Activist atheists, junk DNA and ENCODE

Since the 432 scientist ENCODE Consortium assertion that so far they have detected function (biochemical activity) in 80.4% of the human genome, there has been a lot of whining and gnashing of teeth by activist atheists who commonly use the idea of junk DNA as one of their favorite talking points. Here is a sample of what the whiners are saying:

“That conclusion, that 80% of the genome is critical to function, is simply false, and it’s the notorious dishonest heart of ENCODE’s conclusions.”

“… it makes me mistrust the entire data set — not only are the papers dense, but I have no confidence in the interpretations of the authors …”

“I’ll be blunt. I don’t think Birney has a clue about the biology.”

--PZ Myers

“Most of our genome is still junk in spite of what the ENCODE Consortium says.”

“Who is Richard Myers and where did he get the idea that the concept of junk DNA is an outdated metaphor? Does he have an explanation for all the evidence his statement refutes?”

--Laurence Moran

Why all this anti-science whining and insistence that most DNA is junk? It’s because they believe that random mutation plays a significant role in the creation of the parts of DNA that are functional.  To do this random mutation needs a vast amount of play space in order to accidentally yield functional parts.  Also the higher the percentage of DNA that is functional the more likely it is that random mutations will break existing functionality and will lead to eventual extinction.  This article by Ashutosh Jogalekar explains this perspective in more detail. However, even if a genome consisted mostly of junk it is mathematically impossible for random mutations to produce the design patterns found in DNA.  I have already explained that in part here, here, here and here.

I have two questions for these anti-science whiners:

1) If the vast majority of our DNA is junk, why is the DNA of humans 99.6 percent identical? Shouldn't junk portion of our DNA be able to vary considerably since it isn't under selective pressure?

2) If the vast majority of DNA is junk, why are 95 percent of human diseases relating to DNA associated with non-coding regions?