June 1999 Archives

The cable guy didn’t show. The delivery guy didn’t show. The ergo keyboard I ordered last week is backordered, and won’t be here until next week (my aching wrists!). On the high side, I found a stash of old cassette tapes that I’d forgotten about; lots of cool music to listen to, while I wait for things to happen.

Rooted evolutionary trees are wrong. Interesting fall out from the massive sequencing efforts of the past years. I need to read the actual paper… Link from Honeyguide

Defending the scientific imperative. I think there are interesting parallels between the fabled ‘Hands On Imperative’ of the Hacker Ethic and the motivations discussed in this article. Personally, I find that ‘dreamers’ produce more interesting science, and are responsible for pushing the borders of knowledge outwards. However, we also need the other type of scientist, the practical sort, to fill in the gaps that get left as the dreamers forge onwards.

On a whim, I downloaded and built Window Maker 0.53. I also un-installed the libPropList RPM that came with R5, and built my own. I don’t know which one of those was responsible, but it appears (cross fingers) that I have a Window Maker binary that doesn’t lock up the machine randomly. Of course, it’s possible that the condition hasn’t been triggered yet, but I’m happy for the moment. If you’re having trouble with Window Maker under R5, give those two things a try, and see if it helps.

I’ve been reading The Man Who Loved Only Numbers, and so I’ve come to find that my Erdös number is infinity. It’s likely to stay that way.

Cassini rounds Venus in a gravity assist maneuver. The Saturn-bound probe will get another push from Earth, later this summer. [Link from SciTech Daily

The Nerve Photo of the Day has been running a nice series from Andrew Einhorn; I’m looking forward to the forthcoming gallery of his work.

Couple new weblogs: The NIA and Have Browser, Will Travel [eatonweb for the first; Scripting News for the second]

I’m taking the day off from work; lots of little picking up things to do around the house, and the cable person is coming out to switch us over to digital cable. I imagine I’ll get the tidying up out of the way quickly, and then I’ll probably tweak the site content and layout a bit more. No howls of outrage over the new look have been registered; if you’ve got strong feelings one way or another, let me know at jacobs@azstarnet.com.

I got tired of the old look. Not quite sure how I feel about this color scheme, but I’m tired of dinking around with HTML (for the moment). Still lots of little tweaks to be made around the site, but it’s almost bedtime here.

After a lot of pain and suffering over the past week, I finally gave up on Windowmaker under LinuxPPC R5, and switched to GNOME/Enlightenment. I’m not all that happy; WM is a lot zipper. However, the GNOME/E combo has the distinct advantage of not locking up the whole machine every 30 minutes. It seems as if the problem is starting to show up for other people, so hopefully it will get quashed soon.

Saturday night, I was too lazy to go to the video store, so the wife and I watched Can’t Hardly Wait on HBO. Three comments: (1) It’s pretty cool that the title came from a Replacements song, or that they at least used the Replacements song featuring that lyric. (2) If you haven’t seen this one yet, don’t. Both Say Anything and Some Kind of Wonderful tell basically the same story (it’s a classic, when you get down to it), and have much better soundtracks. (3) What’s the deal with Jennifer Love Hewitt’s disturbingly large head? Is it really much too big for her body, or does it just look like that because of her pencil thin neck?

Salon interviews George Carlin. I wasn’t too impressed with his latest show (which I caught on cable). In other comic-interview-related-news, the Village Voice has an interview with Richard Belzer, who seems much more entertaining. I almost picked up his book during the last Bookstore Pilgrimage, but the budget just wouldn’t allow it. I also had a link to a Chris Rock interview, but I can’t seem to find it. I’m looking forward to seeing his new routine in a couple of weeks.

