papa was a rodeo

Good weekend in the Genehack Compound; got some stuff done, got some relaxing time in, and I must have done some coding, 'cuz my wrists hurt. Hope yours was mostly the same, minus the pain, unless that’s your thing. Now, strap yourselves in, because this is going to be a biggie – I really should have updated on Saturday, but I never got around to it, so today’s going to be extra-jumbo-large.

A link I need to pass around at work: CLEAVER : analyzing microarray data using known biological categories.
Transcribed from’s bio-info section.

Inessential and Scripting News have been talking Napster and mp3s all last week. It’s been a musical weekend here too – while I was doing my BOP coding this weekend, I generally had a disc in the drive, ripping to mp3. In fact, I’m listening to some of the stuff I ripped as I write this. Hey, the Pixie’s Diggin’ for Fire just came on – I love this song. It goes deeper than that too: today’s title is from a Magnetic Fields song that’s been stuck in my head since Friday, when I heard it on, which I generally have on when I’m at work. I don’t usually really listen to the music; it just drowns out the din from the other fattening pens^W^Wcubicles. (I’ve got the same headphones as Jason, in case you care – they rock.) Anyway, he said, winding up the long digression: I can always tell when I’m going to like a song – I start nodding my head to the beat, to the point where I break out of the work ‘zone’ and become aware of the music – which is when I reload the playlist, to see what I’m hearing. I’ve got mp3’s shuffle-playing as I write this – maybe I’ll just note when a song breaks me out of writing mode…

Wired News had a tidbit about SNPs last week. Single nucleotide polymorphisms are places in genes where individuals differ by a single base, and they’re likely to be the key to some of the more profitable results of the human genome sequencing projects, things like pharmacogenetics – adapting medical treatment to individuals based on their genotype.

Just when the Vermont civil union stuff was making me think the country was starting to grow up a bit, Louisiana has to go and ruin it all.

Cool! The crystal structure of a transposase:transposon complex has been solved. More popularly known as ‘jumping genes’, transposons are behind the horizontal gene transfer that I mentioned a while back, and they’re also related to proteins involved in the propagation of retroviruses, like HIV.

Well, somebody had to advocate it – the people behind the cloning of Dolly have come out in favor of human cloning. It’s just a matter of time, folks – we can either talk about ways to do it ethically now, or we can play catch-up.

Giant squid washes up on beach. No word on whether or not the locals were planning to blow it up.

More crypto-zoology news: A possible Bigfoot sighting?

(Music moment: Forgive and Forget, The Get Up Kids.)

Later this month, we’re likely to be able to see a new comet with our naked eyes. I wonder if the religious wackos will make a big deal of a comet in 2000? Surely not… 8^)=

Here’s another story about the efforts to clone the extinct Tasmanian tiger.

(Another music moment: Hallelujah Jordan, the Hothouse Flowers.)

This article raises (but unfortunately doesn’t discuss at length) an interesting question: How much of our world can be modeled by a Universal Machine?

Stolen from somewhere: Natural language principles in Perl. It’s not an accident it looks like a mess; it’s that way on purpose. 8^)=

Here’s an interesting way to think about the “Linux is only free as long as your time is worthless” problem: like free sex.

CNN did a bit of a puff piece on Jon Katz’s Geeks, but there’s some follow-up on Jesse, one of the kids in the book. The book was okay, if you can ignore the broad brush Katz applies when deciding who is and who isn’t a geek. I was disappointed in the short shrift that Eric, the other kid, got in the book. It’s too bad that that’s continued in this story.

The UK is fixing to crack down on cyber-criminals. Of course, the only concrete example of so-called cyber-crime given in the article wouldn’t be a crime in the US – and I’m not even sure it’s a crime in the UK. Any reader feed-back on this?

(Music: Grey Cell Green, Ned’s Atomic Dustbin.)

Workers at Rosetta Inpharmatics (sweet name, BTW) have combined gene expression profiles and computational analysis to accomplish an impressive feat: identifying a previously uncharacterized gene product as a drug target.

Tests of Bt corn under field conditions show no adverse effects on swallowtail butterfly larvae. This contradicts earlier lab research that showed that monarch butterfly larvae were affected.

Why we need Debian. Genehack is produced on a Debian box, and served from a Debian box, in the unlikely event that you care.

A RISKS Digest post says NASA wants everybody to know that a hacker didn’t endanger astronauts, as an article I linked last week reported. Moreover, the author of the RISKS post claims that mission-critical information didn’t flow over the public 'net, which was something I questioned at the time, as I recall.

A draft assembly of the human genome sequence is available at UCSC. Here’s a story about how that came about.

Info on HipCrime, an entity or entities involved in rogue Usenet cancels. An entity dubbed HipClone was pulling this garbage last week, but has been shut down, according to traffic in the Scary Devil Monastery.

Why Perl is bad for you. (From a comp.lang.lisp posting, so consider the source.)

Intro to XHTML.
Nicked from CamWorld.

Salon covers Pottermania. When I was in $LARGE_CHAIN_BOOKSTORE this weekend, I grabbed the first Potter book, just to see what the fuss is about. (Plus it was cheap – US$7 for a trade paperback, at 30% off, ended up below US$5 before tax.) I tore through the book in a couple hours this afternoon – it was decent. I’ll probably read the others in the series, but I can’t see shelling out for hard-covers.

Here’s a comparison of MySQL and PostgreSQL, two free relational database management systems. I think I’ll be sticking with MySQL…

iMacLinux might be useful for LinuxPPC people – or for people having trouble with LinuxPPC.

Hey, all you DC area bloggers – think we should have some sort of party/gathering/happening to welcome Lyn to town?

Seems like there was something else I was going to write about, but I’ll be swelped if I can remember what, and this thing is already probably too long for a Monday – most people probably gave up back at the Grey Cell Green reference. See ya tomorrow…