Respectful Insolence

i-e7a12c3d2598161273c9ed31d61fe694-ClassicInsolence.jpgI’ve just returned from Las Vegas after having attended The Amazing Meeting.. Believe it or not, I was even on a panel! While I’m gone, However, my flight was scheduled to arrive very late Sunday night, and I’m still recovering. Consequently, for one more day I’ll be reposting some Classic Insolence from the month of July in years past. (After all, if you haven’t been following this blog at least a year, it’ll be new to you. And if you have I hope you enjoy it again.) This particular post first appeared in July 2007.

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 JD
    July 13, 2009

    You should introduce Luskin to Craig Venter. Twit o’ tard meets his owner.

  2. #2 MikeMa
    July 13, 2009

    Luskin has been (rightly) called a fool by such a diverse and numerous group he must have it tattooed on his forehead, backwards so he’s reminded every time he looks in the mirror. The little twit needs to go away.

  3. #3 DebinOz
    July 14, 2009

    “Intelligent agents typically create functional things.”

    Yeah, right! The IDtards’ intelligent agent has lousy quality control then.

    Have these people ever wandered around the genetics department of a large childrens’ hospital? I’m not being flippant and calling these children non-functional, by the way (I am the parent of a child with an undiagnosed obscure genetic disorder that caused anophthalmia, bilateral clefts, and other manifestations).

  4. #4 Anon
    July 14, 2009

    Interesting article. I agree that “junk DNA” has nothing to do with ID, and I wish scientists/bloggers would stop engaging with the ID-ers who are trying to make “junk DNA” an ID issue. But one point of clarification: Before and even throughout the 80s and beyond, most scientists did not think that at least one type of what has been categorized as “junk DNA,” namely transposable elements (or, as McClintock called them, “controlling elements”), had any function. When McClintock was awarded the Nobel for her discovery of transposition, there was a lot of skepticism about her ideas and speculations on the genetic control aspect of transposable elements. There really haven’t been many scientists interested in the potential “controlling” (or, in more modern parlance, regulatory) function of transposable elements until recently.