You spoke of non-functional combinations. Actually, there is conceptually no reason you proteins could not be made of beta-amino acids instead of alpha-amino acids. Any proteins that turn out to be non-functional - for any reason - can be weeded out by natural selection, a non-random mechanism. As for the formation of proteins, the physio-chemical mechanisms that would govern this are themselves non-random, so the resulting proteins will not be non-random. We are only just beginning to learn about mechanisms that determine chirality; perhaps alpha-amino acids more easily form peptide bonds that allow the R-groups to move more freely than other forms of amino acids. That by itself could have a tremendous influence on protein evolution.
Kevin L. O'Brien
"Good God, consider yourselves fortunate that you have John Adams to abuse, for no sane man would tolerate it!" William Daniels, _1776_