September 2000 Archives

stormy weather

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Raining and cold — rather a dreary day, all told. Spent most of the day with a vague desire to curl up in front of a window with a book and a cup of soup. has an interview with Ilya Zakharevich of Perl5 Porters fame. Interesting takes on language design, education, and other things.

Thoughts on FrayDay4 from BackupBrain. (Not one of my regulars; scarfed from blivet.) The thing is, every gathering of bloggers is like that; hell, the first time I met someone in meatspace after meeting them on-line was over ten years ago, and I had the same feelings then. All I can say is that it does get better; after you meet people a couple times, things start to feel more symmetric, everybody is more comfortable and relaxed.

Thrilling story of a diving near-tragedy.

Late happy birthday to Graham.

Couple of CueCat links: the Reg’s take on the distribution and privacy stuff, and an Advogato thread on practical uses for the hardware. I’ve got one (fake info to Radio Shack, thanks much), but haven’t had time to hook it up yet. I’d really like to see a CDDB-like mechanism for scanning UPCs from different types of media: CDs, books, magazines. Don’t have time (hmm, I see a pattern) to start a project, but if anybody knows of one that’s looking for a tester or small amounts of coding, let me know.

Wacko alert: The I Ching Binary System And Natural Phenomena. I get this spam at work, by the way.

Wired News overview of proteomics, the Next Big Thing in the bioinfo world. In about ten years or so, we’re going to run out of these massive single-shot solutions, and people are going to realize that the totality of information (mRNA levels, protein levels, protein and mRNA localization, etc) is where the killer app is (IMHO, of course).

Okay, some conservative “leader” up in America’s Dairyland held a demonstration to show people how to correctly spank their kids. Leaving aside my rather conflicted feelings about the whole corporal punishment issue, what I want to know is what the teenaged target demonstratee did to deserve the whuppin’. And do they have to wait for some kid to mis-behave before they schedule these things, or what?

Researchers at Stanford are taking a distributed computing approach to the protein folding problem. I’ll accept that their algorithm works for smaller proteins, even though I haven’t looked at their data at all. My question: is there any evidence at all that the algorithm is going to scale? Are they planning on crystallizing things to check the folding predictions?

New TLD that I’d like to see: .om

Hey — would the person hitting genehack and leaving a referral of http://localhost:1234/Select?FOO drop me a line and let me know what you’re doing? It’s not causing any problems or anything; I’m just a curious git.

Warning: Personal crap and whinging ahead.

I’m giving a lecture Tuesday night, on information retrieval from the Entrez databases. I’ve been working on it for the past several days, and I’m still not completely happy with it. However, I’m also getting pretty tired of thinking about it and tweaking it, and I’d like to get back to my “real work”, so I’m kind of relieved that it’s going to be over in about 23 hours or so.

Anyway (here comes the whinging) the lecture has been keeping me rather busy, and I’ve been short on sleep, and had other Real Life crap intruding, which is why things were quiet over the weekend. I’m also really behind on mail, so apologies to all my correspondents. I’ll (hopefully) be getting to you sometime this week.

And now it’s time to hit the hay, so I can get up nice and early, to finish my slides for the lecture. Might not have much tomorrow or the day after that, but I will have at least one more update this week. If you’d like a short-yet-strangely-compelling email when that happens, join the list.

Another long day. I wonder if this is somehow related to the beginnings of fall? This is the first time in almost 25 years that I haven’t been in an academic environment, so it’s possible that I’m still mentally doing the “back-to-school” buckle-down thing.

I did get to spend some time today writing a style guide for the site I’ve been working on. Being a code nazi is fun! It almost makes up for all the seriously grotty HTML I’ve been wading through.

One of these days, in my copious free time, I’d like to pick up some LaTeX. From this review, LaTeX for Linux might be a good starting point.

Wow — Alan Williams, who you may remember from, was just featured in a SF Gate profile. Sounds like he’s doing well; good luck to him if he’s still reading. In fact, if you are still out there Alan, drop me a line, ‘kay?

Yet another thing that I need to make time to set up: demand dialing.

