I don't understand this argument, as it would apply equally to all features of the theoretical LUCA (protein and DNA sequences, etc). To make it logically sound, I think you have either to include some kind of super-high boundary to getting to other possible conventions (you probably imply this) or, as I have suggested, it may be a particularly good, if not the best, solution (a global minimum, one might say). The first hypothesis is similar to the QWERTY keyboard, which is cemented in place by many factors, whereas the second is more "survival of the fittest."
It should perhaps be noted parenthetically that prima facie the "accident of history" QWERTY hypothesis is at variance with radical Darwinism. JPK On Tue, Mar 19, 2013 at 1:56 PM, David Waterman <dgwater...@gmail.com>wrote: > I believe that the reason all organisms share the convention (more or > less) is that it dates back to LUCA - the Last Universal Common Ancestor of > all extant life. LUCA must have had the basic transcription and translation > machinery that we now see somewhat divergently-evolved versions of in all > cells. This does not answer why that particular convention was "chosen", > but it does count against the idea that it is the best possible system, or > indeed should continue to be selected for (except that mutations to this > machinery tend to be very much deleterious). > > -- David > > > On 19 March 2013 14:34, Jacob Keller <j-kell...@fsm.northwestern.edu>wrote: > >> Never one to shrink from philosophizing, I wonder generally why the codon >> conventions are the way they are? Is it like the QWERTY keyboard--basically >> an historical accident--or is there some more beautiful reason? One might >> argue that since basically all organisms share the convention (are there >> exceptions, even?), that it must be the "best of all possible" conventions. >> I have often wondered whether maybe this particular convention allows for >> the most effective pathways between proteins of significant function, e.g., >> through the fewest mutations perhaps? One certainly cannot maintain that >> every possible protein sequence has been made at some time or another in >> the history of the biological world (go quantitate!) so there must be a way >> to ensure that mostly the "best" ones got made. On the other hand, since >> many organisms share DNA, maybe they had to "agree" on a system (I think >> this is the dogma?). Was there a "United Organisms" convention at some >> point, reminiscent of "Les Immortels" of the French language or POSIX or >> something, to ensure compliance? What was the penalty for non-compliance? >> >> Anyway, I like the question about the methionines, >> >> Jacob >> >> >> On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry <ber...@upstate.edu>wrote: >> >>> Opher Gileadi wrote: >>> >>>> Hi Theresa, >>>> >>>> To add to Anat's comments: Although the AUG codon for the first >>>> methionine and all other methionines in a protein coding sequence look the >>>> same, they are read in a very different way by the ribosomal machinery. The >>>> first AUG is recognized by the initiation complex, which includes the >>>> separate small ribosomal subunit (40s), a special tRNA-methionine, and >>>> initiation factors (proteins) including eIF2. This leads to assembly of a >>>> complete ribosome and initiation of protein synthesis. Subsequently, in the >>>> process of elongation, AUG codons are read by a different tRNA, which is >>>> brought to the 80s ribosome bound to a protein called elongation factor 1a. >>>> This is an oversimplification, of course, but the point is that the >>>> initiation codon (=the first amino acid to be incorporated to the protein) >>>> is read by a special tRNA, hence the universal use of methionine. >>>> >>>> Opher >>>> >>>> Yes, but why methionine? Half the time it has to be removed by >>> N-terminal peptidase to give a small first residue, or by leader sequence >>> processing. Why use a big expensive amino acid instead of choosing one of >>> the glycine codons? Is there an obvious reason, or just "it had to be >>> something, and Met happened to get selected"? >>> >>> And why sometimes alternate start codons can be used? and why doesn't >>> initiation occur also at methionines in the middle of proteins? I'm >>> guessing it has to do with 5' untranslated region and ribosome binding >>> sites. So could the start codon actually be anything you want, provided >>> there is a strong ribosome binding site there? >>> >>> Just being philosophical, and not afraid to display my ignorance, >>> eab >>> >> >> >> >> -- >> ******************************************* >> >> Jacob Pearson Keller, PhD >> >> Looger Lab/HHMI Janelia Farms Research Campus >> >> 19700 Helix Dr, Ashburn, VA 20147 >> >> email: kell...@janelia.hhmi.org >> >> ******************************************* >> > > -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
