Home » 'Junk DNA', Darwinism, Intelligent Design » Arthur Hunt and Steve Matheson vs. the UD Community

Arthur Hunt and Steve Matheson vs. the UD Community

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.

Intronic RNAs mediate EZH2 regulation of epigenetic targets

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

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10 Responses to Arthur Hunt and Steve Matheson vs. the UD Community

  1. Whaddya bet that Matheson replies with yet another definition of “junk”?

    “Hey, I didn’t mean that they didn’t have functional use. Why even the broken bed that gets hauled to the dump has a functional use–it makes the landfill a little higher!”

    Gotta love the creative writing, this is really getting fun now.

  2. This is really exciting to see that ID predictions are already turning out to be much, much, more fruitful than I expected. As someone who really knew very little about ID and was convinced by evolutionists it was religious dogma, it really is crazy to see how much evolutionists, and those who despise ID, will misrepresent it. After reading Meyers book, as well as a few others things, it is incredible how scientific ID really is and how it does make testable predictions!

  3. Robert Sheldon June 11, 2012 at 6:22 pm

    Whaddya bet that Matheson replies with yet another definition of “junk”?

    “Hey, I didn’t mean that they didn’t have functional use. Why even the broken bed that gets hauled to the dump has a functional use–it makes the landfill a little higher!”

    Gotta love the creative writing, this is really getting fun now.

    Is Steve Matheson still partaking in this discussion online? His blog has been dormant since last September.

    I Googled his name, thinking that maybe his blog had moved, and came across this news about his resignation from Calvin College:

    Calvin College letter says professor resigned after student alleged sexual relationship | MLive.com

  4. Jammer,

    GRAND RAPIDS — Calvin College leaders sent a letter to students, parents, faculty and staff Friday saying professor resigned after a student claimed she had a “multi-year sexual relationship” with him, a college spokesman confirmed.

    Matt Kucinski said the letter was sent Friday afternoon. In it, Shirley Hoogstra, Calvin’s vice president for student life, said the student alleged in May this year she had carried out the relationship with biology professor Steve Matheson.

    WHOA! I had no idea. Thanks for the link.

  5. I think it is a safe bet Steve Matheson is out of the ID debate. See:

    Clergy Letter Progject — Steve Matheson and Amy Bishop

    HT: Jammer

    Matheson has presented himself as an example of a Christian and a Darwinist. I think the allegations raised have cast a shadow on his qualification to speak in the name of Christ. He’s free of course to keep speaking in the name of Darwin, that’s fine by me.

  6. For a fleeting second, I thought the New Scientist magazine was being hilariously satirical (though, of course, it wouldn’t have been) about itself, when I read this, in an email blurb:

    “….. find out about those happy evolutionary accidents in this week’s cover story.”

    I was sorely tempted to insert an exclamation mark at the end of it.

    It’s like Forrest Gump’s box of chocolates. You just never know what might turn up next.

  7. I don’t dare give you any estimates about the number of intronic sequences that are found to have a longer life than previously thought, but more and more instances of functional RNAs of intronic origin are being studied. They can differ in their biogenesis (independent transcriptional units, full-length intronic sequences, processed introns…) and may play regulatory roles at different levels.

    This study focuses on a few particular examples, though, and we can not know for sure how general (or not) the phenomenon is. Even if most introns are indeed discarded, my impression is that we are far now from the situation in which all post-splicing introns were considered as automatically degraded and eliminated.

  8. Can someone here point me to the abstracts or talks by Sternberg and Wells at the recent RNA Society meeting? I’m dying to learn just a little bit about the research they are conducting that supports their claims.

    Many thanks.

  9. Nice to see you Art. Your request is irrelevant to the fact it appears Matheson was dead wrong.

    So would you agree your no-longer-esteemed colleague Steve Matheson was wrong about introns?

    That is the more important issue, not whether Rick Sternberg or Jonathan Wells were in attendance of the RNA Society meeting.

  10. Sal, my request is quite relevant to the suggestion that I am mistaken in my criticism of Wells and Sternberg (which was, I believe, one of the main points of all this). Unless you resort to the same funny math that Wells and Sternberg used in their response to Moran’s critique, my point remains unscathed. Which is why I am wondering what recent research results Wells and Sternberg bring to the table. Hence my request.

    Surely, the two ID giants in the field have something other than funny math to offer.

    And I would hope that they did not feel they had to “sneak” into the RNA meeting under pseudonyms. If that’s the case, then it shouldn’t be much of an issue to cite the abstract number. It’s far too late for retractions or revisions of the abstract book and meeting proceedings. No risk of being unmasked, unless these two wish to keep the same pseudonym for future meetings.

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