Is so-called “junk DNA” really useless? What is it doing?

"Junk DNA" was the name given to parts of the genome that do not code for proteins. It was a pretty shortsighted thing to do. We now know that there are DNA sequences that code for RNA that does not get translated to proteins (such as microRNA) and sequences that proteins recognize and bind to regulate other genes. Previously, we believed that biological complexity was a function of the number of genes. Now, we recognize that most of the complexity comes from the way the genes are regulated and that in many ways, the previously junk DNA may be even more important than the protein-coding sequences. It's how the building blocks are used that is more important than the building blocks themselves, which we share with much simpler organisms.

It is likely that some sequences are past remnants or dysfunctional sequences that haven't yet been selected against.. but how much of our genome is truly junk is an open question.