November 2000 Archives

well, they’re not thinking small… >>> The best part of this interview with Michael Tiemann, Red Hat’s CTO:

[ interviewer ] Which distribution do you feel is your main competitor?
[ Tiemann ] Right now our main competitors are Sun Solaris and Microsoft.

well, this could get interesting… >>> The Reg had a story today about how the country code TLD admins (the people who run things like .uk, .de, .us, etc.) are considering moving to alternative root DNS servers. This would pretty much mean the end of ICANN as it currently stands, and would make the currently messy domain name registration thing even more chaotic.

audio candy >>> The new Modest Mouse disk, the moon & antarctica is awesome, if you dig that indie rock noise that’s driving the kids nuts. I got the disk, popped it in the player, and started furiously bobbing my head to the first song, causing passerby to stare, amazed, at the hairy autistic guy driving the gray Saturn. Here’s the lyric that did it:

Your heart felt good it was drippin pitch and made of wood. And your hands and knees felt cold and wet on the grass to me. Outside naked, shiverin looking blue, from the cold sunlight that’s reflected off the moon.
Baby cum angels fly around you reminding you we used to be three and not just two.
And that’s how the world began.
And that’s how the world will end.

damn, there’s a lotta people out there >>> Several other people have beat me to it, but check out this composite picture of the Earth’s night time surface as viewed from space. It’s awesome and humbling and scary, all at once.

$bloggers—; >>> Condolences to the Kempa family on their loss. Kempa was one of those sites that kept slipping on and off my radar screen; I’m sorry that I didn’t read more while I had the chance.

a moment of silence >>> Note to my regular correspondents: I’m going to be taking the next day or so off from email, in an attempt to focus on a few things I need to get done. If you’re expecting a reply, I should be back to you by the end of week.

Y’all stay cool.

clearing out the cobwebs >>> Wow — that break ended up being a bit longer than I expected. Apologies to you regulars who kept pounding on the server while I was gone. I’ll save the personal stuff until the end; that way the blog purists won’t have to sully themselves. 8^)=

are you sure you want to empty the trash, dave? >>> RPG hits the nail on the head with this one.

you talkin’ to me? >>> Is there any real demand for discussion features at Genehack? I’m thinking about gearing up to use BlogVoices, but I’m not going to dick around with it unless people really feel a need.

space bugs! >>> A research group is claiming to have recovered samples of a potentially extraterrestrial bacterium from the upper atmosphere. CNN has a story; ENN has one too. I’m cautious about this, primarily because the group’s announcement doesn’t have any real data to back up the claims. If they’re right, it’s huge, but I fear that eliminating all the other, more likely explanations is going to take quite a bit of work.

got linux? >>> This diary has some interesting things to say about learning to love and use Linux and about interpersonal dynamics in Open Source development. The only bad thing is the second part isn’t out yet…

watch your wallet >>> During my break, I got my parents set up with ‘net access (more ‘bout that later). My Dad was really hot to have a look at eBay; it wouldn’t surprise me if he’s bought something by now. Anyway, when I ran across this primer on eBay scams, I figured I should link it so he could read it. Now I just have to find out if he’s reading this…

Hail, Avatar! >>> Friday, I found Exult, an Ultima 7 engine that runs under Linux. That’s right, if you’ve got the data files (I got mine via the Ultima Collection), you can play Ultima 7 on your Linux box. Appears to work pretty well, too; I killed more time than I have to spare playing around with this this weekend. (Bonus points to the Exult developers for making Debian packages available!)

Word to the wise: there is a lame copy-protection scheme in U7 that requires you to answer questions about the latitude and longitude of places on the world map included with the game. When I hit it for the first time, I was stuck, because my legally purchased copy of the game lacked the lat. and long. lines on the map! (Thanks a bunch, Origin.) Google to the rescue — I found HRUMP, the High-Resolution Ultima Map Project, featuring hi-res scans of the cloth maps that came with the original releases of all the Ultima games.

work-related >>> Some of the people I work with at NCBI do molecular visualization stuff, so I’m sure this list of free visualization tools for *nix systems will be well received.

mail alternatives >>> Anybody out there using GMail or Perl Mail Client? I’ve been thinking about my ideal mail client again, and it still involves some form of SQL backend for my mail archive (currently ~80 MB and growing). Don’t have time to work on it right now, unfortunately, although I am keeping mail storage in mind with my current project (more about that later too).

