Anyone attending ISMB 2007 in Vienna?

Anyone atttending the bioinformatics conference ISMB 2007 (held in Vienna, Austria this year)? I'll be there, along with several fellow alumni of the bioinformatics group from Waterloo -- John Tsang, Tomas Vinar, and Broňa Brejová. Perhaps we could organize a bloggers' dinner or something there if we get a critical mass.

Tagged!

Well, just a few days after I did a "Friday Cat Blogging" (sort of), I find that there's another blogging tradition that I need to follow -- that of a "tagged post". I've been tagged by John Logsdon to follow up on his "eight random facts about yourself" posting and tag eight other bloggers with the same meme.

The rules are:

1. We have to post these rules before we give you the facts.
2. Players start with eight random facts/habits about themselves.
3. People who are tagged need to write their own blog about their eight things and post these rules.
4. At the end of your blog, you need to choose eight people to get tagged and list their names.
5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.

1. I am a native Wisconsinite and my last name is indeed "Badger" (as Wisconsin is known as the 'Badger State', the sports teams of the University of Wisconsin are the 'Badgers' and so many businesses there are named Badger this and Badger that, this was the source of many jokes growing up). Apparently my name has no linguistic connection to the animal or state, though -- 'Badger' is a Scots name and my father's ancestors were Scots-Irish.


2. I don't drive. In the Midwest this fact generally generates gasps of incredulity, here on the East Coast it often generates compliments on the assumption that I've done it out of some noble principle, protesting urban sprawl or pollution or something. But really, given my poor eyesight, reflexes, and sense of direction, it's just better for everyone (including myself) that I stay off the road.


3. My scientific genealogy includes two Nobel Laureates (Rutherford and Chadwick) and well as a winner (Woese) of the Nobel-ish award for evolutionary biologists/ecologists, the Crafoord Prize in Bioscience. Not that that necessarily means anything for my own career -- as stock brokers say, "past performance is no guarantee of future returns".


4. I like languages. Both computer and human. The computer languages I know are Basic, Pascal, C, C++, Smalltalk, Forth, dBASE, Actor, Perl, and Ruby. The human languages I know are English, Esperanto, French, and German, although to be honest, I'm far better at reading than speaking the last two.

5. As if it wasn't obvious from my "Friday Cat Blogging", I'm a cat person. I don't much care for dogs. I find the large ones vaguely threatening, and the small yippy ones are just plain annoying. Plus, they neither clean themselves nor use a litter box. Human infants have similar defects, but I guess inclusive fitness must play some role because all the people I know with infants seem to overlook this.


6. I seem to have an obsession about the former East Germany. I own 27 books about East Germany and listen to albums like "Die Partei hat immer recht" and collections of Oktoberklub songs.



7. My favorite authors are John Crowley and A.S. Byatt. Besides the fact that they both write well, they both seem to be attracted to the Elizabethan and Victorian eras. These eras also attract me because they were also transitional times in the history of science -- the dawn of modern science in the early 1600s and the transition of science from hobby of the independently wealthy to practical career choice in the late 1800s.



8. I like my coffee black, and my art nerdy (Escher) or atmospheric (Hopper).






I tag:
Jacques Ravel
Neil Saunders
Eva
Steve Salzberg
Mike Hu
Naomi Ward (yes, your blog has to rise again!)
John Tsang (You need a blog!)
Marei Dose (ditto)

My 15 minutes (or 30 seconds) of fame

I've worked with people like Carl Woese and Jonathan Eisen who routinely get interviewed by the media, but this is the first time that I've been in the spotlight. In May, Chris Condayan interviewed me along with several other bloggers attending the ASM 2007 meeting in Toronto, and he's edited them into an edition of his MicrobeWorld series dealing with microbiologists who blog.

Besides me, the featured bloggers are John Logsdon, "Yersinia", Tara Smith, Elio Schaechter, and Larry Moran.

