jon@runx.ips.oz (Jonathon Seymour) (07/01/88)
I'm after issue dates for two issues of Nature which have been referred to recently in the Sydney Morning Herald. The first article is about a discovery made by Prof. Paul Schimmel, a professor of biochemistry and biophysics at MIT. It centres around what Schimmel thinks is a second, more primitive genetic code which performs some of the functions of DNA. It was referred to in an article in the SMH on May 17th this year as "appearinging in this week's issue of ... Nature ". Given the media's propensity for distorting reality in order to squeeze it between the cigarette advertisements I wouldn't be at all suprised if the article is a few months old. Today another interesting article was referred to in the SMH. This time the subject was a controversial experiment which seemed to show that "the immune system's antibodies can work even when the solution they are in is so diluted that no antibody molecules are left in it". Powerful stuff. What's more: "the result...was particularly objectionable because it tends to support homeopathy - the discredited practice of using herbs and oils 'attuned' to organs in order to cure ailments in them.....The authors said that shaking the solution for 10 seconds was essential; failure to shake it resulted in a failed experiment" Stories like this last one no doubt excite people involved intimately with the field. For me, a person who has to take a tractor to the monthly issue of Scientific American to plough through to the end, such stories have a quaintly destabilising effect on the keel of my belief system. A Mr. J. Benveniste of the French Medical Research Council was the Chief Author of the report, which appeared in Nature. This story sounds as if it would get into the paper even if a shuttle blew up. So it probably is this week's news. My local library (the Mitchell Library, no less) is about two months behind publication in the issues of Nature. Is there anyone with a more uptodate collection? I would be interested in hearing peoples comments about the two articles I have mentioned. jon.
jyamato@cory.Berkeley.EDU (YAMATO JON AYAO) (07/06/88)
In article <1628@runx.ips.oz> jon@runx.ips.oz (Jonathon Seymour) writes: >I'm after issue dates for two issues of Nature which have been referred >to recently in the Sydney Morning Herald. >The first article is about a discovery made by Prof. Paul Schimmel, a >professor of biochemistry and biophysics at MIT. It centres around what >Schimmel thinks is a second, more primitive genetic code which performs some >of the functions of DNA. It was referred to in an article in the SMH on May >17th this year as "appearinging in this week's issue of ... Nature ". Given >the media's propensity for distorting reality in order to squeeze it between >the cigarette advertisements I wouldn't be at all suprised if the article is >a few months old. >jon. I don't have the magazine in question, but I suspect that the work referred to may be the discovery of the part of the tRNA molecule which determines which amino acid it picks up. The media likes to refer to this as "the second genetic code", for no particularly good reason that I can see. It has actually been established only for one tRNA, by mutating parts of it until it loses/gains specificity, and may not be the same for others. A lot of people said "New genetic code!" to me, and then pointed me to articles which proved to discuss exactly this. As for the homeopathy, I wouldn't get too upset until you actually see the reference. I'll look for it this afternoon. Mary Kuhner genetics, UC Berkeley (but my opinions are my own)
wrp@biochsn.acc.virginia.edu (William R. Pearson) (07/06/88)
>>I'm after issue dates for two issues of Nature which have been referred >>to recently in the Sydney Morning Herald. The article related to homeopathy is in the June 30 issue, which arrived in my mail box today. Bill Pearson wrp@virginia.EDU
ayermish@athena.mit.edu (Aimee Yermish) (07/15/88)
Schimmel &co. found what appears to be the way transfer RNA molecules know which amino acid to pick up. They haven't done the whole code yet, to my knowledge (lots of tedious work, if I'm not mistaken). I had never before realized just how terrible science reporting is in the popular press. I heard and read several totally incomprehensible articles about this discovery before I finally got sick of it and found the real info myself. "Second genetic code" is a nice term to latch on to. The idea is that the "first" genetic code tells you how to go from three bases in messenger RNA to a particular transfer RNA. The code that Schimmel's working on tells you how to go from a particular transfer RNA to a particular amino acid. If you don't charge your tRNA with the right amino acid, plugging it into the right spot in mRNA is worthless. "Primitive" is, as far as I can tell, a poor choice of words. The media is making a big deal out of the fact that while mRNA uses three-base codons, tRNA only uses two bases to specify an amino acid. It's really very simple. There are twenty amino acids used in proteins (some are modified, later, but the argument still holds), and you need a stop codon, too. mRNA has only four possible bases (adenine, cytosine, guanine, and uracil), so it must use three bases in each codon to uniquely specify an amino acid (4x4=16, that's not enough. 4x4x4=64, wayplenty). In tRNA, there are one or two more kinds of bases (pseudouracil is the only one I can think of offhand), letting the cell uniquely specify an amino acid in only two bases (sounds like Name that Tune, huh?). "Performing some of the functions of DNA" Wow, I hadn't even heard that one before. DNA has two functions. It replicates itself and it codes for proteins (and ribosomal and transfer RNA). tRNA can't do any of that, last I checked. Maybe someone else could clarify? --Aimee ------------------------------------------------------------------ Aimee Yermish ayermish@athena.mit.edu MIT couldn't care less about anything I say. (as long as I finish that last paper...)
