Ouch (just kidding Andrew). Seriously I put the word "directly" in there to make a distinction between enhancer elements and other unknown indirect epigenetic effects. It seemed to me that Gore3K was implying that all junk DNA was full of these intronic enhancers and the mystery is solved. Far from it.
Yes, there are those unexpressed pseudogenes (many pseudogenes are still expressed as mRNA only) but they make up a very small portion of what was commonly known as junk DNA.
There are enough of these unexpressed pseudogenes in the genome to make a powerful case against intelligent design. This is basically what I was trying to get across.
In Summary....
About 95% of DNA is non-coding and of relatively unknown function. Some of this may turn out to play an (indirect) role in regulation of transcription, (although much of this DNA is not located anywhere near coding sequences). There is enough of the junk DNA including dead (unexpressed) promoterless pseudogenes and other "mistakes" (in some cases the same exact errors can be found in closely related species) to lead one to believe that the genome was not made by design.
No problem. I consider it an honor to be distinguished for precision. And I must be accurate, because the attack is on the precision. ---All War supposes human weakness, and against that it is directed. ----- General Carl von Clausewitz