I've been meaning to gin up some further contemplations on the ENCODE results, as a followup to my previous article, and in reply to my friend the thoughtful and sober atheistic commenter "Blue Devil Knight" who commented on my article starting here in the comments. But I've been distracted by other projects.
"What is it specifically that the naturalists are having so much trouble handling?"
It's one thing to say that the theory is genuinely flexible enough that wildly different evidential states can fit either way; it's another thing to say that the theory predicts two wildly different evidential states over against itself for conflicting reasons. Either way, though, that means the different evidential states cannot be used as evidence for the superiority of the theory against other theories (although an evidential state in itself could still be used as evidence against another theory).