I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.Fortunately, there are some smart people who post comments on Uncommon Descent. They have told Bill that the concept of junk DNA is explicitly non-Darwinian. It was proposed by scientists who didn't feel the need to explain everything as an adaptation.
I don't know how many times we've explained to Bill that not all evolutionary biologists are "Darwinists." I know I first told him four years ago but I'm sure there were others before me. He seems to be a very slow learner.
One of these years he'll realize that there's more to evolution than just natural selection.