small world >>> Until the recent news of his death, I hadn’t realized that the author of ping, the internet command-line tool I use second-most (after ssh) lived in the DC area. Mike Muuss is gone, but his web page lives on, for now.

long-term plans >>> Lewis Carroll’s Symbolic Logic has been on my ‘to read’ bookshelf since my sophomore year in college (‘bout ten years now). I’ve taken a crack or two at it, but never gotten all that far. On my next foray, however, I’ll have some help! Seriously, if anybody wants to start a book club (meatspace or net-based) around reading this sucker, I’m in.

wheels and the re-invention of >>> A while back, I talked about writing a ‘driver’ script to automate ripping and encoding MP3 files from CDs. I got a quick-and-dirty version working (and I’m still using it, matter of fact — have to remember to send those module patches back to the original author…), but I also recently ran across grip.e, which is a more completely generalized solution to the same problem.

read docs, then build >>> After months of kludgey syncs between my Visor and my Linux desktop, I finally read some documentation and realized my error (failing to include USB /proc filesystem support). Now I can hot-sync just like under the MacOS or Windows! gnome-pilot is pretty slick, too.

choppers >>> Pregnant women who are planning to nurse might not want to look at this picture. The rest of you go right on ahead.

DWW defense, take 2 >>> I’m participating in Day Without Weblogs again this year (must start gathering links!). I’m not going to get into the fray over whether it’s worthy or not, but I did want to correct a mis-understanding of Al’s. When he asked:

What would I accomplish by blacking my page for a day? Will I put us one step closer to a cure? Raise awareness or do anything to educate the public about the continuing scourge of HIV? Will it add a day to the life of any HIV patients?

It became apparent that he didn’t get the point of DWW. Al, we’re not turning our pages black, although I’m sure black will be a prominent design feature on 1 Dec. The point is to provide links to AIDS/HIV resources. I’ll quote Brad from the About DWW page:

The idea is a simple one: On December 1, replace your ordinary weblog or index page with a simple page like this (this is the page I put up on World AIDS Day last year), displaying the DW^2 symbol and providing links to websites that offer information about the AIDS pandemic and how to get involved.
Alternatively, leave your weblog in place, but display a DW^2 icon and pepper your weblog with AIDS education links.

If you do participate, you will be raising awareness (or at least trying). Raising awareness might just lead to some AIDS/HIV patients living longer, or even to some researcher having the critical insights that lead to a new treatment, or even a cure. I think it’s especially important for bloggers with biomedical backgrounds to participate, because we often wander into areas of the web that non-biomed people don’t get into, and we can explain some of the more technical aspects of those areas in more easily understandable language.

Anyway, that’s my justification, and my call for participation.

audio knowledge >>> At work tomorrow, I’ll hopefully get time to listen to the Larry Wall interview from the Paula Gordon show.

the rest of the story >>> Every year, the President pardons a turkey or two, ‘round Thanksgiving time, and sends them off to live out their natural lives at some sort of turkey old age home. Ever wonder what it’s like at the Presidential Turkey Rest Home? A Washington Post writer investigated, and found out that things might not be as you think…

food phear >>> Also from this weekend’s Post, Tacogate: There Is Barely A Kernel of Truth presents a take on the StarLink corn controversy that’s rather different than others I’ve seen. I’m not sure I buy the part about minimal allergy concerns due to a lack of exposure, but then again, I’m not an immunologist, either.

random thought >>> Found scribbled in my notes from a work presentation of about two weeks ago:

Watching a PowerPoint presentation that consists entirely of web browser screenshots is like showering with your socks on

I mean, come on! The machine’s got a fargin’ web browser, doesn’t it? Why not just show us the damn site in the damn browser? Even if it’s not stable enough for that, you could at least make some fake pages more quickly that you can make a PowerPoint slide show, right?

irony of the day >>> Tonight I was eating a bit of dinner and watching the movie Hackers on the Sci-Fi channel (hey, the pickings were slim; what can I say?). They returned from a commercial break with “We now return you to Hackers, presented by Cisco Systems, powering today’s Internet”. I almost spewed my Spaghettios, I was laughing so hard.