Speaking of net access, I applied for DSL again, after getting turned down by Covad earlier this year. I’m trying with PhoenixDSL this time. Here’s something I don’t understand: if I applied before and was bounced, how come the ‘put your phone number in’ forms don’t just turn me down right away? Or, if by some miracle my previously inadequate CO has been re-provisioned or something, why didn’t Bell Atlantic Verizon let me know that? I want to give people money in return for a fast connection! Why is this so hard?

I’m glad to hear that Jessamyn is doing okay. Lor and I are headed up to Vermont later in October to pay a visit, and we’re both really looking forward to it.

Genome Biology had a series of articles about electronic publishing in the biomedical sciences earlier this week. I thought Paul Ginsparg’s article summed up my viewpoint fairly well: electronic publishers should really be trying to do more than just replicate paper journals. Sadly, most journals seem to be happy just generating PDFs that people can print out. It saves you a trip to the library, but that’s about it. Scientific journalism is about communication; it would be nice if some of the online journals started to really emphasize this.

Al Gore’s Mom invented Perl.

Have a good weekend…

Ouch. Whadda day — the move, trying to cram a day’s worth of work into the half day I had net access for, unpacking, ARRGHH! And it’s not going to get better anytime soon. On the plus side, I had a decent idea today about the project I’m working on — now if I could just get some time to code…

On the off chance you don’t see it somewhere else: a professor at the Art Institute in Chicago commissioned a group of scientists to make a transgenic albino bunny that expresses green fluorescent protein (GFP). Looks like a normal white rabbit, but under the right UV wavelength, the bunny glows. This is a pretty cool hack; it was intended to cause controversy (err, I mean “spark discussion”), and it’s looking like it might just do that.

Idea borne out of lack of sleep, offered gratis: Given the recent release of green catsup, can other color-enhanced foodstuffs be that far behind? Take your average beef cow, clone in a bit of GFP, and presto! GlowSteak. Secondary marketing opportunities (e.g., the black lights to make it glow, sauces with fluorescent proteins of different emission wavelengths for contrast, etc.) abound. I really think this one’s a winner. Oh! And not just limited to the meat eaters, either — how about a really green salad? Glowing bran muffin? MMMMMMM.

And now I’m going to stagger off to bed. If you’ve sent me email recently, I am working on getting back to you, but it might be a day or so. Tomorrow’s going to be quiet ‘round here, but I expect to be back in full force Thursday night/Friday morning. See you then.

Shaping up to be a busy week on the work front — tons of stuff to do, plus an office move thrown into the mix for fun. Hopefully won’t be as quiet ‘round here as last week was, but don’t be surprised.

Long time readers might remember that I’ve ranted before about why I don’t typically link to things on Scripting News, despite Dave’s sometimes insightful writings. (And despite Dave and Frontier being instrumental in me starting Genehack in the first place.) One of Dave’s recent posts provides a capsule summary of the reasons, and also summarizes why I think editing ‘live’ files without proofing them is a Bad Thing. Maybe it’s my academic background, but I always think of the ‘net as equivalent to print, and putting something on the ‘net as equivalent to committing it to the historical record. At that point, the content should become inviolate. You want to post follow-ups, or retractions, that’s okay — just don’t retroactively edit the content. That’s my viewpoint, anyway.

WebMake looks interesting. One of these days, I’m going to code on BOP again, I swear…

WANT! Santa, please take note.

Okay, so we’ve apparently got some terrorist CD-ROM, supposedly from the bin Laden group. (Not gonna bother to dig up a link; try CNN or something.) My question: why are we releasing this information? Wouldn’t it be better, assuming that the thing is real, to just sit back and utilize the info to more easily foil terrorist plots and stuff? What am I missing?

AAAS advises against augmentation of human abilities via genetic engineering. Although it seems like they’re hedging their bets somewhat. Despite the fact that I think this is going to happen sooner or later, I think the idea of some sort of committee to develop guidelines is a good idea. Where do I sign up?

I had one more link, about a expression profile XML DTD released by a biotech company, but I just posted it on NodalPoint. So jump over there and have a read if it sounds interesting.

