Instruction manuals

DNA uses three-base "words" for each amino acid building-block for a protein.  Some of the words, though, have alternative functions as punctuation, as in "start sequence" and "stop sequence."  Our remote ancestors settled into these punctuation conventions so long ago that most current life on Earth uses the same ones, but it seems that a few organisms here and there employ a different system.  That wouldn't matter so much if all their DNA did was talk to their own cells, but bacteria and viruses have a way of spreading their DNA around somewhat promiscuously.  What a mess it seems this would make, if DNA from a system with one convention for "start/stop" ended up in the genes of a system with another.  Somehow, they work it out.