The hilarity of this post is hard to ignore. Cordova is actually trying to give the ID creationist movement credit for the discovery that "junk" DNA has lots of functions (as well as suggest that acknowledgement by Sternberg in a review article is some how proof of ID science).

That's an interesting suggestion. I'll have to figure out how to get on this scam, you know, making vague statements then taking credit for others' work. Like, I could say, "we don't know everything about non-coding DNA, there must be something as yet undiscovered" then when they discover something new like miRNA or retrotransposons I can demand my Nobel even if contributed nothing.

Never mind the importance of actually doing benchwork, I can just say my BS theory predicts this or that, and then when other people discover anything I get to claim victory. That's a brilliant idea. It apparently also works when one makes the claim about a decade after the discovery, you see in reverse-vampire conspiracy world, the DI and ID always existed and were always right. Anyway, here's a simple image of what we know about the DNA in a human cell.



As you can see, we've figured out a lot of what that "junk" is, and considering introns were discovered in 1978, promoters were hot stuff as early as the mid-eighties, transposons were discovered in the 50s in corn resulting in Barbara McClintock's 1983 Nobel, and retrotransposons and various other repeat elements that have undergone recent hot study were really discovered as a result of the Human Genome Project which began in the early 1980s it's pretty much insane for the DI to suggest that they had any impact on this science. The sheer arrogance of it is actually pretty extraordinary.

It's also an interesting claim that missing out on the functions of "junk" DNA was the greatest mistake molecular biologists have ever made. And was it ever really a mistake that a majority of us made? I remember back when large portions of DNA were found to be non-coding, not everybody thought that meant they served no purpose. Hell, our lab has been studying that junk for about 20 years looking for things and finding lots of interesting and important pieces of non-coding DNA. To say that it wasn't until the DI or ID showed up that scientists started looking at noncoding DNA is a joke. This has been a hot pursuit for decades. It's almost as funny as when they claim evolution isn't important for molecular biology. In the last 3 days we've had a bunch of talks from visiting researchers, and in every single one they mentioned evolution as a guiding principle in figuring something or another out. I guess I've been more attuned to it lately. For example, in pretty much every talk I saw the researchers used VISTA for conservation analysis of non-coding DNA regions. It's a wonderful program. You enter regions of genomic DNA and it aligns them and shows you areas of conservation. It turns out the areas that are mostly highly conserved across species are usually where the important gene-regulatory cis-elements are. Take for example this little alignment I just did of human, mouse and chicken smooth muscle alpha-actin promoter sequences.



What this shows us is the conservation of sequences between the three species in the sequence immediately preceding the smooth muscle alpha actin coding sequence. The closer the line is to the top - or 100% conservation - the more the sequences have stayed the same over millions of years of evolution. It's helpful because it points to what is important for gene regulation. A promoter might have an element 30 thousand bases away that is critical for regulation of a gene, all the intervening sequence might be completely unimportant, and VISTA will show you essentially what selection has deemed important enough not to change.

Interestingly, when the mouse actin promoter was first put into a transgenic mouse with a reporter gene on it, they only included the first few hundred base pairs (where most the conserved elements and CArG binding sites are), because in tissue culture that was enough to drive expression. However, in the animal, the thing didn't work, the reporter didn't get expressed where smooth muscle actin was. So, our lab looked both forwards and backwards through the promoter and gene and found not only did you see conservation of a elements -2.6kb back (in mice and rats, but not in chicken), but you also had a conserved CArG element in the first intron. We then cloned this sequence that included the -2.6kb and the first intron (out of the rat actually), put the reporter gene on it, and voila, beautiful recapitulation of the expression of smooth muscle alpha actin in the mouse.



The other interesting thing our little Vista plot shows us is that huge portions of sequence still appear to be "junk", that is, they don't appear to do anything, and nature hasn't seen fit to conserve them across species. Often times, researchers create artificially short promoters that take the various conserved regions and cut out thousands of intervening base pairs and they recapitulate endogenous expression perfectly. So to say that "junk" DNA doesn't exist, is well, still unfounded, especially considering papers such as this one in which researchers demonstrated entire megabase regions of DNA could be deleted from the mouse genome, with no ill effect. One day we might figure out a use or reason for so much extraneous DNA, but to say the "junk" hypothesis has been fully disproven is still unfounded, almost as unfounded as suggesting ID had anything to do with discovering additional functions in non-coding DNA (like scientists really sit around reading the output of the DI for anything but laughs).

Also what's this bizarre need for design to mean that everything has a specific function? Aren't we biasing our supposedly non-Christian, or non-deity based "scientific" theory towards a perfect creator? After all, why can't the Raelians be right? Maybe we were designed by imperfect aliens who weren't paying too much attention to the details, or had problems with foresight? And what kind of designer would create our system of cranial nerves? What a complicated inelegant train wreck those are. Why would a competent designer make sure childbirth was so painful and dangerous? What kind of idiot made our urogenital system in general? Reproduction and waste disposal using all the same equipment? Why do men get nipples? What idiot designer would make our terrible system of sinuses. Why does their designer theory need everything to fit into its specific cubby-hole? Why couldn't there be waste, inefficiency, redundancy and mistakes in their designers plan? There's a good explanation for why evolution by natural selection would come up with such inelegant solutions, they just had to work, they didn't have to be pretty. But why would a designer, especially a perfect one, screw these things up?

It's one of the signs of the underlying assumption of ID, and one that the IDers are continuously deceptive about. There is only one possible designer they are interested in pushing, and their assumptions how a designer would operate are the proof. They know which designer they're trying to justify. The fact they won't acknowledge that it's specifically the god of the bible they're pushing as designer is just more proof of the fundamental deceptive nature of the DI.

Labels: Sal Cordova, uncommon descent