RAZD writes:
3. Personally I don’t think any DNA is junk, just that the purpose is not known or understood enough. Consider that it takes a considerable expenditure of energy to produce these sequences, and that if they did not serve a purpose that they would be eligible for being weeded out by selection, especially in stressed populations (starving, insufficient nutrients, etc), and that is not happening.
There is some indication that sheer bulk of DNA carries some selective benefit. Bases added to DNA simply for the sake of bulk are legitimately called junk.
Sample reference of many: Cavalier-Smith, T.
Skeletal DNA and the evolution of genome size. Annu. Rev. Biophys. Bioeng. 11:273-302 (1982). Ref pinched from bibliography of
Evolutionary Principles of Genomic Compression by David C. Krakauer.
We also know that different parts of the genome have different selective pressures. Some sequences are highly conserved; others are not. In fact, this is one way of identifying sequences that have some importance, even if we don't know their role! One mystery is that some high conserved sequences were deleted from mice, with no apparent effect. This remains a mystery.
Ref:
Are Ultra-conserved Elements Indispensable? by Dr Mae-Wan Ho (ISIS press release, 16/09/04).
But by comparison there are other parts of the genome where mutations accumulate at pretty much the same rate as they arise, indicating no selective pressures at work. This is indirect evidence for junk, I suggest.
Cheers -- Sylas