01 February 2008

Weekly sampler 4

This week's theme is, um, "fun with biology." Seemed apropos after all the bickering I did this week. Which I'll mention as well.

1. So I assume you saw that Craig Venter's outfit produced the first "synthetic genome" recently. All this means is that they synthesized a very long piece of DNA, and included within it all the components known to be necessary for bacterial life. The simplistic line is that this is "synthetic life"; the standard scientific caveat is that this human-made genome hasn't been used to direct an actual organism. Yet.

2. And I'm guessing that you heard that the makers of this synthetic genome included within it a "coded message." The message itself is pretty uninspiring. ("METHINKS IT IS LIKE A WEASEL" would have been perfect, but anything would be better than the name of a company and its techies. Boooooorrrrrring!)

3. Well, what kind of message would you put into a genome? And by the way, it's not a completely silly question; it will soon be easy enough to do, and will take the place of name an asteroid/star after yourself/loved one as the latest vanity gift. Want to check it out? First you need to have a look at the alphabet that's available. Don't worry – it's not just A,T,G,C. That's the DNA alphabet, which is translated into the protein alphabet. The means of translation is what is commonly called the genetic code: each three-letter DNA "word" is translated (via RNA) into a single amino acid, a string of which adds up to a protein. There are 20 different amino acids in nature, and scientists have devised a single-letter abbreviation system to facilitate the display of protein sequences. So, here's your alphabet:


LetterAmino acidLetterAmino acid
AAlanineMMethionine
CCysteineNAsparagine
DAspartatePProline
EGlutamateQGlutamine
FPhenylalanineRArginine
GGlycineSSerine
HHistidineTThreonine
IIsoleucineVValine

KLysineWTryptophan
LLeucineYTyrosine

You may have noticed that we're missing some very useful letters. Two vowels are out (O and U) and you'll have to do without B, J, X and Z. The Venter folks used V in place of U (a neat trick), but I don't know what we'll do for an O. (I guess we can use Q in a pinch.)

Still, you can do a lot with an alphabet like that, starting with "Methinks it is like a weasel." (But not "in the beginning.") And you can search genomes to see if they contain favorite words or secret codes just for you. (Is "ELVIS" in the human genome? Yep. "LIVES"? Yep. "ELVISLIVES"? Alas, no.) Want to try? Go to the Protein Blast page at NCBI, enter your word or phrase in the big box at the top, select "Non-redundant protein sequences (nr)" for your database, and enter "human" (or any other interesting species, or nothing to search all genomes) in the organism box. Click on the Blast button at the bottom, and ignore the window that comes up first; it will probably report that it hasn't found any "putative conserved domains" and will give you an estimate of how long you'll have to wait for results (mere seconds, usually). Then...presto!

You might get nothing of course, or you might get a report of X number of Blast hits on the sequence. Scroll down to see the various alignments, which might only encompass part of your search string.

'STEVE' hits dozens of proteins (some "hypothetical"); here's a partial screen shot of the results for 'STEVE' in the human repertoire, showing what the alignment looks like:
The alignments, perfect in this case, are indicated by the subtle red arrows. When I Blasted 'STEPHEN' the best match I got was 'STEPHE.'

So much more fun than biblical numerology, if you ask me, and Carl Zimmer seems to agree: he's sponsoring a contest to see who can find the longest word embedded in protein sequences. I'm gonna work on it!

4. Another way to waste time: GenePaint, a site full of anatomical maps, for the purpose of revealing gene expression patterns. Just what I need, Shelley.

5. Some of the bloggers at ScienceBlogs are having a book club of sorts, simultaneously reading and blogging on Stephen Jay Gould's hefty opus, The Structure of Evolutionary Theory. I haven't read it yet, and maybe now I won't have to.

6. Instead, I'm reading H.W. Brands' biography of Ben Franklin, The First American. Very interesting; expect some quotes to find their way here.

7. Seen any good science blogging lately? Send me a heads-up – I'm hosting Tangled Bank next week and I'm looking for submissions, especially from bloggers who might not know about this excellent carnival.

8. Some seem to think I've been too hard on Tony Campolo. Well, check out what I wrote about Jerry Coyne in response to his brainless outburst in response to a blog post about "hopeless monsters." (There was a related discussion on Greg Laden's Blog in which I commented further.) See? I'm an equal-opportunity basher.

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