Last week, Wired had a puff piece on a database-mining assistant that’s being aimed at the bioinformatics/genomics market. The need for the product is definitely there, but I’m not sure if this is the way to do it. Wouldn’t it be better to set up the databases (e.g., Genbank) so that this type of correlation was already present?

the lack of updates over the past few days can be attributed to two things: (1) my stupidity and, um…that explains it all, come to think of it.

i foolishly decided to upgrade my linuxppc installation to R5 on Sunday night, instead of waiting for the weekend. Murphy licked his chops, and I’ve spent the non-work hours of the last couple of days fighting to get back to a functional spot. I’m still not quite there; this update is coming to you from the mighty Work Honker (don’t tell anybody…)

Birthday gifts that are just too cool: new geek hat, world domination shirt, and Crytponomicon. (Check out the Crytponomicon review on /.; there’s not much more to add. If you haven’t read it yet, you should be soon…)

this is going to have to be it for the moment; i’ve got a ton of bookmarked stuff to sift thru, and i’ve got to re-compile most of the software i use on my home box, and get back to work on the GUI front end for genpage, and figure out how to use all the nifty new features of the latest release of the latter…

I just realized that my dates have been off all week. Fixed that problem…

From Rebecca’s Pocket, I found out about the Viridian Notes, a design movement started by noted author Bruce Sterling. Lots of interesting stuff in there, at exactly the point when I don’t have time to dig into it. Following this chain of links, I also learned that Bruce Sterling has a new book out. Looks like a trip to the bookstore is in my future.

I think I’ve linked to Unobserved Utterances before, but I’m doing it again in the hopes that this will remind me to add it to the Daily Dose.

In the Just A Matter Of Time dep’t., a biotech firm announced that they had cloned a human embryo and taken it to the edge of implantation — in November. Two comments: (1) It is possible that this announcement has been made to lay groundwork for an IPO or a round of VC courting? Financials in the biotech sector have been a little low, and ‘any publicity is good publicity’. (2) The media fallout on this one is going to be even more interesting than normal, me thinks…

I haven’t been into the mp3 thing too much; my home box is a little too under-powered to play mp3s without slowing down everything else, and downloading lots of 3 and 4 MB files over a modem link sucks. With the new work box however, both limitations have gone away, and I’ve been browsing around mp3.com for interesting stuff lately. A couple of recommendations in the ‘indie/alternative’ category: The Sacred Monkeys of Bali (mp3s here) and Noah’s Red Tattoo (mp3’s here).

Harold Varmus, director of the NIH, is making waves with a plan for electronic publishing of bioscience research. I don’t understand what the fuss is; the physics and computing communities have had online archives, preprints, and publishing for quite a while. Look at what they’ve done, and steal the successful bits…

It would be cool if the NIH went with this software; collaborative on-line peer review would be pretty cool. Slashdot for scientists. Maybe somebody should hook Rob Malta up with Harold Varmus and see what happens.

Continuing with the academic publishing theme, a recent Salon piece discussed the politics of authorship. From what I’ve seen, the situation isn’t quite that bad in the biosciences. The author also presents the following conclusion:

So why all the reluctance to address such issues? Perhaps it’s because scientific communities usually consist of two groups with distinct interests and very different powers. The likely victims of misappropriation of authorship are the junior scientists with no power to legislate the rules of authorship. The senior scientists, on the other hand, might change the system, but in the sense that it clearly benefits them, they have little incentive to do so. Since senior scientists no longer have a supervisor who can easily appropriate authorship from them, and no longer need famous honorary names to help greasethe wheels of publishing, they have no reason to perceive the issue as a problem.
I hate to disillusion anyone, but that’s basically the situation in every hierarchical power structure in the world. It’s not a science problem, it’s a human power structure problem.

Brig admitted to me that the real purpose of her weblog portal was to cause massive amounts of time wasting. I, of course, have fallen into her evil trap…

While I’m on weblogs, a couple new ones that I might end up following: lemonyellow and bespoke.