I have to say, though, whoever did that screenplay got quite a few things right about geek culture and hacking. Clearly, somebody did their homework. Unfortunately, somebody (else?) got about twice as many things wrong, but…

and now, the personal info-dump >>> Okay, that’s all the external stuff — all you blog purists can leave now; you lot who are interested in the details of my life gather round.

After we got the news last week about my grandfather’s passing, Lor and I quickly got some plane tickets to Kansas City (via the financial assistance of good ole Mom and Dad; thanks!). We had a bit of trouble there, due to a lost FedEx package, but a three-way call between Lor, our travel agent (Lor’s sister-in-law Leigh), and US Air cleared that up. I went out to JC Penny’s about 9 pm Saturday night, and discovered that walking into the menswear department and announcing “I need a suit. Now.” isn’t as satisfying as you might think.

Sunday, we flew to KCI via Pittsburg. Despite the impending holiday, things went smoothly. Met people from my mom’s family (grandparents, aunt, cousins) at the airport, and had a visit with them at the grandparents’ house while waiting for Mom and Dad. After that, traveled to the nursing home to pick up people from Dad’s side of the family (other grandmother, aunt, cousin) and went to the visitation at the funeral home. After that wrapped up, we drove the 1.5 hours back to my hometown, Lyndon, and collapsed into bed.

Monday morning we got up and made the 1.5 hour drive back for the funeral proper. The church service went okay, but I was less than impressed with the minister. I had the honor of being a pallbearer, which involved much less organization than I expected (it was sort of a just-in-time system). The graveside service was rather chilly. My cousin read a moving eulogy that had rendered everyone in attendance a bit weepy. Following the funeral, we made the 1.5 hour trip back to Lyndon, had a nap, had some dinner, and then got piss-drunk (well, at least I got piss-drunk) with friends and family. Sort of a Midwestern Protestant wake, if you will.

Tuesday, I got my parents’ newly purchased computer (running Windows Me Harder!) connected to the ‘net and caught up with email and the web. We flew back on Wednesday on a direct flight from KCI to National — flight was a bit more packed than the two on the way out, but still not too bad, considering it was the day before Thanksgiving.

Thursday, we did Thanksgiving over at Lyn and Steve’s place — quite delicious, and quite fun. The rest of the weekend, I played catch-up of various kinds, until Sunday, when I played hooky and hacked on some BOP code (yes, the BOP project lives!)

And now it’s about an hour past the time when I intended to be in bed; I fear tomorrow is going to be a very long day indeed. Hopefully I’ll get time for another update in a day or two…

My paternal grandfather died last night, at about 8:15 pm CST. He had been in declining health for quite some time, so his death doesn’t come as a shock. My father, who was there when he passed, said that the end was peaceful, and without pain. I regret that I wasn’t able to make it back before the end, but Lor and I will be headed back to the Mid-West for the funeral services, sometime in the next couple of days. If you’ve got a spare good thought, please earmark it, not for Lor and I, but for my grandmother, who has survived her husband of many, many years, and for my father and his siblings, who have a difficult time still ahead of them.

please ring

| No Comments | No TrackBacks

p1Ty m3!!!!1!! >>> Sitting here waiting for Lor to call; should be doing work stuff, but can’t get motivated. And the mail server is apparently a bit wonky, cuz the stuff I mailed myself from work isn’t here yet. sigh Somebody send me some mail or Gabber me or something.

sad, really. >>> No, it is — because I’m blogging this with the thought that I could add the output to my Daily Dose pages: “tvguide is a Perl script that reads the tv listings from and outputs them in a table format.”

now it can be told >>> perma-link texicon? Reader Paul Nagai contributed his theory.
Damn, I didn’t think anybody would figure it out for a while…

boys on the radio >>> by Hole is playing on the ole MP3 rotation right now. I’ve been searching for something else to blog, as I sit here waiting for the phone to ring, but I’m not finding anything. Plus Mozilla just crashed, so I’m gonna say the hell with it. Maybe tomorrow will be better…


| No Comments | No TrackBacks

lost weekend >>> I had Friday off work, and Lor left Saturday morning to go to a conference, so I spent most of the weekend totally geeked out with one thing and another. Got a local news server set up (INN and suck, for those interested), got bookmarker working (so I can use different browsers without worry), and finished up my CD->MP3 script, ripdriver. If anybody wants that, let me know — it’s not quite ready for public consumption, but it could be cleaned up pretty easily. I also played around a bit with Nautilus, after I found some Debian packages. shrug It’s pretty cool, but I’m not ready to switch away from gmc yet — not that I use a graphical shell all that much to begin with.

