It's been almost three years since I created a blog post on What is the "dark matter of the genome"?. I noted that the term was popularized by the philosopher Evelyn Fox Keller who was opposed to the concept of junk DNA. She preferred to think that most of the genome was full of functional sequences that hadn't yet been discovered. The term "dark matter" was her way of emphasizing that most of the genome was a mystery but it wasn't junk.
Since then, the term "dark matter" has been increasingly used by scientists, especially those in the field of genomics. I think it's for the same reasons that Evelyn Fox Keller described. These scientists spend a lot of time and effort analyzing entire genomes for biochemical activity of various sorts and they don't want to admit that they are mostly looking at junk DNA. That's why I summarized my position like this ...
