small ncRNAs, such as snoRNAs, small nuclear RNAs (snRNAs), piRNAs or miRNAs39, 40, their expression being coordinated with the intronic context from which they originate. In addition, a recent study reports close to 80,000 and 40,000 long intronic expressed sequence tag (EST) contigs in human and mouse genomes, respectively41. They suggest that 80% of all spliced human protein-coding genes have transcriptionally active introns41. Nevertheless, long ncRNAs arising from intronic regions have so far received little attention from researchers.
…
These findings support the model in which ncRNAs carry out a function at the interface between DNA and specific chromatin modification marks, through stabilization of the association of PRC2 with chromatin. Intronic RNAs arise as candidates to carry out roles as ‘transcription factors’ that are responsible for fine-tuning mammalian transcriptional programs.
This article also overturns a claim by Steve Matheson that was highlighted by Uncommon Descent in Sternberg Plasters Matheson where Matheson says we can only claim about a dozen introns have function:
The human genome contains at least 190,000 introns (though it’s been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth. That’s 768 million base pairs. And biologists have identified “important functional roles” for a handful of them. How many? Oh, probably a dozen, but let’s be really generous. Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function, and gosh, they’re snipped out of the transcripts and discarded before the darn things even leave the nucleus. We might return to this topic, since it’s interesting and there are more layers of duplicity in the “junk DNA” fairy tale that Meyer has included in his book. But Meyer has done significant damage to his credibility by including it. In my view, he showed his cards.
Contrast Matheson’s uninformed assertions with the recent article cited above:
Intronic sequences contain a number of ncRNAs (conservative estimates suggest that 65% of noncoding transcripts map to intergenic regions and 35% to intronic regions38), including many well-characterized regulatory small ncRNAs, such as snoRNAs, small nuclear RNAs (snRNAs), piRNAs or miRNAs39, 40, their expression being coordinated with the intronic context from which they originate. In addition, a recent study reports close to 80,000 and 40,000 long intronic expressed sequence tag (EST) contigs in human and mouse genomes, respectively41. They suggest that 80% of all spliced human protein-coding genes have transcriptionally active introns
Which pretty much demolishes Matheson’s assertion that we can claim only a dozen introns have function. Matheson is plastered again. Further, does a non-coding RNA need to leave the nucleaus to have function? I pointed the flaw in Steve’s analysis which led him to make his mistakes:
This is illogical. This is like saying, “I don’t know what function this part has in the space shuttle, therefore this part is useless.”
A human is arguably more complex than a space shuttle. How presumptuous then to assert something has no function merely because function hasn’t been perceived yet. Lack of perceiving function in an intron is not the same as the intron having no functon….that is Mathesonian reasoning…
Matheson insinuated that unless we know how something functions we cannot assert it has function. Not true. We can provisionally predict something has function before we know all the details of how it functions if we have other clues to suggest function. Sternberg laid out the case in Matheson’s Intron Fairy Tales. These recent discoveries vindicate Sternberg’s prediction.
Matheson said that Meyer’s prediction of the large scale function of “junk DNA” was an error. Too bad for Matheson, in light of the most recent peer-reviewed paper, it appears Matheson was in error by large margin.
PS
Recall, it was Matheson who said: The Discovery Institute Needs to be Destroyed
Your Discovery Institute is a horrific mistake, an epic intellectual tragedy that is degrading the minds of those who consume its products and bringing dishonor to you and to the church. It is for good reason that Casey Luskin is held in such extreme contempt by your movement’s critics, and there’s something truly sick about the pattern of attacks that your operatives launched in the weeks after the Biola event. It’s clear that you have a cadre of attack dogs that do this work for you…I can’t state this strongly enough: the Discovery Institute is a dangerous cancer on the Christian intellect, both because of its unyielding commitment to dishonesty and because of its creepy mission…It needs to be destroyed, and I will do what I can to bring that about.
Steve Matheson,
Open Letter to Stephen Meyer