Respectful Insolence

I really shouldn’t do it.

I really shouldn’t go perusing the blog of the house organ of the Discovery Institute’s propaganda arm, Evolution News & Views, as I did yesterday. I’m not as young as I used to be, have a family history of cardiovascular disease, and am not in the greatest of shape. Reading idiocy such as what regularly appears there surely cannot be good for my blood pressure or my general health, nor can it be good for my mind. Still, for you I nonetheless delve deeply into the muck of logical fallacies, half-truths, distortions, and misinformation that spews forth from the Discovery Institute, keeping my eye out for when it intersects with an area of interest to me, the intersection between medicine and evolution. (It’s the same reason that, even now, I still occasionally visit Bill Dembski’s home for wandering sycophants, Uncommon Descent, to see what DaveScot and the rest of the “intelligent design” anti-evolutionists are up to.) This time around, I came across an article at EN&V that was so breathtakingly idiotic that at first I assumed that it could only have come from everybody’s favorite creationists neurosurgeon, Dr. Michael Egnor, the Energizer Bunny of anti-evolution.

Surprisingly, my first instinct was wrong. It was Casey Luskin, flak extraordinaire for the Discovery Institute, crowing about how he thinks that “junk DNA” somehow disproves evolution. He finished his little exercise in scientific mendacity with a howler so amazing that I literally could not believe that I was reading something so stupid, even from him. But first, some lesser idiocy, to whet the palate:

It’s beyond dispute that the false “junk”-DNA mindset was born, bred, and sustained long beyond its reasonable lifetime by the neo-Darwinian paradigm. As one example in Scientific American explained back in 2003, “the introns within genes and the long stretches of intergenic DNA between genes … ‘were immediately assumed to be evolutionary junk.’”

Yes, because Scientific American is such an authority on what evolutionary biology says. Hint to Casey: It’s a popular science magazine, targeted to the educated lay public. It’s not a scientific journal, and this wasn’t a scientific review. But, hey, a little thing like that’s never stopped our mighty Casey before, from getting up to bat and striking out, has it? (The difference, of course, is that, unlike the fictional Casey of the famous poem, our mighty Casey never hit a homerun before he came up to bat this time; so his striking out again is not a spurprise.) So let’s see Casey whiff:

But once it was discovered that introns play vital cellular roles regulating gene production within the cell, John S. Mattick, director of the Institute for Molecular Bioscience at the University of Queensland in Brisbane, Australia, was quoted saying the failure to recognize function for introns might have been “one of the biggest mistakes in the history of molecular biology.”

With all due respect, Dr. Mattick appears to be overstating the case considerably. Granted, my perspective only goes back to the late 1980s when it comes to what has been going on in molecular biology, but for as long as I can remember molecular biologists have been trying to figure out whether “junk DNA” has functions. Remember “junk DNA” is a rather poorly formulated term, as it simply means any DNA that doesn’t code for a protein.” However, it’s long been known that segments of junk DNA have functions. Some are promoters; i.e., segments of DNA that regulate the production of protein from specific genes. Some are enhancers, which differ from promoters primarily in that, unlike promoters, they are not usually contiguous with the gene whose function they regulate; enhancers can be many kb away from the transcription start site of a gene. Heck, I cut my teeth in graduate school doing promoter bashing (deleting sequences in a promoter to see which ones are important for driving expression of the gene to which the promoter is attached). That was in 1991, long before the thought of using junk DNA as an argument against evolution was but a gleam in a creationists’ eye, and I’m not particularly important. Even so, at least since the late 1980s there has been considerable effort devoted to elucidating the function of so-called “junk DNA” because a lot of scientists have long suspected that at least some of it has functions that we just haven’t figured out yet. ID has nothing to do with it.

With that background in mind, Casey’s great “revelation” seems even more stupid (if that were possible):

Now it’s turning out that this “mistake” of ignoring function for junk-DNA may have also hindered discovery of the causes of colon cancer. A news article from Science reports: “Three independent groups have hit on the first common genetic variant that appears to raise the risk of colorectal cancer, albeit by a small amount, and which they estimate is found in half the world’s population. Although rare genes have been linked to the disease before, this is the first evidence of common DNA–and also notable because it falls outside a gene, in so-called ‘junk DNA.’” The Washington Post also reported that causes of Type II diabetes may be linked to malfunctions in non-coding “junk” DNA.

