|MadSci Network: Biochemistry|
L-sugars and D-amino acids certainly exist in nature as free molecules and as the products of racemization of their respective enantiomeric partners in proteins and carbohydrates, and D-amino acids have even been found to have a role in normal brain function, but in general it is true that D-sugars and L-amino acids are the norm. The fact that usually only D-sugars and L-amino acids are found in natural biological macromolecules certainly could be used as an argument for intelligent design because currently there is no scientific understanding as to why that should be the case. However, I would not call it a "compelling" argument simply because one could always argue that just because there is not a scientific understanding now of why only the given enantiomers exist does not mean that there won't be one in the future. An evolutionary argument can be made for their predominance as follows: if one imagines that life arose from a prebiotic primordial soup in the form of a self-replicating molecule of some sort, and that this process was catalytic in the sense that molecule A makes more molecule A and molecule B makes more molecule B, one can imagine that if randomly there got to be more A than B, this would quickly have a "snowball" effect in which the amount of A relative to B gets greater and greater, and if this means that A uses up all of a critical resource for the reaction, i.e., a catalytic surface, then B would be eliminated. If from A all subsequent life arose, then if A was D-sugars or L-amino acids (or something that energetically would be expected to lead to only them and not the opposite) all subsequent life would contain them. One could also argue that A had some inherent advantage in replication, but you don't need to, and as you say there is no known advantage to the predominant molecules. Ultimately, this is really a philosophical question. Those of a more scientific persuasion can always argue that we just don't know the data yet to construct a "scientific" theory explaining the phenomenon (any phenomenon around which this kind of debate happens), while those of a more theological persuasion can always argue that there is a sentient, guiding force behind what behavior they seek to explain. Or to put it another way, one side will say we just don't know enough yet, and the other side will say it is God. Since it is logically impossible to prove (i) that what one doesn't know either exists and hasn't been found yet or doesn't exist, or (ii) that God either exists or doesn't, then there is no way of resolving this conflict. All that can really happen is for physical data to arise that leads to a plausible scientific explanation for whatever you are talking about and for this explanation to be accepted by the vast majority of people. But for cases in which that hasn't happened, logically one can't argue that it will happen or that it won't; you either believe that it will or you believe that it won't.
Try the links in the MadSci Library for more information on Biochemistry.