HT: Larry Moran
According to Michael White it is:
What you should really know about the concept of junk DNA is that, first, it was not based on what scientists didn't know, but rather on what they did know about the genome; and second, that concept has held up quite well, even in light of the ENCODE results. Among the reasons that scientists in the 1970s and '80s began to believe that much of the genome is non-functional was the observation that very similar species could have very different genome sizes. There is no reason to believe that similar species require dramatically different amounts of functional DNA, and thus something other than functional requirements must explain differences in genome size. Scientists also discovered that our genomes contain parasitic, virus-like elements called "transposons" that have the ability copy themselves within our cells. This DNA ecosystem makes our genomes more like a jungle than a precision machine. At the latest count, transposon-derived DNA makes up at least half of our genome. The transposon-derived sequences in our genomes do not have to be explained by invoking some useful function for it. There is no mystery here: this DNA is there because it can replicate.