Dear Taz,
A) Regarding one's quest for proving random mutation, i.e., in mutation spots,
While I'm amazed at Peter's tenacity to disprove random mutation in certain theorized mutational spots (if you will in my meager understanding), it makes empirical sense to me. For how can the mutation spot possibly be random when it must be determined? Else random mutations (if they were indeed random) would almost always invite detrimental mutations more than beneficial ones (eg. 999 to 1 or whatever). Thus the whole concept of random mutations is a misnomer for determined ones at mutation spots.
How deterministic vs random are these mutation spots, really Taz?
B) Who and how could one assert an organism's consistently occurring gene is non-functional: Are you asking us to believe:
1) We empirically know it has no function whatsoever,
2) That it does not and/or will not react with protein factors, genes, and/or harmones.
3) That its presence is totally arbitrary and expendable in the grand scheme (if you will) of the organism's posterity.
4) That it doesn't even serve as a functional gene-molecule for nucleotide connectivity or other functions.
In sum, I don't see molecular genetic proof against beneficial random mutation as even necessary to prove that mutation spots must be determined. Such relational determinants must exist (in part at least) to enhance beneficial mutation.
Again, beneficial random mutation seems a contradiction in terms, regardless of mutation spot characteristics; better phrased I might state them perhaps as: beneficial deterministic mutation.
My heralding "beneficial deterministic mutation" does not imply complete non-randomization events occurring at the gene level; please don't misunderstand me. I only imply that detrimental mutations are the only truly random mutations.
Is it that black and white, really; I think so.