Via one weblog or another, I ended up at the Computer jokes section of the rec.humor.funny archive. That’s joining the ‘Read at Leisure’ book mark section…

A Fox News story on the

first application of cloning to rescue endangered species. In order for this to work, we’re still going to have to clone a sizable number of critters from each species; otherwise the species will bottleneck, and we’ll end up with a genetically ‘brittle’ species, with insufficient diversity to respond to environmental changes. (You could argue, of course, that if the species had sufficient diversity they wouldn’t have become endangered…)

I think I may have finally found a use for those 286 PCs I accidently purchsed…

Murphy evidently heard me talking about a more frequent update schedule, and ate my web content Zip disk as a sign of approval. So, I’ve been back home to retrieve the tarred archive, and now I’m back at the lab. I’m not too happy with the Zip disk shuttling solution, but I haven’t come up with anything stunningly better.

One of the things that got lost was the source for the gooeyGenpage GUI. Back to the drawing board on that one, I guess. It’s ok; after browsing the sample chapter of Learning Perl/Tk, there are several things I could go to make the geometry management a little bit cleaner.

Here are those screenshots I promised yesterday: One and Two. Both are 1280x1024 jpgs of about 200 K. One shows some nice transparent terms; Two demonstrates my usual browsing configuration. Both feature gobs of dockapps and GQmpeg.

On a mailing list, I asked about setting the reply-to header back to the list, and someone whose name escapes me pointed me at “Reply-To” Munging Considered Harmful. Sure enough, my mailer does have a reply-to-all command…

There’s a new issue of Perlmonth up. I haven’t had time to get thru all of it, but I’m lookingforward to the Perl/Tk section.

On Macintouch, Ric pointed to Apple-flavored Unix, a collection of information about running a *nix on your Mac. John Morrow, a fellow-TFUG-er, has got similar information on Free UNIX for your Macintosh. I dig that ‘Think REAL Different’ graphic!

I’ve been meaning to add these links to the Daily Dose for quite some time: Alan Cox’s diary and Telsa Cox’s diary.

I’m waiting for that birthday cash to roll in before ordering LinuxPPC R5. However, I’m also downloading it a little early (I’m impatient, you see) from ftp://ftp.cdrom.com/pub/linux/linuxppc, a nice fast West Coast mirror site. I’m getting consistent 300 K/sec throughput on the UA ethernet.

On Flutterby the other day, Dan pointed to an article about G.W. Bush. I just got around to looking at it today; I’m fairly pissed. A tip for the crypto-fascists in the crowd: the key part of the word is crypto; saying things like “there ought to be limits to freedom” just takes all the mystery out of it. So, ole’ Jeb is out of contention for 2000. I can feel my gorge rising at the thought of voting for Mr. Tipper ‘PMRC’ Gore, too. Maybe it’s time to look into postdoc opportunities in Canada…

H. sap. genome almost 90% complete. Cool.

I’m experimenting with a slightly longer form of writing for GeneHack updates; let me know if it really bugs you. I’m also going to be moving towards smaller, more frequent updates since I’m expecting to be spending a lot more time at work. The speedier net connection will also make surfing much more pleasant, so I’ll be doing most of my daily info download there.

I spent a good part of today poking around with Perl/Tk. I can see that a trip to the bookstore for another O’Reilly title is in my future. My immediate goal is to develop a front-end for editing genpage configuration files and launching genpage runs. I got the basic GUI (26 K gif in new window) implemented, now I just have to fill in all the callbacks. (The grey buttons are the un-implemented ones.) I’m calling it gooeyGenpage, but suggestions for better names are welcome. I expect to have a working version out by this time next week for people to pound on.

I took some screenshots of the new work box, but somehow they got munged between work and home. I’ll take some new ones once I get into work and then put them up.