werner@aecom.YU.EDU (Craig Werner) (07/17/88)
In article <6209@bloom-beacon.MIT.EDU>, ayermish@athena.mit.edu (Aimee Yermish) writes: > > "Second genetic code" is a nice term to latch on to. "Second genetic code" was never used by the original authors. It had its origins in the nature commentary that appeared in the front of the issue. > you need a stop codon, too. mRNA has only four possible bases > (adenine, cytosine, guanine, and uracil), so it must use three bases > in each codon to uniquely specify an amino acid (4x4=16, that's not > enough. 4x4x4=64, wayplenty). In tRNA, there are one or two more > kinds of bases (pseudouracil is the only one I can think of offhand), > letting the cell uniquely specify an amino acid in only two bases > (sounds like Name that Tune, huh?). Actually in another recent paper, it was shown that a tRNA made completely out of DNA (well,with 1 ribonucleotide at the end since the 2'0H is needed for charging) was recognized and charged with the correct tRNA with only slightly different kinetics. It has been known for some time that native tRNAs (without modified bases) work just fine. Secondly, while a "pair" of bases was cited in the popular reporting, it is unclear whether, this means a dinucleotide or a base-pair. It is important because a dinucleotide has 16 possibilities, while a base pair only contains 8 (or only 4 unless 3D structure is important, which it probably is). The structure described by Schimmel et. al. is a base pair, so basically it turns out that they solved the Alanine-recognition problem and very little else. Consider the following analogy. In Exon shuffling experiments of the MHC,it was shown that the two outer domains contained all the information to present antigen and be rejected as foreign in grafts. The third domain didn't matter in these experiments. Well, the third domain is relatively conserved, so the shuffle actually didn't change anything of importance. It took old-fashioned mutant searches (Potter, et. al) to show that the third domain was crucial. Similarly, changing a base pair in a tRNA turned it into an alanine tRNA, but there are other cues that are based simply on tRNAness that get missed in the shuffle, as it were. -- Craig Werner (future MD/PhD, 4 years down, 3 to go) werner@aecom.YU.EDU -- Albert Einstein College of Medicine (1935-14E Eastchester Rd., Bronx NY 10461, 212-931-2517) "But I digress..."
pell@boulder.Colorado.EDU (Anthony Pelletier) (07/19/88)
(sorry, I tried to mail this, but it bounced--just hit "n" unless you are the original poster) I think you got a couple of things mixed up here. The "two-base code" is a bit of a misnomer. They only did the work for one tRNA; unlike translation, information for which must be constrained in a physical space (the A nd P sites of the ribosome), there is no reason that all tRNA sythetases need use the same number of contacts or even contacts on analogous parts of the molecule. One might imagine, for example, that the variable loop might be important in some cases, not in others. John Ableson has found that one cannot construct efficient amber suppressors for all tRNAs. That is, altering the anticodon to CUA does not mean that it will work. I have not heard these data for a while, but some of the inefficient tRNAs were so because they were not charged properly. Thus, even though the rest of the molecule is unchanged, the cognate synthetase does not recognize and/or transfer the AA. Also, recall that there is a tremendous amount of structure-information in tRNA. The possibility for allosteric effects on a binding pocket by changes elsewhere in the molecule are strong. Put this in an evolutionary context. It is imagined by many that tRNAs were self charging, at first--it is clear that RNA can be catalytic and it is clear now that specific binding sites for amino acids can exist in RNA (See the article by Mike Yarus in the 6/24 Science). If that is true then proteins were added later. Why should proteins developing contacts with different tRNAs all interact with the same spot? There are plenty of good reasons why the number of spots will be limitted. But some variation should be expected. Regarding functions of DNA: In NO WAY could it be said that a function of DNA is to "replicate itself" as you say. DNA does not do that. True, self complimentarity does provide for the mechanism of replication. DNA's main role is the storage of information. What I think schimmel meant was that his tRNA does store information. In the RNA world (before DNA and protein) imagined by most scientist, catalysis and information storage were performed by small RNAs. The ancient "code" was the way pre-tRNAs interacted with amino acids. Later, after protein synthesis was developed a bit, this was helped along by proteins (until you can code for proteins, you can't really use them). Anyway, personally, I think Schimmel is stretching the importance of his work a bit. One professor in our building who shall remain nameless put the article on his notice board with the caption "what an Asshole." I have to be more kind since Schimmel gave me a clone I needed for a rather important experiment. There were other points I was going to make, but...back to experiments. -tony
norm@ochoa.bcm.tmc.edu (Norman Furlong) (07/20/88)
In Aimee Yermish's article (ayermish@athena.mit.edu) on July 14th, he states: >I had never before realized just how terrible science reporting is in >the popular press... >"Second genetic code" is a nice term to latch on to. The idea is that >the "first" genetic code tells you how to go from three bases in >messenger RNA to a particular transfer RNA. The code that Schimmel's >working on tells you how to go from a particular transfer RNA to a >particular amino acid. Here here! The press had no business making Schimmel's discovery appear as important as that of the FIRST half of the genetic code (DNA triplet to amino acid). Schimmel & co. have contributed to the field, but this is a far cry short of unlocking the SECOND half of the genetic code, the protein folding problem: how the sequence of amino acids directs the 3-dimensional structure of the gene product. Let's hope the press doesn't continue to cry wolf every time a new discovery comes out of the lab! Norman B. Furlong, norm@tmc.edu Office of VPIT Baylor College of Medicine Houston, Texas 77030