Relay-Version: version B 2.10 5/3/83; site utzoo.UUCP Path: utzoo!utgpu!water!watnot!watmath!clyde!ima!haddock!johnc From: johnc@haddock.UUCP Newsgroups: sci.bio Subject: Re: information content of DNA Message-ID: <430@haddock.UUCP> Date: Tue, 7-Apr-87 15:24:54 EST Article-I.D.: haddock.430 Posted: Tue Apr 7 15:24:54 1987 Date-Received: Fri, 10-Apr-87 03:22:13 EST References: <2840@ecsvax.UUCP> <11189@teknowledge-vaxc.ARPA> <978@aecom.UUCP> <425@haddock.UUCP> <1010@aecom.UUCP> Reply-To: johnc@haddock.ISC.COM.UUCP (John Chambers) Organization: Interactive Systems, Boston Lines: 87 In article <1010@aecom.UUCP> diaz@aecom.UUCP (Dizzy Dan) writes: >In article <425@haddock.UUCP>, johnc@haddock.UUCP (John Chambers) writes: >> One observation I haven't seen yet is the peculiarity of DNA called "reading >> frames" This effectively triples the number of amino-acid sequences a given >> chunk of DNA encodes. Multiply this by two for the complementary strand. >> Granted, it is very rare that all six readings actually code for something >> in real life. But this doesn't have much to do with the information content. > >Forget rare, there ain't no such animal. Although multiple reading >frames have been observed in phage, and transcription from complementary >strands observed in a variety of organisms (most recently, mice) there >is no documented example of anywhere near the six possible readings >coding for functional polypeptides. Come now, isn't it a tad early to make such a declaration? The literature has on the order of 100 genomes published, all but a handful being viruses. A couple of real cases of overlapping genes have been discovered; both are in viruses. From this you are going to presume to predict that there are no cases at all in higher organisms? You have more chutzpa than I. > The implications for molecular evolution for such a scheme would > be disastrous. No, they'd only be disastrous if such overlaps were common. It seems clear after just a little thought that selection would tend to eliminate overlapping genes, perhaps replacing them with replicates that can then mutate independently. Simple info-theoretic calculations would predict that such multiply-read stretches of DNA would be rare; they wouldn't be impossible. I'll go out on a limb myself, and predict that when we finally get entire genomes of vertebrate species, we will in fact find a few overlapping genes. The frequency will be much lower than you would expect in a random list of nucleotides, but they will be found occasionally. BTW, there is one mitigating factor that allows them slightly more often than you'd expect: There are many codings for most of the amino acids. Of the 64 possible frames, there are only 21 amino acids and a stop code. This means that it is possible (although difficult) to make slight changes to one of a pair of overlapping genes without changing the other. But it'll still be quite rare. >Organisms apparently think little about the advantages of compact >genomes, prokaryotes included. Rather there seems to be something about >having a lot of "junk" DNA that's beneficial, if I may be allowed this >ounce of teleology. Granted, we may one day realize that much satellite >and intron DNA may have functions we don't even dream about today, but I >truly doubt that coding for proteins will be one of them. The same thing goes for programs. Most of my programs contain some junk that I hope is never used. I call it "debugging code", and it is turned on by something like a -D5 option on the command line. If you don't know about such an enabling option, you might well look at the code and decide that it is worthless and can never be executed. Consider also the use of #ifdef in C to supply parallel chunks of code that can never be activated together: #ifdef SYS5 ... #endif #ifdef BSD ... #endif #ifdef XENIX ... #endif How do you know that some of the "junk" DNA isn't like this? I sorta suspect that my DNA comes loaded down with similar "junk" sequences that can become enabled by some circumstance that probably won't happen in my lifetime, but happened often enough to my ancestors that the stuff passed the Darwinian tests and got passed on. The fact that current researchers can't explain it is interesting to me, but not to my genome. Note that genetic "diseases" like sickle-cell anemia and diabetes are already known to be adaptive in certain environments. If such downright damaging genes are "adaptive" in some populations, you'd expect a lot of the apparently-innocuous DNA to also be adaptive somehow. Also, the literature already contains some descriptions of stretches of DNA that have regulatory functions rather than coding for amino acids. Also, sometimes DNA (more often RNA) ends up curling around, interacting with itself like an enzyme, and modifying its own function. This could easily activate stretches that otherwise appear to be dummies. It's not well understood yet, but wait a few more years. -- John Chambers (617)247-1155 <...!ima!johnc> [The above opinions are my own; for a small fee, they can be yours, too.]