And this breathless “update”:

Wired Magazine’s blog network is now reporting that “junk”-DNA’s regulatory function may be the key to improving the techniques used to treat diseases in gene therapy: “[T]he findings could explain why gene therapy that transfers genes but not junk DNA hasn’t fulfilled its promise, and [one scientist] illustrated it thusly: ‘And we know what happens when a foreman doesn’t turn up on a building site: you get the tea-drinking and wolf-whistling, but not much building.’”

The amusing thing about all this is that “intelligent design” creationists like Luskin are trying to convince you that “Darwinism” has blinded scientists to the possibility that these untranscribed stretches of DNA might have functions. Give me a break! In cancer research (my field) exploring those stretches of DNA has long been an interest, given that chromosomal breaks and alterations have long been known to be involved in the pathogenesis of cancer from the very earliest days of cancer research in the first half of the 20th century, a fact that became more important after Watson and Crick worked out the structure of DNA and then later in the 1960s the genetic code was worked out. Indeed, I’m involved in a project right now to study a gene involved in the pathogenesis of melanoma. The way we learned of its importance is when disruption of noncoding sequences that regulate its expression resulted in melanoma in transgenic mice. Moreover, one of the hottest areas in cancer research right now is the study of microRNAs. MicroRNAs are short RNA sequences that regulate the expression of other genes by binding to complementary sequences in their transcribed RNA and blocking the production of the protein product of these genes. (I’m involved in studying microRNAs in my lab as well.)

Of course, even with these discoveries of new functions in former “junk” DNA, there is still a lot of DNA in the genome whose function is not yet known, and it’s certainly possible that much of it doesn’t have a function, although it’s also likely that there is a considerable amount of it that has functions that we have yet to identify. So how does the existence of stretches of DNA that don’t code for proteins and don’t (yet) have identifiable functions support “intelligent design.” Here’s the really hilarious statement by Luskin making that connection:

How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?

My head almost exploded when I read that one. There’s not a single disease the understanding of whose pathology, etiology, or treatment has been the least bit illuminated by ID. In fact, when you boil it all down, this is the only rationale ID apologists use to claim that ID predicted that “junk DNA” might have function, “… design theorists recognize that “Intelligent agents typically create functional things.”

Yep, that’s it. That’s all there is to it. This “prediction” is trivial and has been made by scientists for many years. Of course, nothing in ID predicts which regions of DNA might have a function and what that function might be, but, worse, ID seems to predict that every last nucleotide must have a function of some sort. After all, to quote the above, Intelligent agents typically create functional things.” Using that “logic,” any nonfunctional DNA would be evidence against ID and could arguably falsify ID. Luskin traps himself with an absolutist statement.

In contrast, Mike over at The Questionable Authority points out that it is in reality evolutionary theory that is guiding scientists to the sequences of “junk DNA” that are likely to have function. This is because, now that the technology for whole genome sequencing is becoming faster and more ubiquitous, not to mention cheap enough that it doesn’t require a Manhattan Project-level effort to sequence a genome (as it did for the Human Genome Project), the genomes of more and more organisms are being completely sequenced. The results show that, in among this “junk DNA,” there are stretches of DNA that are very similar (i. e., “highly conserved”) between organisms. Evolutionary theory tells us that when DNA sequences are highly conserved they almost certainly have very important functions. This is because organisms can tolerate mutations in unimportant sequences, whereas mutations in critical sequences are more likely to be deleterious and therefore selected against. By honing in on those sequences, scientists will eventually be able to figure out what their function is:

David Haussler of the University of California, Santa Cruz, and his team scanned the genome sequences of man, mouse and rat1. They found more than 480 ultraconserved regions that are completely identical across the three species. That is a surprising similarity: gene sequences in mouse and man for example are on average only 85% similar. “It absolutely knocked me off my chair,” says Haussler.

The regions largely match up with chicken, dog and fish sequences too, but are absent from sea squirt and fruitflies. The fact that the sections have changed so little in the 400 million years of evolution since fish and humans shared a common ancestor implies that they are essential to the descendants of these organisms. But researchers are scratching their heads over what the sequences actually do.

