Alu questions

After Friday's abbreviated post on human origins, I got this question in my email:
I had to go out and look up what Alu elements are on Wikipedia and started on Shen's paper but wasn't able to get much comprehension of the paper. Would you be able to make a quick post about why the Alu elements in gene-coding sequences would be a bit of happy news for YECs? (or were you being facetious?)
I wasn't being entirely facetious. I'm referring to the longstanding interest of creationists in rudimentary (AKA "vestigial") structures and "junk" DNA. I addressed vestigial organs here and here. In that last post, I made this important point:
A more subtle mistake is the insistence that vestigial organs have no function, that they are true evolutionary leftovers that are just waiting to be eliminated from our bodies. This leads to the equally fallacious response that by demonstrating a function - any function - the vestigial argument is nullified. In response to this reasoning, Steve Matheson made a great analogy to the function of a 1989 Yugo: Just because you can turn a Yugo into something useful, like a mailbox or port-a-potty, doesn't make it any less a vestigial car. In fact, it makes its car-ness all the stranger, since its automotive attributes have nothing to do with its function as a mailbox or whatnot. See my point? Having any function does not mean something can't be a vestige. I personally prefer to use the old term rudimentary structures for what we now call vestigial organs.
The key to understanding potential creationist excitement over the Shen et al. paper is this section from their introductory paragraph:
Historically, Alu elements were regarded as "junk DNA" with no apparent function. However, studies in the past decade have revealed diverse roles for Alu elements in gene regulation and genome evolution.
Shen et al. provide us with many more examples of Alu elements that are somehow involved in gene expression. I think this will excite those creationists who are looking for functions to assign to transposable elements ("junk DNA") like the Alu elements. I remain intrigued but unconvinced that this would somehow negate evolutionary arguments about transposable elements in general. Specifically, if Alu elements are really just gene regulatory elements, why do they look like transposable elements? Or to paraphrase what I wrote before: Just because you can turn an Alu element into something useful, like a gene or gene regulatory element, doesn't make the Alu any less a vestigial transposable element. In fact, it makes its transposable element-ness all the stranger, since its transposable element attributes have nothing to do with its function as a gene or whatnot.

That said, I do tend to think that we've barely scratched the surface in our understanding of Alus, TEs, and the noncoding regions of genomes. I just don't think our ignorance makes for a very good slam-dunk argument against evolution. Ignorance rarely makes for a good argument against anything.

Feedback? Email me at toddcharleswood [at] gmail [dot] com.