im me, baby >>> Oh, and I also installed Gabber, a GNOME-ed up Jabber client. If any of you out there would like to add me to your Jabber group, I’m If you’re only on ICQ, my user number is 96897923 — add me to your list, if you’d care to.

yah, pull the other one… >>> Annoying Wired News article on bioinformatics that I saw last week. Starts out okay, but then gets all pie-in-the-sky-y when talking about computational simulations of cells. I was rolling my eyes after I read this:

“Here you’ve got a situation where I believe you can predict things the pharmaceutical industry would not know by any other method,” [Alan] Watson [chairman of Oxford Bioscience] said.
The program can tell researchers that a certain heart drug, for example, will cause the left ventricle to expand.

Look, I am, near as I can tell (since there’s still not a good definition of the word and all) a bioinformatician. I’m as jazzed about the possibilities of computational biology and the genome project and the massive (hopefully positive) impact it’s going to have on all our lives. That said, that last sentence is utter and complete hog wash. “Programs” don’t, can’t, and won’t ever “tell researchers” anything. Programs predict, following which, another, likely completely distinct group of researchers will do actual experiments, with actual experimental organisms (even possibly human ones) to test those predictions. The predictions may, in fact, be borne out — but it wasn’t the program that told the researchers that, it was the bench work.

more stuff to read >>> Speaking of bioinformatics, I need to take a good spin through The Gibbs Motif Sampler homepage at some point. My “To Read” list is bulging at the moment; I’m working through a calculus text (for remedial reasons), and Lyn gave me a bunch of reports from the National Research Council when during our ( == Lor and I’s) recent dinner with her and Steve. sigh About two weeks with nothing else on my plate and I could catch up…

bonus tip of the day >>> Run Linux? Use Netscape for web browsing? Want to get rid of that annoying ‘Shop’ button? Do this.

‘bout time >>> A group of bio-scientists is agitating for free on-line access to the research literature. They’ve taken the step of publicly pledging to stop publishing in closed literature in September, 2001. Unfortunately, they’re willing to accept delays between print and on-line publication of up to six months — I’d prefer that there be no delay at all…

weep >>> I caught an HBO special called “Women in Sport” yesterday. Not something I would have watched on purpose; I fell asleep with the TV on, it was showing when I woke up, and I got sucked into it. By the end of the show, I was stuck between sorrow for my species and anger at the same — I hadn’t known, for example, that women weren’t allowed to run marathons before 1977. I hadn’t known this was because of fears that the long run might damage their uteruses. I hadn’t known that the first woman to compete in the Boston Marathon (she registered using her first initial instead of her name) was attacked by an enraged race official during the race, and disqualified, for no reason, after she finished.

If you get a chance to see this special, I recommend it.

totally random access >>> I should really be getting ready for work, but this is about the first time I’ve had to put down a few thoughts, so I’m grabbing it while I can..

Election: Boy, this is a bit more excitement than anybody expected, eh? Too bad about Nader not making the cutoff. Sometime Tuesday night, while watching the returns, I had the idea that the Libertarians could do a lot better in 2004 if they ditch Brown for someone with a bit more media pizzaz. You know, a celebrity candidate, a la Ventura. I’m thinking Ted Nugent, but that parts still a bit fuzzy for me.

Nader as a spoiler: I think this strip sums up my feelings about this particular issue. ( The Boondocks rulez, BTW.)

Comics: Speaking of comics, did everybody notice that both Dilbert and Doonesbury have started running the same-day version of the strip on the web, instead of delaying by a week or two? That puts me one step closer to being able to ditch my dead-tree newspaper subscription…

MP3 rip-driver: About half-way done with this little project; hopefully all the way done by this weekend. Thanks for all the emailed comments and suggestions; I’ll be getting back to y’all directly.