The most likely scenario is that they control the activity of indispensable genes. Nearly a quarter of the sequences overlap with genes and may be converted into RNA, the intermediate molecule that codes for protein. The sequences may help slice and splice RNA into different forms, Haussler suggests.

Another set may control embryo growth, which follows a remarkably similar course in animals ranging from fish to humans. One previously identified ultraconserved element, for example, is known to direct a gene involved in the growth of the brain and limbs.

[...]

The presence of exact copies in different animals suggests that even tiny changes in the sequence of these segments destroy whatever they do, and have been weeded out during evolution. Non-essential regions of DNA, by contrast, tend to accumulate mutations so that the sequences vary in different organisms.

This is the power of evolutionary theory. It’s a power with not even a modicum of which “Intelligent design” has yet been able to dazzle us. This comparative lack of predictive value and utility is the reason that Luskin’s speculation that an ID perspective would have led to the discovery of the causes of colon cancer and diabetes sooner than evolutionary theory is so divorced from reality as to deserve ridicule, in the very same way that Dr. Egnor’s frequent claims of that evolutionary biology contributes “nothing” to medicine are.

Comments

  1. #1 daedalus2u
    July 18, 2007

    If biologists worked from an Ingelligent Design viewpoint, they would never compare genomes of different organisms. What reason would there be for comparing them? There is no reason for them to have the slightest bit of similarity.

    Any similarities can only occur because God did it. God put those similarities there for a reason, that reason being to trick us into thinking that evolution was correct. No doubt that is part of His plan to trick those who are wise.

  2. #2 ERV
    July 18, 2007

    That last sentence almost made my head explode too.
    For the obvious irony, and also because Behe just told us in his new book to give up trying to treat malaria because his god is making malaria resistant to our drugs.

    “Think of all that time, money, and effort evilutionists have been wasting on malaria! If only they had accepted the Intelligent Design Paradigm!”

  3. #3 Clark Bartram
    July 18, 2007

    Well to be fair, it wasn’t absolutist. He did say typically right? He can’t really be wrong with a convenient escape term like that.

  4. #4 Bronze Dog
    July 18, 2007

    Imagine this: It’s 2027. A guy shouts that we could have prevented 9/11 if we abandoned the whole materialism of relevant security and intelligence studies and instead spent our time assuming that Nostradamus was right and that all of his writings must predict something.

    Not quite a perfect analogy, but I think it’s funny enough for a comment.

  5. #5 David D.G.
    July 18, 2007

    Bronze Dog,

    I think that’s a splendid analogy, both hilarious and wonderfully parallel with that fool’s claims.

    ~David D.G.

  6. #6 ZacharySmith
    July 18, 2007

    This is a really a great example of the vacuousness of ID.

    Conservation makes perfect sense in an evolutionary context.

    Of course, an IDiot can claim that significant genome conservation across several species reflects god’s use of a common platform, much like the way car manufacturers use the same frame for several different models.

    On the other hand, if there were no significant conservation, then the IDiots could say, “Well, the big guy was feeling a bit whimsical one day and decided to try several different things.” Of course I doubt they could tell us why or when god (er, umm, I mean “The Designer”) got playful in the lab.

    ID can explain everything – which means that it can really explain nothing.

  7. #7 trrll
    July 18, 2007

    I’m not sure where this idea got started that “junk” DNA is synonymous with noncoding DNA. When people first started talking about junk DNA, it clearly referred to “selfish” DNA that was completely without any current function and provided no selective advantage to the animal. After all, the concept of noncoding DNA was well understood, going back to the dawn of molecular genetics, and there was no need for a synonym. While the presence of important regulatory elements in noncoding DNA was known, the junk DNA concept was important in that it stressed that one could not assume without evidence that a stretch of noncoding DNA possessed a function, because evolutionary theory allowed, and indeed predicted, that there would be junk sequences that were without function. This raised a significant research question: how much of noncoding DNA is actually junk, and how much has as-yet unrecognized functions? The suspicion that a lot of noncoding DNA in some (but not necessarily all) species might be junk arises from the observation that apparently similar species can have dramatically different amounts of DNA.

    The notion that the junk concept caused scientists to ignore the possibility of unrecognized regulatory elements or other functions in noncoding DNA is of course an utter fantasy. Notably, the discoveries of new functions for noncoding sequences have all come from laboratories who have based their investigations on evolutionary reasoning, not from ID/creationists who now claim after the fact to have “predicted” such discoveries, and presumably “woulda, coulda, shoulda” have made those discoveries themselves–except, of course, they didn’t.

