Sal Cordova Quote Mines Nature (I'm shocked!)

I just knew it. The second I read this abstract I just knew that the Uncommon Descent cranks would dust off their old "Junk DNA" harangue and suggest that if it wasn't for them, no one would believe that all that non-coding DNA had a purpose. Sal Cordova obliged, and it's the usual embarrassing misread of our literature.

Heaven forbid that scientists should be so brash as to not infer purpose into everything without studying it first. I've been waiting to use "promiscuous teleology" in a post, I guess this is my chance. But that's not even necessary in this case, this is such an egregious misreading of this result by Cordova that we can nail him just on his lack of reading comprehension and knowledge of biology, let alone his historical revisionism. That is if we're not assuming he's being purposefully dishonest - given his history of quote-mining that wouldn't be stretch.

Let's start with a timeline of non-coding DNA:

The most important thing to remember about creationists is their complete inability to appreciate a timeline. In this case, the term "Junk" as applied to DNA originated in 1972 with Susumu Ohno. It was kind of a null hypothesis - that there was no obvious function for such huge amounts of non-coding DNA so some of it might just be filler.

Evidence already existed in 1972 for the function of some non-coding DNA. Probably starting from the discovery by Barbara McClintock of transposons it was known that repeat elements and non-coding regions could serve a functional and/or evolutionary purpose.

The creationists however, make it sound as though once Ohno suggested the junk hypothesis, that all biologists just sat on their hands and stopped working on non-coding DNA. However biologists were already intensely studying it - contrary to the rather idiotic assertions of the evolution denialists that ignoring junk was some great "mistake" that we're trying to recover from.

A decade before this Jacob and Monod figured out the lac operon - and that it was controlled by a promoter or a non-coding region. The terminology of junk, while popularized widely, wasn't believed. It's not like all the molecular biologists in the world took the cue from Ohno and just dropped their pipettes and walked away. Non-coding DNA was an active field of study at the time, if anything the only false assumption was that things like promoter regions would only be immediately adjacent to genes - within 100 base-pairs - and that it was then hard to account for all that additional space between genes. That is, until around 1981 with the discovery that upstream promoter elements could be thousands of base pairs away.

Promoter research was intense throughout the 80s, and with the advent of PCR in 1984, molecular methods became exponentially more powerful. Day by day, the function of non-coding elements of the genome was being analyzed and dissected. Promoters were being used to drive expression of transgenes in experimental animals, they were being mutated. Regulatory elements were being discovered as well as the transcription factors they bind. In other words, no one thought that non-coding DNA was really junk. After all, the best way to find the regions that were important was through conservation analysis - which requires that natural selection preserve the most important regions for gene regulation. By comparing a similar sequence across species, the areas of high conservation turn out to be the ones that are responsible for controlling genes, the intervening sequence that his highly mutable is often just spacer. But that's not the only thing discovered in non-coding DNA, even without funding from the Discovery Institute, rebel scientists studying the junk against the wishes of the Darwinian orthodoxy have discovered in humans things like micro-RNAs, non-coding RNAs that appear to be critical for gene regulation. They've discovered various RNA molecules that are critical to protein function, and some that have their own enzymatic functions. For decades following Ohno's suggestion of the null hypothesis (creationists do have a problem distinguishing between hypothesis and theory) functions of non-coding DNA were being elucidated.

But what does the creationist mind of Sal Cordova think of this timeline? Well, apparently the study of non-coding DNA started in 1997.

Behe 10 years ago, in Darwin's Black Box (DBB) suggested junk DNA may not be junk after all. Behe has been vindicated by the facts, Miller refuted.

Wow. What a stunning insight from Behe! Decades after every other scientist in the world began to study and decode the function of non-coding DNA, he figured out it might be useful for something. What a genius! Give that guy a Nobel! He predicted, from the future mind you, what would happen in the past! What an accomplishment!

Not content to just let it go at that level of idiocy, Cordova then, true to his nature, quote-mines the article:

Finally, there is at least one other interesting fact in this article: "the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution". This means these designs NOT attributable to natural selection. Features in the genome have been shown not to be likely products of "slight successive modifications". How I love science!

At least one other? Holy crap is that an understatement. This has got to be the most important paper in transcription in years. As Razib points out in his analysis, there's enough here for 5 or 6 papers full of interesting facts. But onto his allegation that these results are a sign that, " these designs NOT attributable to natural selection". Aside from the obvious promiscuous teleology (hehe), what is Cordova's major failure in reading comprehension? Can anyone figure it out?

Well, aside from the obvious hilarity of a creationist using the results of sequence conservation analysis across different mammals for his advantage, the answer of course is in the very next paragraph, which as a creationist quote-miner, Cordova would never bother to report. From the Science Daily article.

According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species' genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction. As this pool turns over during evolutionary time, researchers speculate it may serve as a "warehouse for natural selection" by acting as a source of functional elements unique to each species and of elements that perform the similar functions among species despite having sequences that appear dissimilar.

It's also worth including this passage from the Nature paper.

Surprisingly, many functional elements are seemingly unconstrained across mammalian evolution. This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism. This pool may serve as a 'warehouse' for natural selection, potentially acting as the source of lineage-specific elements and functionally conserved but non-orthologous elements between species.

You see, these elements are "functional" in that they do something, but not necessarily to the benefit of the organism. It suggests rather than part of being an integral part of the "design" of an organism, they are merely tolerated. They aren't harmful enough to effect survivability, and not critical enough for natural selection to maintain them under constraint. They may serve a long-term advantage for natural selection - that has yet to be determined - but they certainly aren't critical for the function of the organism.

If anything, this is the opposite of what intelligent design would predict. These sequences have a function, it's just not particularly useful for the organism.

That's some good quote mining there Sal.