Netscape: That’s it — I’m done with Netscape. I know I’ve said this before, but I just spent about 20 minutes shutting down six Netscape windows, because, for some reason, the app freaked out and ate all my RAM and most of my swap. (Yes, I could have just kill -9’d it, but I wanted to see how long it would take to shut it down the normal way.) It’s all Mozilla from here on out…

Tttthat’s all, folks: Time for me to bathe and get to work — hopefully, I’ll be able to write a real update tonight. All a special note for all the email correspondents I’ve been neglecting for the past couple days: you’re next, before the update. Really. Pinky swear.

it’s not a journal… >>> …but occasionally it has journal-y stuff in it. Lor’s back in town (yay!), so I can finally go to work at a decent hour, which means I have the time to a morning update. Had a good weekend — I spent some time on Saturday upgrading to XFree86 4 (it just entered the unstable branch of Debian), which entailed fixing some font problems. Decided to clean up the CSS for this site a bit too — let me know how that looks for you. The upgrade also prompted me to make an extensive investigation of what packages I had installed (via dselect), so I’ve gotten rid of some cruft and found some new toys to play with. Saturday night, Lor and I had dinner at the home of Lyn and Steve, which was very nice.

some design notes >>> I also cleaned out my MP3 directory this weekend, since a bunch of the stuff I’d ripped myself was truncated, encoded at the wrong bitrate, or had the wrong ID3 tags. I went through all the stuff that I didn’t rip and normalized the ID3 tags, and set up a sane directory structure. I’d like to start re-ripping things (I mean, that 10 gigs is just sitting there — might as well make it earn its keep!), but I’m a little unhappy with Grip, which is what I’ve been using to drive the ripping. I think I need to write some Perl to tie together cdparanoia and lame, so here are some notes on doing that:

I think I’m going to need two scripts: one that (a) queries CDDB (or FreeDB) for album information, (b) drives cdparanoia to rip the tracks to WAV files, and (c) makes a log of these WAV files, with all the info needed for properly ID3 tagging the end product MP3 file. This script will be run interactively, so error output can happen on STDERR. The second script should (a) read in that log file (which may contain info about WAVs from >disk), (b) MP3 encode each track using lame, setting the ID3 info appropriately, (c) remove the WAV file, and (d) move the MP3 file to its permanent home. Since this script is going to be run as a cron job in the wee hours of the morning, or during the day while I’m at work, it needs to log the results of all operations, and then mail that log to me.

As long as I can find a Perl module on CPAN that will query a CDDB-like database based on what disk is in the CD drive, I think I should be in business…

umm, wes… >>> Where were you last Saturday night at 0300 GMT?

Just one week after Microsoft admitted to a major breach of its security, another hacker by the name of Dimitri claims to have gained access to several of its Web servers.
Using a known security hole in M$’ Internet Information Server software - which should have been fixed with its own patch - Dimitri hacked into the servers and uploaded a text file called Hack the Planet.

(Bolding mine.)

(More info at InfoWorld.)

Seriously, I wonder if Wes is going to be questioned by the Feds over this? Seems like the kind of brain-dead thing they might consider…

joy >>> Peapod is now doing grocery delivery in our area. Now if they’d just team up with Trader Joe’s as well as Giant, I’d never have to go to the grocery store again…

more on banking >>> More about the recent banking dilemma: Previously, I had said we were going to use a combination of our bank’s website (to pay bills) and GnuCash (for checkbook register-type stuff). Now, we’re thinking about using for the latter functions. Anybody out there have any feedback about onmoney? The nice thing about using them is that we can then access the info from anywhere — which means if Lor’s on the road, she’s got as much access as I do from home.

male-hood >>> Every time I look at this strip, I laugh my ass off.

soon to be pointless, but… >>> So, Mike quotes Drudge on some internal Bush polling numbers showing the Gov leading Gore in several key states. My inner pedant is forcing me to point out that the numbers quoted are “within the margin of error”, and without knowing what that margin of error is, you can’t really evaluate them. If we assume a ‘typical’ margin of error of 2 to 4 percent, the Florida and California results become meaningless, and the Michigan result becomes much more marginal (with a 4% margin of error, the spread between the candidates could be as low as 1%).

