Junk DNA and the foundation of eukaryotic complexity

I've been considering some new ideas for my capstone thesis.  In 2004 for my science writing class, I wrote a paper about the possible function of Junk DNA.  You can download and read my paper here.  I was reluctant to post it because when I reread it now I don't necessarily agree with all of the conclusions that I came to.  Now, I think that the idea that most junk DNA is regulatory is probably just wrong.  I argued that biological complexity scales better with genome size than with gene count and that perhaps some junk DNA has a regulatory function. I explored the potential roles that micro RNAs, RNA interference and introns might play in the specification of complexity in higher eukaryotes.  My main reference was the work of John Mattick who argued that the genome may contain regulatory networks he called Endogenous Controlled Multitasking.  I just did a search on him on nature.com and he has done a lot more work since I last looked at him mostly in the area of micro RNAs.  This week, I am going to spend some time catching up on this stuff.  I think it has a great potential to turn into my thesis.  Even though my original idea might have been wrong, this is still a hot area. Perhaps a small percentage of junk DNA is functional.  It doesn't all have to be functional for this to be an interesting area for study!