  8. #8 Alison
    July 18, 2007

    The “Intelligent Design Paradigm” hasn’t produced one single piece of testable, reproducible evidence for anything AT ALL in the years it’s existed. Why in the world would any sane individual say it could produce evidence of the functions of ANY DNA faster than biologists could? This boggles the mind. All ID has produced so far is guesses, and “predictions” that amount to “Yeah, we thought that would happen. See this vague phrase that didn’t mean anything at the time we said it? Well, that’s really what it meant. So there.” Gack.

  9. #9 Scott Beach
    July 18, 2007

    Casey Luskin and the other proponents of Intelligent Design have NEVER stated ID in the form of a hypothesis that can be subjected to scientific scrutiny. ID is nothing more than a propaganda campaign.

    Mr. Luskin personally acknowledged to me that the Discovery Institute’s statement “The theory of intelligent design holds that…” is a DESCRIPTION of ID, not the statement of a scientific theory. See http://intelligent-design-hypothesis.com

  10. #10 Ginger Yellow
    July 19, 2007

    “How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?”

    That’s an easy one. They’d never have recognised these causes of disease, because they’d simply have given up when they found something they didn’t understand. After all, that means it’s designed!

  11. #11 James Collins
    July 19, 2007

    Here is the honest truth: “How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?” AMEN!

    Of course the author and self made investigator believes in evolution. It’s sad that a scientists who is supposed to believe in the scientific method, gets so riled up that he nearly blows a fuse. That’s what happens when someone can’t show evidence for their belief. In this case the belief is that evolution created human beings, ETC. How utterly wacky to believe in something that they can’t even describe the what, where, and how it all started.

    The sum total of evolution ‘science’ is the suppositions of those who postulate on old bones and new enigmas.

  12. #12 Bronze Dog
    July 19, 2007

    Riiiiight. Scientist use the scientific method and evolution to find conserved lengths on non-coding DNA (since useful and especially necessary bits of DNA are expected to be conserved according to evolution) and dinker around until they found a use. They’ve known it’s had a use for decades.

    Then the IDiots come along, claim credit because they held the faith that everything has a purpose when it was the scientists who discovered it had a use, rather than just sit and presume like the IDiots did from their Public Relations armchairs.

    Sorry, but it’s quite clear that ID is what’s operating on an a priori assumption of function, rather than actually investigating. That’s why they’ve been doing no research at all. All they can do is try to spin history from merely lucking out on one issue into an unimpressive “I told you so” when evolution already told us so.

  13. #13 pough
    July 19, 2007

    Here is the honest truth: “How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?” AMEN!

    An assertion followed by an amen. I like it. Sounds all sciency and truish, with not a whiff of the religion that has so far unfairly held back the obvious and undeniable truth of the as-yet unformulated Theory of ID. Can I get another amen?

    Of course the author and self made investigator believes in evolution.

    This one had me scratching my head. Are there any non-self-made investigators? When was the last time some child was plucked off the street to be forced into a life of enforced investigatortude?

    Orac, your real-life job doesn’t happen to involve research does it?

  14. #14 mark
    July 19, 2007

    The sum total of evolution ‘science’ is the suppositions of those who postulate on old bones and new enigmas.

    You don’t read much, do you? (Comic books don’t count.) Every week Science has research articles about evolution. Some deal with fossils, but many report on investigations in all sorts of fields. I just read one about how a bacterium was induced to take up an entire 1.08-million base alien genome, with implications about horizontal gene transfer, a mechanism of evolution.

  15. #15 wrg
    July 19, 2007

    An assertion followed by an amen.

    Assertion, you say? I don’t think I can find one. All I see is a question, albeit rhetorical, followed by an amen. Just what is “the honest truth”? I mean, normally, when someone tells me “this is the honest truth” I then expect to hear a true statement. What’s being stated?

    “This is the honest truth: What did I have for breakfast? Hallelujah!” doesn’t make sense.

  16. #16 ZacharySmith
    July 19, 2007

    Hey there, James Collins.

    You got something better than evolution? Bring it!

    Please be so good as enlighten us: What is the theory of Intelligent Design and how can it be tested with the scientific method?