Hopefully, that will satisfy the pedant in me for this particular election season…

satisfaction >>> Today was a good day — a good, solid day. Spent most of it building and refining Perl code to parse some text files and insert stuff into a database, then decided to update the software on my workstation — which involves compiling a whole load of stuff. See, I’m pretty used to the environment I use at home — Gnome with Sawfish — and so when I got to NCBI, I took some time and built most of Gnome 1.0 in my userspace. Now I’m upgrading it to 1.2, and re-organizing things a bit in the process. The problem is, there’s not much GNU stuff available at work — most of the common *nix programs are Solaris-flavored. Add in the fact that I don’t have root on the box, and in the end, I end up with about half a Linux distribution compiled into my $HOME…

against future need… >>> had a tutorial on building coding Gnome apps in Perl recently. had a Squid configuration HOWTO. (Squid is a caching HTTP/FTP proxy, which can have the effect of really speeding up your web browsing.) Maybe if I read this, I can figure out how to reduce Squid’s memory footprint a bit…

Info on automatically updating Junkbuster config files. (Junkbuster is a filtering HTTP proxy — it blocks banner ads and such, which also improves the speed of your net connection.)

must-haves >>> Tom over at Ft. Boise had a list of his most-used software the other day, and I thought I’d share mine too:

Program Used for Use Open Source? Free
(as in beer)?
XEmacs Writing, coding constant yes yes
Gnus Mail and news constant yes yes
Netscape Web browser constant no yes
Gnome Terminal command line stuff constant yes yes
Sawfish Window manager constant yes yes
J-Pilot Visor sync and desktop PIM daily yes yes
Sitescooper web site scraping into Visor format daily yes yes
Genpage HTML preprocessor (used to produce Genehack) almost daily ;^)= yes yes
Mozilla web browser weekly yes yes

Plus a slew of command-line tools — fetchmail, analog, ssh. This isn’t everything I use, of course — just the things I’d be hard pressed to do without.

(‘Constant’ in the table means that basically I open the app when I login, and have it open and running all the time.)

first, they came for the readers >>> Last month, David Pogue had an editorial in MacWorld about privacy in the ‘net age, basically arguing that people were being way too paranoid and that they should find better things to worry about. Can’t find a link to the piece, but I think he might even have trotted out the “if you don’t do anything wrong, you don’t have anything to worry about” meme. It was easily the most wrong-headed piece of opinion masquerading as tech journalism that I’ve seen in recent memory (okay, maybe I just need to get out more).

Want an example of why? Look no further than the Tattered Cover case in Denver, where cops want bookstore records so that they can track down somebody (or somebodies) who was running a meth lab. Sure, at first that might seem like a reasonable thing to try — but even leaving aside the ‘slippery slope’ arguments, there are legitimate purposes behind making sure a purchase. Gag gifts, for one; book collecting, for another. Of course, we have to expect that during the War on Drugs, there are going to be some collateral casualties, like our civil rights.

odd search queries leading to genehack >>>
pictures of jewish women
tipper gore nude
research articles on the way people dress
scay movie

In some cases, I can almost understand why somebody did the search, but why, in the name of all that’s semi-intelligent, did they click through to my site?

nodalpoint >>> Yesterday, for some reason, SciTechDaily had a link to an interview with William Gibson, about his new book All Tomorrow’s Parties. Bit odd, since I’ve had the book for awhile now (it’s got a 1999 copyright), so “new” is a bit of a stretch. Interesting interview, however.

Meanwhile, Salon has a piece about Bruce Sterling and his new book, which actually appears to be new. Sounds like I might need to wander towards a bookstore this weekend; it’s been a while.

rna world >>> Looks like a small RNA molecule that regulates development in worms (C. elegans, to be specific) is universally conserved in metazoans. A big portion of the molecular biology world tends to think of RNA as that unimportant molecule between DNA and protein in the Central Dogma — and it drives the people who work on RNA nuts. Some of those people have been saying for years that RNA would play key roles in regulation of gene expression, and now it’s starting to look as if they’re right.

at the core >>> I have a certain tendency to think of Michael Moore as a funny, slap-dash kind of guy. I think it’s because time dulls the memory of how dark Roger & Me and Moore’s later TV shows were — they were funny, but whistling-in-the-dark funny. From reading his latest letter, however, it sounds like he’s stopped whistling, and started shouting.

welcome back >>> Indirection is back on the air.

knowing your limits… >>> …is a good thing, I think. I’ve still got some links squirreled away in the goodie bag, but I think I’ll save them for later this weekend.

(While I’m getting meta, I removed the sidebar, and slapped some reasonable sizes on the layout table — let me know if it’s still too wide.)