As a side note, figuring out what, if anything, "junk DNA" does is something being researched at the moment, since it otherwise seems strange that so much of DNA would not be being used. the amount of junk DNA also tends to increase with organism complexity, from what I've heard, while the amount of genes do not, which suggests ot a lot of people that it has some other important functuions that haven't been worked out yet, that do not involve proteins.
one theory has to do with evolution: that people/all creatures are essentially made of different insensate cells which got together, because it was beneficial for them. In time, as the whole organism evolved, some of these unnecessary cells lost their function (like the human appendix), but their genome still remains within, becoming 'junk DNA' (otherwise known as non-sense DNA).
The other thing that is interesting is this: diseases which kill, tend to start from the ends of the cells. Also, all cells die natural programmed deaths: there is a time frame for life. The process is known as apoptosis: programmed cellular death. Enzymes known as telomerases are responsible for 'eating' up DNA sequences.
It is because of this that we have death. Since on a micro-level, what is death but the loss of genes.
Man seeks for immortality. But the only cells that are immortal are cancer cells. Their telomerases have stopped functioning. So cancer cells are the only ones that grow and grow, and live forever. (perhaps poetry has it right, intuitively: that death is the only immortal thing. Ironically, immortality is to be found in what brings death.)
Which brings us back to junk DNA. Quite a large proportion of them are found at the end of the cells. So when the telomerases start eating up DNA, these go first. In essence, they become infantry soldiers who fall first in the line of fire, such that the important leaders (ie, the sense DNA) are still protected for a while.
That's one postulated function.