Here's a bit from his latest post on Evolution News & Views (sic [Perspectives on ENCODE and Junk DNA].
The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.That's pretty good for someone who posts on a blog that also publishes stuff from Jonathan Wells and Casey Luskin. I wonder if they talk to each other?
On the other hand, the observation that the genome is buzzing with activity underscores what proponents of ID have been saying for years: not knowing what something does doesn't constitute evidence that it's doing nothing. Moreover, it wasn't long ago that Laurence Moran and PZ Myers were telling us that the genome is not even pervasively transcribed and that this amounted to evidence that the majority of our DNA is junk.
On the other hand, it's not perfect. I've been arguing for years that there is good solid evidence that most of our genome is junk. I have never used the argument from ignorance that Jonathan attributes to me.
Also, I have never denied that the genome is pervasively transcribed. Instead, I have argued that pervasive transcription is something that one expects given what we know about DNA binding proteins and transcription. I've pointed out that the vast majority of our genome is transcribed very rarely—about one transcript per day in 100 cells—and this is consistent with accidental transcription. This is noise. The product is junk RNA and is has no function [Useful RNAs?] [Junk RNA] [Pervasive Transcription] [How to Frame a Null Hypothesis] [How to Evaluate Genome Level Transcription Papers ].
I discussed this thoroughly when I reviewed Jonathan Wells' book The Myth of Junk DNA [Junk & Jonathan: Part 6—Chapter 3]. Perhaps Jonathan McLatchie hasn't read my earlier posts?
Contrast McLatchie's post with that of Jonathan Wells [A Dishonest Intelligent Design Proponent?].