In which the Discovery Institute mocks me and reveals its ignorance...again.

You must be doing something useful if the Discovery Institute, that bastion of intelligent design propaganda, devotes an entire post to your article.

This time it was the piece on junk DNA that I wrote for Scientific American. Here's what the DI folks had to say:

Darwinian "Science" in Action

Evolution News & Views  October 9, 2012 5:53 AM | Permalink

Someone forgot to put Scientific American blogger Ashutosh Jogalekar on the list to get the memo on massaging the ENCODE results. Darwinists used to say a genome scattered with junk is just what you'd expect from natural selection. Now they say the reverse, that a much more fully functional genome is just what you'd expect. (See here for David Klinghoffer's note on Richard Dawkins's remarkable change of heart.)

But in the immediate wake of ENCODE, poor Jogalekar was still carrying on with the old talking point ("Three reasons why junk DNA makes evolutionary sense").

We think his third paragraph is most revealing:

But what I found astonishing was why it's so hard for people to accept that much of DNA must indeed be junk. Even to someone like me who is not an expert, the existence of junk DNA appeared perfectly normal. I think that junk DNA shouldn't shock us at all if we accept the standard evolutionary picture.

In other words, because Darwinism is true, "much of DNA must indeed be junk." Theory trumps evidence. That's Darwinian "science" for you.

As usual, the DI's interpretation is chock full of misleading statements. Let's address the objections in short order:

1. Yes, I was not on the ENCODE memo because the whole point that people like me, Larry Moran and Ryan Gregory were making is that the ENCODE results misrepresented the lack of significance of junk DNA by having their own, very liberal, definition of "functional" DNA sequences. Several posts criticized the widely disseminated impression provided by ENCODE that "80%" of DNA was functional. The DI of course jumped on this bandwagon with alacrity since it fit like a jigsaw puzzle piece into their worldview that most or all of the human genome had to be "designed". As many commentators mentioned, the 80% quip was a PR disaster.

2. The "old talking point" is old precisely because it fits well into standard evolutionary theory. The DI wants to make it sound like scientists were for junk DNA before they were against it before they were for it again. This of course proves that scientists are a confused lot who are not sure about anything...

The truth of course is that "junk DNA" was always a misnomer since we did not know what function, if any, the sequences of DNA regarded as "junk" would turn out to have. Now some of them (but a small percentage) did indeed turn out to be functional in the true sense of being coding or regulatory elements. But the fact is that many of them are still non-functional by these same definitions. 

What scientists were saying is that some DNA which was regarded as "junk" might turn out to be functional, and in fact it has been found to be so. However, there is no reason - based on standard evolutionary interpretations which I explored in my post - to assume that most DNA would have a function. Will we find function for some more DNA in the future? Absolutely. Does that still mean that most DNA is functional? Of course not. Thus, contrary to what the DI would have us think, believing that some junk DNA would turn out to be functional but also believing that most DNA might still be predictably "junk" are not opposed viewpoints. The DI would have us believe that they are and this then becomes a convenient vehicle for them to insinuate that scientists are not sure of anything.

The last statement is just a gross misunderstanding of the scientific method:

In other words, because Darwinism is true, "much of DNA must indeed be junk." Theory trumps evidence. That's Darwinian "science" for you.

No, the accurate way to say this is that "evidence supports theory". The DI wants to give the impression that we "Darwinists" used two sets of evidence, one contradictory to the other, to support our pet theory. But as I have indicated, it's a straw man to proclaim that these two sets are contradictory. Both pieces of evidence are entirely consistent with a standard evolutionary interpretation in which some junk DNA does turn out to be functional without providing any reason to believe that most junk DNA would also be the same.

It's not that hard to understand. At best the confusion is a result of confusing nomenclature and bad PR, not a failure of evolutionary theory that the DI would perpetually have us buy into.