And now, I’m off to bed…

What happened to getting this up last night? Blame it on my ISP; I couldn’t get online until almost midnight, and at that point I just grabbed my mail and went to bed. Today was spent on yet another IKEA run; had to be done today, as some stuff we had back-ordered finally came in. Anyway, let’s get down to it…

While I was unable to get online, I watched the Olympic opening ceremony. We’re not a bad species, when we put our mind to it, although I do wish someone had gagged Costas and Couric.

Gnobog is a GNOME-ish bookmark organizer. Can’t install it at the moment, cuz the Debian package is b0rken, but it looks useful.

Heh — Debian package description for the Flash plugin:

Flash/ShockWave is a Macromedia invention for wasteful webcontent.

Review/recap of a recent meeting on gene prediction in genome-scale sequences. Sounds like things are getting interesting… For the non-bioheads in the audience, the issue is that when you sequence an organism, all you get is a bunch of seemingly random data. Finding the important and interesting parts is a big problem, and traditional techniques don’t scale at all to whole genomes. This is where the computational stuff comes in, and it sounds like we may be getting a handle on at least the easy parts pretty soon.

Okay, where can I get the bumper sticker? Or maybe a tee shirt…

The English is a bit fractured, but this page shows you how to replace the buttons on a Palm with clear ones. Why would you want to do this? Well, after you replace the buttons, you put colored LEDs under them, see…

Making friends with grep. Pretty basic level stuff, but if you’re a *nix beginner, this is worth reading. By the “which do I do more often” metric, grep is more important to me than sex.

Opps. Guess I missed Behind the Curtain; shooting is tomorrow. Oh well, I’ll just buy the coffee table book.

Large gallery of erotic photos by Peter da Silva, who some of you may know from the Monastery. I particularly liked this one, this one, and this one. (That last one features a naked male ass, so watch it as necessary.)

Anybody want to take any bets on whether any of the issues raised by Don Gilmour get addressed in the presidential debates? Didn’t think so.

I’d really like to point you to some of the content on, but they’re using a totally brain-dead set-up that won’t let me. Near as I can tell, incoming links to internal pages are getting redirected to their front page, presumably so that those umpteen annoying ads can get loaded. Losers.

Top Ten Tips for working with CVS. I really hope ORA keeps doing these top ten tips lists; the two I’ve seen have been outstanding.

Pro bio-tech recap of the World Forum.

Goodbye to the Miss Waldron’s Red Colobus. posts over-heard snippets of conversation. I sometimes wonder if people are listening to some of the conversations I seem to typically end up in, and what they think if they do.

K5 K0untd0wn. I’m so glad they’re coming back…

That’s not a beer belly, it’s an organ!

Scathing review of the Debian installation process. I have to say, I run Debian, and have had no problems with installs, updates, or anything else. It does require a bit more ‘get-up and go’ on the part of the user, but if you think that’s a bad thing, Linux might not be for you.

Blog rolling: I’m aghast; my personal map of the universe has come unsprung, and I’m not sure how to fix it. The reason for all this discombobulation? Mike has ditched Bush for Brown. The heavens are all a-tremble, I tell ya.

The project I spent all last week working on is coming together. There’s still quite a bit left to do, but it’s mostly tweaks. That should all get done tomorrow, Ghu and my wrists willing. If you want, have a look. I’d dig feedback, too; we haven’t done a whole lot of user testing.

Okay, it’s getting to be time to get to bed. Next week is going to be another bear, but hopefully I’ll be a bit better on the update tip. Enjoy the rest of your weekend.

echo ho ho ho

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Okay, the next couple days have stretched a bit. Got some stuff to ‘blog too, dammit. Expect to see an update here sometime tonight.

Things are going to be quiet ‘round here for the next couple days, as I work on getting a web-based work-related project up and running. Sorry ‘bout that.

plans i make

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This has been a really odd, off week. I’ve been struggling with the next phase of my project at work, circling around the problem and looking for a place to get a grip on it, and I’m not having much success. The frustration from this is bleeding over into everything else, and basically I’m ending up an unhappy camper.

Interesting story about how Perl is used to help assemble the OED.

Talking about rape research can be unpopular, apparently. Unfortunate, because understanding why it happens might help prevent it from happening.

