Wells addresses this argument in: Jonathan Wells on Darwinism, Science, and Junk DNA. Before analyzing his response, it's worth reviewing what he wrote in The Myth of Junk DNA.
In chapter 5, Wells talks about sequence conservation as evidence of function—specifically the fact that the sequences of some potential pseudogenes are more conserved that would be expected if they were really pseudogenes [Junk & Jonathan: Part 8—Chapter 5]. That's an important argument and, if true, it would point to a function. The irony is that Wells doesn't believe in common descent so, from his perspective, these are not conserved sequences due to negative natural selection. Nevertheless, he is happy to use evolutionary arguments whenever it suits him.
What about the reverse argument; namely, that lack of sequence conservation is a indication of lack of function? Wells is not so happy to use that argument, as he explains in his latest posting.
Not so. Although sequence conservation in divergent organisms suggests function, the absence of sequence conservation does not indicate lack of function. Indeed, according to modern Darwinian theory, species diverge because of mutational changes in their functional DNA. Obviously, if such DNA were constrained, then evolution could not occur.Wells is arguing that evolution requires change. Therefore, sequence conservation is not what "modern Darwinian theory" would predict. Instead, it predicts that sequences in different lineages should change!
In 2006 and 2007, two teams of scientists found that certain non-protein-coding regions that are highly conserved in vertebrates (suggesting function) are dramatically unconserved between humans and chimps (suggesting… rapid evolution!). More specifically, one of the teams showed that one unconserved region contains an RNAcoding segment involved in human brain development.
He picks two papers from the scientific literature that purport to show rapid sequence changes in regions that are functional. Wells is trying to discredit the idea that lack of conservation implies lack of function and he's using a few specific examples to make the case.
In any case, the idea that lack of sequence function indicates selection for function rather than evidence for nonfunction cannot be sustained by cherry-picking a few controversial examples from the literature. Wells' argument is silly, and it's made even more silly when you realize that he doesn't actually believe in evolution.
Furthermore, the analysis by “paulmc” assumes that the only thing that matters in nonprotein-coding DNA is its nucleotide sequence. This assumption is unwarranted. As I pointed out in Chapter Seven of my book, non-protein-coding DNA can function in ways that are largely independent of its precise nucleotide sequence. So absence of sequence conservation does not constitute evidence against functionality.This point is valid but it's not consistent with his first point. Either lack of sequence conservation indicates lack of sequence-dependent function or it doesn't. If it does, contrary to his first point, then one can still explain sequences that aren't conserved by invoking functions that require bulk DNA but not specific sequences.
Wells spends very little time on these kinds of functions, which is surprising since they represent the only real possibility to establish that junk DNA isn't really junk. He discusses enhancers, chromatin organization, centromeres, nucleus organization, and the idea that junk DNA could act as a lens in mouse eyes [Junk & Jonathan: Part 10—Chapter 7]. None of these make the case for most of our genome having a function.
If junk DNA is really a myth then there should be some good explanations for why we have massive amounts of DNA in our genome that has all the characteristics of nonfunctional DNA (lack of sequence conservation). Wells does not give us these explanations. Instead, as we see in his posting, he wants to deny that there's a connection between lack of sequence conservation and lack of function. But he's happy to accept evidence that sequence conservation implies function.
Isn't that strange coming from someone who doesn't believe in common descent, natural selection, and "conservation"?