I've been carrying on a conversation with a commenter by the name of John at a post or two over at Biologos. He began by saying that he couldn't see a coherent ID inference for the start and stop codons in the cell.
[A brief explanation: Messenger RNA makes a copy of a strand of DNA that codes for a protein. The first triplet of nucleotides, or the "start" codon, always codes for the amino acid methionine, whereas the last triplet of the strand, or the "stop" codon (of which there are three possible permutations), never codes for any amino acid.]
After much give and take between us, John finally came up with what I consider to be a good challenge for the ID hypothesis. Proteins achieve their function by folding into their specific shapes. In order to do this, it is important to have many or most of the correct amino acids in the correct positions. Because the stop codons do not code for any amino acids, when the ribosomes produce the protein, there is no problem of the stop codons coding for an unwanted amino acid. However, this is not the case with the start codon. Whether or not the protein calls for methionine at the first postion, methionine will be at the first position. Often this could interfere with the correct folding of the protein. So a second process is needed to remove the methionine before the protein can fold and function. From a design perspective this does indeed seem needlessly inefficient. It would seem that a much better process would be for the start codon not to code for an amino acid, also.
So the challenge is for the ID proponents to figure out why an intelligent designer would have used methionine for the start codon, instead of a codon that does not code for an amino acid. And until an explanation is produced, John's challenge weakens, to some extent, most ID hypotheses.
Of course, there may already be a good explanation that I'm not aware of. Any readers who know more about this should feel free to comment.