In the continuing fallout (no pun intended) over the Bt corn-monarch butterfly study, ENN has

a piece with comments from John Losey, the scientist responsible for the study, downplaying the applicability of the study to real world conditions. The obvious question is why that fact wasn’t featured more prominently in the original paper and press releases. The answer, of course, is because would have made crappy news if that was done. In other genetically modified food news, the that many of the scientists appointed to advise the British government on GM food issues have ties to companies in the GM food sector. (Link from Robot Wisdom.)

The Rev Michael Reiss, ethical adviser to ACNFP, said he thought the system was flawed and “genuinely lay people” should be given seats on advisory committees. “Also, at some point you need to involve the sceptics on these committees,” he said. “For reasons of fairness, expertise and public confidence, the whole spectrum of public opinion must be included.”

I’m all for including the “whole spectrum of public opinion”, but several things need to be remembered. First, we mucking with the only ecosystem we’ve got right now; messing it up would be a Bad Thing. Second, that ecosystem doesn’t pay much attention to national boundaries; some yahoo in Outer Mongoland can release a bug just as easily as a highly trained scientist in the US or Britain. Third, there are a lot of hungry people out there who really need more productive food crops; it’s difficult to care about the environment when you’re starving. Finally, the problem with including “genuinely lay people” is that by the time you’re competent to evaluate the benefits and risks of something this new and complex, you’re not a layperson anymore. (Insert stock rant about opinions, entitlement, and chuckleheads here.) I’m not sure what the answer is, but I am sure it’s a lot more complex than it will get made out to be.

I’ve got 3 or 4 more things bookmarked to point at, but I think I’ll just mail the URLs to work and decide what to do with them later. It’s just about bedtime…

Yesterday’s failure to update was due to a system meltdown. I’m basically back up to speed; luckily, most everything important was backed up in preparation for the move to the new honker. However, I did lose my mail spool file, so if you sent mail this week, please send it again.

the honker Here’s the spec’s on the new work box. If I’m real lucky, it will be delivered today; sometime next week is more likely.

  • Asus P2B-LS motherboard
  • Pentium II 450 MHz/512K cache/MMX
  • 9 GB ultra wide SCSI hard drive
  • IDE Zip drive
  • 48X IDE CD-ROM
  • Digiview 17” 1600x1200 monitor
  • Matrox G200 AGP video card
  • SoundBlaster AWE 64

Comments or suggestions for an easy Red Hat install are welcome, but I don’t expect any problems…

micro-rant Got the new Wired yesterday. I can remember when it was about cool people doing cool stuff, and the fact that people were getting insanely rich was irrelevant. Now Wired is about people getting insanely rich, and cool stuff is irrelevant. Unfortunately, I think I already re-sub’d for another year. Sigh…

car In addition to the system meltdown, I also found out yesterday that the recurrent problems with our 1997 Saturn SL2 are mystifying the techs at the local dealer. They had to do some sort of conference hookup with the techs in Spring Hill, which resulted in re-wiring some parts of the electric system. We’ve been very happy with the car, but this whole series of events is making me very nervous.

stuff Some stuff to download and/or look at:
There’s a new Window Maker out; builds fine under LinuxPPC. The download link for genpage got fixed, but I haven’t played with the new tarball yet. A couple of links from memepool: Bart Simpson waggin’ his ass and an on-going rerun of Calvin & Hobbes. On the information radar front, Wes is back, and I think I need to start looking at AntiOnline more. Finally, over on Flutterby, Dan’s linked to a piercing site. (That link has pictures of body parts you can’t show on broadcast TV; you’ve been warned.) First, OUCH! Second, how do these people get through metal detectors?

No real update again today. I’m very, very close to ordering the box for work; unless something odd happens tomorrow, I’ll be ordering a honker from a local wholeseller. Details tomorrow. For now, I’m off to bed early, because I have to get up and take the car to the dealer. More about that tomorrow also. Some links that I thought were interesting, but don’t have time to comment on extensively: Unobserved Utterances, a new weblog; A Linux Journal interview of Larry Wall; and an interesting exploit of search engines.