Chris
It should be pointed out that the judgment that so much of a genome is
"junk" is based on the phenotype's view of things, not the gene's. From the
point of the "junk" genes themselves, they are not junk. They are
evolutionarily successful in that they have found a way to survive by
hitching rides along with productive or useful genes.
Further, a scientest believing in purpose *might* be content to label 95% of
the genome "junk." For example, if he removed that 95% of the genome and the
resulting organism was (let us suppose) still fitted to its normal
environment, he might well conclude that it was "junk." We already know that
some genes are parasitical on other genes, so why might there not be genes
that are not particularly harmful but not useful either?