The evidence is pretty clear: there is little (and likely none) "junk DNA".

http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001...

Not only is there no junk DNA, but the evidence shows that the controller regions of DNA are often in close approximation spatially with the genes they regulate, despite being quite separated linearly on the DNA strand.

Any theories out there as to how this situation came about simply by an accumulation of random mutations? How would such a random process lead to essentially 100% functional DNA? And how would all these controlling regions happen to end up spatially adjacent to their respective genes?