March 1999 Archives

Neal Stephenson has written an absolutely amazing essay about GUIs, command lines, and how the differences between Morlocks and Eloi map onto current computer users. Put down that copy of Programming Perl and go read this instead.

The upcoming issue of PNAS has several interesting looking articles:

If I had a spare couple of thousand bucks, I’d pick up one of these!

Ohhh…Linux Software Encyclopedia

It’s been over two weeks since the last Window Maker release — I’m starting to jones pretty bad for a new version…

Macintosh Word 98 bugs page

Another LinuxPPC page

It’s too bad that this site is so cheesy, and has nothing to do with bioinformatics.

So, I finished Holy Fire for the second time. On the first read, I didn’t care for this too much, but now I think I can see what Sterling was trying to say. I’m not sure I can articulate it, but I think I might understand it.

I’m suffering from the post-late-night-hacking-binge blues, so I haven’t been keeping up with a lot of media (including the scientific ones). Hopefully, I can play catchup in the next couple of days.

So tired…

Oh, where to start…so many things to talk about…

My report on yesterday’s Biology Career Day is on the Rants’n’Raves page.

I finished Open Sources. Overall, it was a good read. It was interesting to note how people with different public prescences wrote differently. In general, the more well known people (Linus, Larry Wall, rms, esr) were much easier to read, much less overtly technical, and much more enjoyable (in terms of pleasure reading). There’s probably an interesting corrollary about achieving success (or at least being well known), but I’ll leave that as an exercise for the reader. 8^)=

On Friday, during the 11 hour marathon of bathroom upgrades, I caught a mini-documentary/ad/fluff-piece on the making of the upcoming movie The Matrix. The plot-line sounds like a blatent rip-off of Jack Chalker’s The Wonderland Gambit series, right down to the Alice in Wonderland references, and I’m interested in seeing the credits, to see if he’s mentioned at all. The effects, however, looked astounding! Heavy use of that stop-action-and-pan-in-a-circle popularized by the recent series of Gap ads. Nice CGI stuff. Some BladeRunner-esque disutopic backgrounds (shades of Giger, really). However, I think my once-a-year movie theater pilgrimage is going to have to be dedicated to The Phantom Menace…

Cool Science: This story reports on a Molecular Cell article presenting results which suggest that measles, mumps, HIV, ebola, and a host of other virii may share a common evolutionary origin. I haven’t seen the research article, but I’m initially skeptical. Horizontal gene transfer has got to be ruled out to make this conclusion firm, and it’s not clear how that was done, or even if it was questioned. Regardless of the evolutionary aspects (interesting to only a few bio-geeks), this opens the possibility that HIV treatments may be useful for blocking the spread of other viral species.

I’m going to a Career Day event at the University of Arizona today, so this will probably be the only update for today. I’ll post something about the event, if I hear anything interesting.

I picked up a copy of Open Sources last night; so far it’s been pretty interesting.

A few more pages put up, and a lot of nasty little errors stomped on. Check out the MacOS part of the (hard|soft)ware heirarchy, specifically the MacOS screenshots.
And yes, it’s about 9 hours later, and yes the people are still banging away in the bathroom. And, oh, by the way, yes, I’m going to be late for my bowling league because of this, and yes I’ve got to piss so bad I can taste it, but No!, I’m not annoyed…

I’m hanging around home today, with not much work to do (I need to get some time in on the G3 at work, and crunch those numbers). I’m at home because a gang of nice people is ripping all the tile out of my bath and replacing it, or something. I’m not really clear on what the landlord told them to do. Anyway, it’s giving me some time to hack on this site. For example, the Personal heirarchy is up.

I finished Heavy Weather. The genetics part at the end always really bugs me — Sterling just doesn’t get the lingo right. Chromosomes, for example, have arms, not branches. And what the hell is an intron scan supposed to be, anyway? The chrolophyll hack, though, is a mega-tasty idea, one that I think we’ll get around to implementing one of these days.

Zyvox is a new antibiotic that’s passed FDA approval. Proper use is a major issue — should we just deploy it, or hold it in reserve for use when all other antibiotics have failed?

The latest gamma-ray burst was caught live, thanks to an ad hoc satellite net. Apparently, the bursts look so impressive because they’re beams, rather than ‘fireballs’.

Mini-rant: Why aren’t there any biological science stories under the CNN SCITECH section? I can understand why all the biological stuff under HEALTH is focused on human biology, but there’s no reason for SCITECH to exclusively focus on astronomy, physics, and computing. Don’t get me wrong, those are cool topics, but so are molecular biology, genetics, and biochemistry!

Un-intentional irony?: Check out this PCWorld article, featuring Tim Berners-Lee talking about how the Web is still too complex. Check out the truly nasty interface around the article, including the really unnecessary small fixed-font for the body of the article text, and the ads for everything under the sun. Wonder how many cookies your browser was just sent. Read the section about privacy. Laugh.

