August 2000 Archives

Watched Magnolia last night. Wow. If and when we get a DVD player, I’ll be grabbing it on disc — just because I know I missed stuff…

Yay! Amanda’s back! At least for a bit, anyway…

In a twisted way, I can understand getting hazed to join an athletic team. I still think it’s wrong, and all, but I can understand it. But who the hell gets hazed to join a church group?

An interestingly contrarian view of working in IT. (Stolen from the SDM, since I saw somebody grousing in there the other day about /. using things without credit…)

Judge rules LAPD can be sued under RICO statue.

Pregnant mom to be monitored daily to protect fetus.

Last two items make me feel slightly more random about US society than normal.

GTK-XEmacs had a release yesterday. I’ve been using the CVS version, updating and rebuilding every weekend, and it’s been rock stable. William M. Perry has done an absolutely fantastic job on this project.

The BioPerl project has started using Wiki. Time to learn that now, I guess.

Here’s Abigail’s YAPC::19100 talk on JAPHS and other obscure signatures. Interesting not only for the Perl bits, but for the (highly effective, IMHO) way the deconstruction of the coding tricks is presented.

Following up on last week’s pig cloning/xenotransplantation virus transfer worries stories, a Massachusetts-based biotech firm has announced that they have a line of miniature pigs that seem to be unable to transfer porcine endogenous retroviruses (PERVs, and who came up with that acronym?) into human cells. Of course, they don’t sound all that sure:

“It appears that these animals don’t contain replication-competent PERV in human cells. We don’t know why.” [ said a company spokesperson ]

Those key words “appears” and “don’t know why” are making me just a wee bit leery of running out to get some pig organs implanted.

Good day at work yesterday — the last couple weeks have been spent doing a lot of planning, designing, and thinking, and even when I was coding, it was support stuff in libraries. Yesterday, however, I finally got the first functional bits written and tested. I finally feel like progress is being made.

Today was a Monday’s Monday. Everything took longer than expected, I couldn’t concentrate on anything to save my life, and really fun things kept happening. Example: the Meta key on my keyboard got stuck down. Swapping out the keyboard demonstrated it wasn’t really the keyboard, but rather the Sun-PS/2 converter box doohickey. Recommended solution: reboot. Okay, but I have to give a password to do that, and that password contains a number, and I’ve got Meta-number combos bound to commands in my window manager… Oh yah, big fun all around.

Systems Software Research is Irrelevant. One note, the ‘Irrelevant’ part probably doesn’t mean what you think. This is an interesting read, and it’s by Rob Pike, so it probably deserves a look, even if you don’t agree with what he has to say.

Some links for the “when I have time” alternate reality that I may one day inhabit: PSGML tricks and Colorizing with emacs and psgml.

Interesting SciAm piece on Ensembl and DAS, which are systems being developed to collaboratively annotate the human genome. (“Annotate” means to pick out the genes and control bits from the gimish of sequence.) I concur with David Lipman’s point that there may be issues with the quality of the annotation, but I hope that this could be partially solved via some sort of trust or reputation metric.

The seven don’ts of Usenet. My life would be immeasurably better if people followed these rules, not just on Usenet, but mailing lists as well.

Maybe then I wouldn’t find things like “When your systems administrator works for the mob” quite so amusing. Or at least not a source of tips for future use anyway.

K5 is coming back! Yay!

Fun weekend — IKEA run, movie watching with Lor, some design work for a work-related project. Not enough time, all things considered. In fact, the first paragraph of the 25 Aug entry over at All Too Cozy pretty much sums up how I’m feeling — too much stuff, not enough time.

Human Gnome Project Completed.

Esther Dyson says “The music industry encourages stealing by making people feel justified in doing so.

Galeon packaged for Debian.

Freaky web search referral of the week: “Free photos of nicked women”. Is this some kink I’m unaware of?

Skud takes on Quality versus Quantity in the Open Source world. On one hand, I think she’s right, but on the other hand, it’s much, much easier to start writing something on your own than to have to grok an existing code base. And that’s not even dealing with having to fit into the culture of an existing project, which can also be tricky.

Follow-up on Friday’s canine leishmaniasis story — it’s now been found in 21 states.

Yes! Yes! Wow! Go read Beyond Alchemy now. Clay Shirky Gets It. One tiny pull quote from a longish (and did I mention excellent?) piece:

What had previously looked like a one-way chain from DNA to phenotype is now looking like a chaotic network of two-way forces, and a good motto for the biological frontier in the age of fully sequenced genomes might be “It’s More Complicated Than That.”

(Aside: my personal biological research mantra for the past four or five years has been “it’s more complicated than you think”.)

So, to the TAM crew, spot on article, and thanks for the link. Say, how much does this “unofficial bio-guru” gig pay, anyway? 8^)=

Native Americans aren’t having much luck getting ancestral remains and artifacts back from museums.

One of the movies we watched this weekend was Liberty Heights, the latest(?) Berry Levinson life-in-Baltimore piece. