But more recently, we've learned a lot more about some of those non-coding regions of DNA. Although they don't specifically code for proteins, there is now evidence that at least some of the non-coding regions seem to be important in turning genes on and off, and thus they may be important in directing the timing of development, among other things. That has led to the currently popular view that there is no junk DNA. At scientific meetings, the discussion sometimes gets a little heated.
But does the finding that some non-coding DNA is useful necessarily mean that there isn't a lot of junk? It's hard to imagine that cells are so efficient that they have managed to eliminate all junk from DNA when it occurs. If a junk sequence did no harm, what would cause it to be selected against during the course of evolution? In all likelihood it would just remain there forever. And that's exactly what "junk DNA" proponents believe.
And so the debate rages on. Before you decide where you stand on the junk vs. no-junk debate going on in biology today, read the fairly well-balanced article in the New York Times.