Yet another “let’s make a plain ole browser out of Mozilla” project: Skipstone. Haven’t tried it yet; anybody care to comment? I’ve backslid from my commitment to use Mozilla, and Galeon has been too unstable for me to use regularly, perhaps because of my “aggressive” browsing style (I tend to pop open new windows to follow links, rather than having them open in the same window; it’s not uncommon for me to have five or six browser windows open at once).

I summon the vast power of CERTIFICATION!

Philadelphia police infiltrated protest groups during the Republican National Convention? I’m shocked. (Ob80’s: Not!)

Awesome, wonderful interview with Helena Cronin, evolutionary biologist. Touches on genetic determinism, how we should be using knowledge from behavioral studies in shaping policy, and several other areas. This is the link to follow today, if you follow no others.

Analysis of coprolites demonstrates that at least some Anasazi were cannibals. More interesting than the confirmation is watching the fall-out; apparently the idea of cannibalism in Southwestern Native American populations is controversial.

Last week, a Maryland police officer trailed a man through the District, and into Virginia. At some point, the man ended up dead, and now an autopsy has shown he was shoot in the back. The officer is claiming he was in fear for his life after the man repeatedly rammed his car into the officer’s unmarked vehicle, and that is why he opened fire. So far, nobody is asking the obvious question, “Why didn’t you just drive away?”

Rebecca wrote up a weblogging history today, including some perspective and opinion for good measure. It’s a good read, if you’re interested in this little subculture we’ve got going here.

This seems like a good time to point out that Genehack is about two years old this month — I say “about”, because the archives go back to September 1998, and there was some older content that I never bothered to archive, but I don’t think I called it a “weblog” until April of 1999 or so. Whatever; as these things go, I’ve been here a while, and I’m fixin’ to stay around. 8^)=

And, while I’m blog-rolling, I’ll just say I think Jorn’s “Sustaining Subscriber” experiment is a pretty cool idea, and I’m curious as to how it’s going to work out.

The Saga of El Cabeza Del Oro!. Because we could all use a bit more surreality.

I’m thinking about getting a hollow plug for one of my earholes. I really like the way this looks, with the hoop threaded through the plug. Bit worried about jamming the sucker in there myself, however — anybody got any stories they want to share about this?

Pretty full weekend ahead: DC ‘blogger gathering tomorrow night (mail for details, if you’re interested — you don’t actually have to ‘blog to attend; we’ll let slavering fans in too. grin), couple other parties, and a big stack of crud to wade through. Whee. See y’all on Monday; have a good weekend.

Okay, so the 10 pm EST thing didn’t happen. Mea culpa. I forgot that tonight was the meeting, and I kinda had to go to that, for reasons I won’t go into here. It was my first DC Perlmongers meeting, and I had a pretty good time. Scored a spiff Perl Mongers hat, too. Woo. Alright, into the breech…

Here are some Gnome-ish toolbar icons for GTK-XEmacs. On my TODO.

Wired News had a piece last week on the Lego Desk guy. I need to get back down to the Potomac Mills Lego outlet and pick some stuff up — my pre-adolescent Lego jones is returning…

I’m not sure allowing the Boy Scouts to receive federal funds is okay. Sure, let them use the federal lands, I don’t see a problem with that, but giving them some of my tax money? I certainly wouldn’t want it going to a (hopefully hypothetical) Aryan Scouts group which didn’t allow anybody but straight white kids in, and I think the difference between my extremist example and the real Scouts is only a matter of degree.

Gov’s off the net!” sez report. But will they listen?


Another graphic for the office…

The top ten Linux tips also contain some good ones for people using any sort of Unix-like OS.

Email leading to death of written English! Film at 11! This meme seems to have a period of four or five years between appearances, in my experience. On another note, check out this quote, from the same article:

Researchers from the McCann-Erikson advertising agency, who interviewed more than 100 children aged 5-11, concluded that traditional letter-writing will be of no more use later in life than the history lessons pupils learn.

What’s more scary, that researchers from an ad agency are getting involved in educational policy, or that they’ve apparently already decided that history is useless?

The Big Picture Book of Viruses has some pretty cool photomicrographs, like this one, the first ever view of the Ebola virus., for all your Perl documentation needs.