Tara seems to think that she is too "animated", but I think she is undervaluing the value of animation. After all, this week, the animated Ratatouille beat out the latest "Die Hard" movie....

I could complain about my segment too, but it's probably pretty representative of me (not that I tend to talk into phones without calling someone first...)

Not your typical Friday Cat Blogging

There's a tradition in blogging culture termed "Friday Cat Blogging". in which bloggers post light-hearted articles on Fridays, with the clichéd example being pictures of one's cats. Well, as you can see, I did post a picture of Bella Cat Badger, perched upon my closet door as she so often is, but I actually have a more serious reason for bringing up the topic of cats this Friday -- Driscoll and colleagues newly published paper "The Near Eastern Origin of Cat Domestication" (probably not open access, unfortunately). Anyway, as the article involves both cats and phylogenetic inference, how could I resist?

Small wild cats live (or have lived) in many places in Europe, Africa, and Asia. So an obvious question is whether domestic cats in different parts of the world are more closely related to their local wild cats (evidence of independent domestication events in different parts of the world) or to wild cats from one part of the world. Driscoll and colleagues addressed the issue by two different methods: making a neighbor-joining tree from short tandem repeat (STR) profiling (basically DNA fingerprinting) of 979 cats and by making a maximum parsimony tree from the sequence of the ND5 and ND6 genes from the mitochondria of 742 cats. The cats contained a mixture of wildcats, feral domestic cats, and domestic cats of various breeds sampled from Europe, Asia, and Africa. Both analyses supported the conclusion that the closest ancestors of both European and Asian domestic cats are wildcats from the Near East. However, the mitochondrial data suggests that there are at least five maternal lineages within that group.

Secret Messages in DNA...no

There were a lot of blog postings about the evolution articles in yesterday's NYT (for example, JE's, Coturnix's and Larry's), but I don't recall anyone mentioning Dennis Overbye's article. I realize that making fun of bad science journalism is getting to be a rather repetitive joke, but this one is just weird. The article is combining two different topics. The first is about a Japanese group that encoded "E=mc^2" in DNA and introduced it into E. coli. That's a cute but in the end rather useless trick, rather like using DNA to solve cases of the traveling salesman problem (which people have also done). Apparently, the Japanese group seriously thinks that DNA in living organisms could be a practical data storage method, and claims that the problem of mutation could be solved be using multiple copies (which would only slow down the decay, not halt it).

It gets more disturbing in the second half -- apparently actually taking seriously the idea that messages could be hidden already (by aliens?) in our DNA. I mean, everyone is amused by finding phage proteins that actually contain the word "PHAGE" using single letter amino acid abbreviations, but that's different from actually assigning meaning to the coincidence. The numerous falsified "solutions" to the Voynich manuscript, the supposed Bible Code (and the facetious Moby Dick code), and the endless reinterpretations of Nostradamus suggests that people can find secret messages even when none exist. What's the point of encouraging such nonsense by even seriously considering it in a major newspaper? I expect a crank volume on messages in our genome any day now -- in fact, were I less scrupulous, I'd write it myself under a pseudonym -- I'm sure it would sell.

Greatest BBC Headline ever

"FBI tries to fight zombie hordes". Okay, I know the author knows he's being clever, and probably the people who actually have to deal with compromised Windows machines are already sick of the slang term "zombie", but still, I never expected to read such a Romero-esque headline at the BBC except maybe on April Fool's day.

Not that the zombies in the article affect me other than sending me more spam -- I'm a Linux and OS X user...

Genome of DNA Discoverer NOT Deciphered

Do you recognize the man in the picture? It's Friedrich Miescher, the Swiss biologist/biochemist who discovered DNA in 1869. So, when the NYT announced today that "Genome of DNA Discoverer Is Deciphered", I was really excited, despite the annoying (and incorrect) use of "decipher" to mean "sequenced". Just think! Sequencing the genomes of Victorian scientists is now in our grasp! Who will be next? Darwin? Maxwell? Faraday?

But alas, it isn't so. It's just Jim Watson's genome.