Damn! My best-to-date Angband character just bought the farm. Time to start over…

Wow! Free online access to Trends journals at This expires in June, but it’s a sweet deal nonetheless. I still wish online science journals could switch over to an advertising-supported open access model, or that the online publishing that’s so popular in the physics world would take root in the bioscience community.

Finished Idoru. Gibson’s definitely at his most trippy in this one, and I kept seeing parallels with American culture (which I guess is one of the points). For example, do the Slashdot crew count as otaku? How about the User Friendly crowd?

The Canadian Bioinformatics Supercomputing Center looks like it has a lot of nice resources available.

After Idoru, I picked up Heavy Weather for about the fifth time. Sterling is some ways more amazing than Gibson, despite, or perhaps because his futures seem much more plausible.
What do you hack? I hack genomes.

I just re-read Speed Tribes, and now I’m working through Idoru again. It’s a fairly trippy combination. I think I want a Sandbenders. is mirrored at Armageddon.

I went to a computer science seminar yesterday, to hear about a new method of multiple sequence alignment. I wasn’t too impressed, but giving a talk to two groups as different as biologists and computer scientists has to be fairly difficult. There has to be a way to do it without boring both groups, however. The software that was being talked about can be found on the web.

Flutterby is back on the air. Whew!

What a crappy day this is shaping up to be. The external CD-ROM I tried to hook up didn’t want to work either, and I can’t tell if it’s a problem with my box, or with the ancient drivers I was forced to use. Hey, that’s a thought: I wonder if my Apple CD-ROM driver could have gotten corrupted somehow…something to check out, the next time I boot back into the MacOS.

Alien Hand Syndrome

J. D. Salinger Bananafish home page

I’d like to get the rest of the old site up and running tonight, but that’s probably not realistic. Of course, my stellar hit counts tell me I’m not disappointing too many of you.
/me shouts into the Void

Lotsa work to do today…

Wes returns from spring break, so Hack the Planet is running again. Check out what he has to say about OS X Server and Darwin…

Well, the Linux Screenshots section of the site is back up.

Am I the only one who can’t get into I need my fix!

Ooohh..I’m just a procrastinating little bugger…the Links section is back up also.

It’s a gorgous day! Spring is here, I think. Now it’s back into the MacOS for me…

gdict is a cool little GTK+ app that looks up words in the MIT dictionary server.
(I put up a screenshot of the gdict app.)

My periodic Angband playing is picking back up.

Gsh is a cool looking graphical *nix shell.

My CD-ROM died yesterday. If anybody has a cheap SCSI-1 CD-ROM for sale, let me know (

Today’s work requires me to reboot into the MacOS — that should make for a nice change.

I’ve been struck by the User Friendly productivity virus. (See the UF site for the Archives.)

Also from User Friendly, the Universal Truths page.

The new wmakerconf is pretty cool.

From Flutterby, a nice quote page.

Iowa attempts to make English official state language - This seems like a really bad idea, but I’m not sure I can clearly state why.

Scientists doubt speedy gene reading machine - This is the same sequencer from the Wired story, below.

The BOFHCam is cool, but I got a bigger kick out of the PFY stories. Maybe it’s because they ring oh so very true…
Seen on Flutterby.

There’s a new version of the Protein Information Resource site up at

NEWWWSBOY looks pretty cool. This could be the Frontier-replacement I’ve been looking for. Course, I don’t know when I’m gonna have the time to get it running under my account.
Is a permenent Net connection too much to ask for? I think not…

Whatta day! Things got off to a rocky start. I’ve been having some mini-buffer troubles in XEmacs 21.2b12, so I decided to try to downgrade to v20.4. I forgot I’d already tried to build that without success, which is why I’m running 21.2b12. And, of course, I didn’t remember until after I’d nuked my current install…

After I got XEmacs rebuilt, I decided to switch mail readers. I’ve been using KMail, but the XEmacs screwup convinced me I need to clean out some disk space. So, KDE had to go, which meant bye-bye KMail. I downloaded Arrow (and the required libraries), and it built ok. I’ve got to say I’m a little bit under-whelmed, especially considering how long it took to compile.

However, my old friend Postilion has improved since I last checked, and that’s the client I ended up going with. Looks nice, runs fairly fast, and doesn’t take up a load of room. The built-in mail database is nice also, given my tendancy to save most of the email I get.

The other thing that went out with KDE was the kdm graphical login screen. This I was actually prepared for. I grabbed, which is a sweet little xdm replacement. It’s really the finishing touch for a box running AfterStep or Window Maker.

Now that I’ve spent a large portion of the day futzing with my personal box, it’s time to grab some dinner, and head to the lab. The nice G3 there should be free, so I can write some nice Perl code, and hopefully get some work done.

Wired News says the human genome project is going to be done earlier than expected. That’s good, maybe we’ll be able to figure out how it a little bit quicker now.

MacCentral has a nice Linux article today, as well as a new Linux Reader’s Forum. Now, if they’d only get rid of those <FONT SIZE="1"> tags…