If we’re going to have to live in a dsytopic science fiction universe, couldn’t we pick something other than the Steve Jackson Games Car Wars one?

This weekend, I found out that Hal (of Blivet) lived in the same small Kansas town I grew up in! We never overlapped, and I don’t think I know any of “his people” (as we say in the Mid-West), but it’s still a pretty cool “small world” kind of thing, and I thought I’d share.

Ugh. Reading back on this update, it’s not really my best work — it’s too rushed, and things don’t really flow, and the writing, well, it reads like it was quickly dashed out, with very little revision. Which, actually, it was. Sorry ‘bout that, but if I start trying to fix it, it’s never going to get posted. Hopefully, as the week goes on, I’ll begin to get more caught up with my backlog of stuff. Speaking of which, still working on the email tip — be patient, and know I’m going as hard as I can.

Wow, is it Tuesday already? What the hell happened to my nice long holiday weekend? I was planning on having an update today, but it’s just not going to happen. (Actually, I was planning on having lots of things done that didn’t happen. sigh) Anyway, this is just a short little note to let you know that tomorrow’s/tonight’s update will be a bit earlier than normal (look for it around 10 pm EDT) and a bit larger than normal (I hope). For all my email correspondents, I’m working on those replies too, and hope to be all caught up before I collapse into bed tonight. Now, it’s time to get to work…

Just enough time to slam out a quick update before getting back into work for another exciting day of database/CGI coding. Yesterday, I was thinking about the part in Cryptonomicon where Randy is locked in prison, and trying to decode the old messages without being phreaked. Stephenson has one of the best descriptions of the amount of mental ‘state’ that coders carry: “juggling flaming chainsaws”. The stuff I’m doing isn’t like that — it’s more like building a wall out of very tiny bricks — making sure each brick is positioned just so — and then pounding the fscker into place. Seems like slow going while you’re doing it, but at the end of the day — well, lookit there, it’s a wall!

Odd search engine referrals for the week:
finding interesting conversation topics for therapy
marijuana friendly vacations

Speaking of hits from search engines, my plea from July 11 has fallen on deaf ears; I’ve been getting 3 or 4 hits a day against that particular phrase. Bit upset about that, but I guess looked at in one way, I’m poisoning the results just a little bit…

Okay, I haven’t read it yet, but I’m pretty sure any Harlan Ellison interview is worthwhile. And that title graphic is so getting printed out and hung in my work cube!

ESR flames Linus. Strikes a cord with me because I was one of those kids who never studied in high school. Actually, I didn’t really have to start studying intensely until about junior year of college (he said modestly) and it was hard to get into that groove.

Fish are getting smarter. This is pretty cool!

If you’re in the dark about the whole transgenic foodstuffs thing, have a look at Transgenic Crops: An introduction and resource guide:

The goal of this web site is to provide balanced information and links to other resources on the technology and issues surrounding transgenic crops (also known as genetically modified or GM crops). The site’s authors are engaged in plant genetics research and teaching at Colorado State University. They receive no funds from companies involved in transgenic crop development, nor are they affiliated with groups campaigning against such crops.

Cool and interesting article about the diversity of life found around seamounts. Cool pictures, too.

FAKtory is a forthcoming GPL’d fragment assembly system. Not much there yet, tho.

Gosh, it appears that in the wake of the recent DeCSS decision, the MPAA is acting like a big bully. Anybody surprised? Interesting to note that the portion of the decision that they quote in their C&D letter also bans “linking any Internet web site, either directly or through a series of links, to any other Internet web site containing DeCSS.” Given the nature of the web, and the “big cloud” net topology study of a couple months ago, this means that a large portion of the sites on the web are in violation of this injunction.

Interesting legal hack — two Texas women are set to marry. The interesting thing here is that one of the two is a post-op transexual. The union has been deemed legal because she is genetically XY (i.e., male). I’d never considered this particular situation before, but I think it really points out the arbitrariness of being against same-sex unions.

Mental note: buy Bike.

Okay, just time to bang out a reply to some emails, shower, and jump on the train. Don’t know if I’ll be updating Monday or not, as it’s a holiday here in the States, and I might just take advantage of my day off and sleep all day. Or something. Anyway, have a good weekend, and I’ll see you later.