  17. #17 Dave S.
    July 19, 2007

    In fact, when you boil it all down, this is the only rationale ID apologists use to claim that ID predicted that “junk DNA” might have function, “… design theorists recognize that “Intelligent agents typically create functional things.”

    This is not even a prediction of ID. ID “theory” is incapable of making any predcitions on the nature of the designer.

    So they tell us anyway.

    Unrestricted intelligent agents can as well create scads of functionless things.

    ID really is that useless.

  18. #18 Chas
    July 19, 2007

    Thanks to “trrll” for clarifying the etimology of the term “junk DNA.” Orac seems to regret that the term “junk” was used in the first place, but the term is in keeping with the persistent arrogance of some evolutionists.

    Orac rather cavalierly dismisses the conclusion of Mattick and follows with an appreciated humility (“there is still a lot of DNA in the genome whose function is not yet known”) and a very dimenished arrogance (“it’s certainly possible that much of it doesn’t have function”) in using the term “junk.”

    Concerning the use of an “intelligent design paradigm” versus a “Neo-Darwinian” one, I have two questions.

    First: Why are so many scientists today using the “reverse engineering” method of research and analysis if the intelligent design paradigm does not the “least bit” illuminate the understanding of “a single disease?”

    Second: If Mike, over at The Questionable Authority, and Orac are correct that “it is evolutionary theory that is guiding scientists” in the discovery of functional “junk DNA” then why were the results of Haussler’s research so “surprising” to him that he would comment: “It absolutely knocked me off my chair.”

    There are at least two very obvious reasons why Haussler was so surprised that he almost fell out of his chair.

    First: Haussler must not have used evolutionary theory a priori to guide his research. If he had the results would not have been surprising at all, but would have been a priori predicted. Orac assures us that evolutionary theory has this “power” of “predictive value and utility.”

    Second: I would suggest that the other reason has to do with the implications of the discovery that the sea squirt does not share even one of the 480 ultraconserved regions of the human genome. About 80 per cent of the genes in both the mouse and the sea squirt genomes are also found in humans and other vertebrates. Yet while the mouse genome contains identically all 480 ultraconserved regions examined, the sea squirt genome contains not one.

  19. #19 Bronze Dog
    July 19, 2007

    Unrestricted intelligent agents can as well create scads of functionless things.

    When you’re feeling mad or glad or sad, buy Doo-Dads!…
    [Chorus]
    You’ll be glad!
    [/Chorus]
    …Doo-Day!

    Orac rather cavalierly dismisses the conclusion of Mattick and follows with an appreciated humility (“there is still a lot of DNA in the genome whose function is not yet known”) and a very dimenished arrogance (“it’s certainly possible that much of it doesn’t have function”) in using the term “junk.”

    Yeah, because baseless proclamations from the ID crowd are much less arrogant. Isn’t that avoiding the issue, though?

    As for thinking it’s possible that something might not have a function, how’s “I don’t know for sure but maybe it’s possible” arrogant?

    First: Why are so many scientists today using the “reverse engineering” method of research and analysis if the intelligent design paradigm does not the “least bit” illuminate the understanding of “a single disease?”

    Following Egnor’s wordgames, are we? Wikipedia is not a scientific journal.

    Second: If Mike, over at The Questionable Authority, and Orac are correct that “it is evolutionary theory that is guiding scientists” in the discovery of functional “junk DNA” then why were the results of Haussler’s research so “surprising” to him that he would comment: “It absolutely knocked me off my chair.”

    Context, please.

    Second: I would suggest that the other reason has to do with the implications of the discovery that the sea squirt does not share even one of the 480 ultraconserved regions of the human genome. About 80 per cent of the genes in both the mouse and the sea squirt genomes are also found in humans and other vertebrates. Yet while the mouse genome contains identically all 480 ultraconserved regions examined, the sea squirt genome contains not one.

    I’m rereading, rereading, and I don’t see anything really remarkable about that at the moment. Perhaps you’d better spell it out slowly for us.

  20. #20 Bronze Dog
    July 19, 2007

    Oh, wait, missed it. Disregard the call for context.

    I don’t see why he’d be so surprised. I wasn’t. I mean, I’m sure finding it might be surprisingly cool, maybe, but not unexpected or counterintuitive. At least not to me.

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