Our published claim that most “dark matter” transcripts can be explained as by-products of the process of transcribing known genes holds: whether they are functional remains to be seen, but the notion that because they exist they are likely to be functional violates Occam’s Razor”.
van Bakel et al., in response to an article from the Mattick lab which criticized several aspects of their study entitled “Most ‘dark matter’ transcripts are associated with known genes”, published in PLoS Biology last year.
Here’s another quote from the Hughes Lab response:
We believe that Clark et al. misinterpret what can be claimed from much of the literature in this area, and fail to acknowledge known weaknesses in some of these studies”
Here I am with Tim Hughes:
And here I am with John Mattick: