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 Tuesday, January 14, 2003
Public Release: 13-Jan-2003
Journal of American Chemical Society
Expanding the genetic code: the world[base ']s first truly unnatural organism
From time immemorial, every living thing has shared the same basic set of building blocks -- 20 amino acids from which all proteins are made. That is, until now: A group of scientists say they have, for the first time, created an organism that can produce a 21st amino acid and incorporate it into proteins completely on its own. The research should help probe some of the central questions of evolutionary theory.
Contact: Beverly Hassell
b_hassell@acs.org
202-872-4065
American Chemical Society
[Eurekalert - Biology]
Okay. This is one of those articles that makes me say 'Okay.' They have manufactured a bacteria that has a new metabolic pathway that creates a novel amino acid. The bacteria is able to incorporate this novel aa into a charged tRNA molecule that will recognize a normal stop codon. (There are 3 stop codons which do not normally have a charged tRNA that bids the codon. One of these, the Amber codon is not used very much in E. coli so it can be shanghaied for this new use.) So, they can now place an unusual amino acid at the end of a protein, althoug h translation will still occur, adding more and more amino acids onto the end of the protein. So I do not really see how this 21st amino acid can be effectively incorproated into a useful protein, permitting selection to have any effect. Plus it is a derivative of phenylalanine so I am not sure just how novel it is.
Now there are lots of instances of bacteria using very unusual amino acids for all sorts of things. Seleno-cysteine is one example. So I went out on the web and used google to get some examples. And it turned out to be a small world. I quickly found this link to work at Scripps (where one of the authors of the JACS article above had come from). It discusses in much better detail the work being done by Peter Schultz. Peter was in the same class as I at CalTech and has done some very interesting work over the last 25 years. The thrust here is that by inserting amber codons into gene seuqneces through site-specific mutation, they can accurately place novel sidechains in the protein. Now this makes a lot of sense and would have lots of really interesting implications. They are detailed in the article from Scripps which is very well written. But this article is over a year old and they keep talking about unnatural proteins. But in these cases, they added the unnatural amino acids to the growth media, where it could be used to charge a tRNA. The JACS article added a novel metabolic pathway to make the new amio acid INSIDE the cell, meaning that it did not need to be added.
This is a exercise but I think that SHultze's approach has greater flexibility in examining the effects of a wide variety of novel amino acids. Then once you found something really interesting, you could try to engineer a bacterium that made the novel amino acid of choice. 11:53:16 PM 
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Consequences of Linkrot. The first lesson is that linkrot is incredibly rapid. The second lesson is that it thus becomes critically important not just to link but to quote--and to quote extensively. The third lesson is that not even fear, surprise, and ruthless efficiency can defeat linkrot. If you want your links to be worth anything in two, three, or five years, download *all* the pages you're linking to to your hard disk. Idle Words: I've been working with some of the many... [Semi-Daily Journal]
This is very true. Quoting a little of the info will always be important for context, even if the link no longer works. While copying the entire piece would violate copyright, there are definitely fair use aspects here. It is why I sometimes go through my blog's history. A lot of what I blog is for my own us, kind of like a personal secretary. Being able to reconnect with this older info is important in many contexts. So recheck important links and if linkrot has taken hold, I'll use google to see if I can refind the info. In some cases I will then bring it whole into my world so that I can be sure never to lose it again. 10:44:44 PM
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Now playing: The human genome. Researcher downloads data to iPod [InfoWorld: Top News]
Several people have done this but it is very cool, nonetheless. The human genome on something you can carry in your pocket. I remember having to use printouts of DNA sequences and trying to find restriction enzyme sites in them by hand. Getting a TRS-80 was a huge event, since we could write programs that would so this in the computer. Where will data manipulation of DNA sequences be in another 20 years, when I will be getting close to getting Social Security? (assuming it still exists.) 10:35:13 PM
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Well, I have not talked much about the Foundation that several of us from Immunex have started but it has been taking up some of my time. We have website for it that I administer, along wiht mailing lists, etc. We have been having meetings and raising money. Lots of fun stuff. One of the main aspects of this foundation is that we want it to be similar to Immnuex. Low hierarchy; anyone can participate; we want ideas from everywhere. On that note we held an Educational Forum tonight for donors and prospective donors. We invited several speakers: Lee Hoo, Lee Hartwell and Chris Elias. These were scientists and philiantrhropists who could help us focus our views and give us some keen insights. At least that is what we hoped.
It was even better than that. We had about 60 people attend for 2 hours: 30 minutes of socializing and 1.5 hours of tallks and discussions. It was very exciting. We got some very good responses from the attendees and the speakers were outstanding. They did a wonderful job helping us see where we might want to go and what fun it will be. I am very charged up about this now. 9:57:33 PM
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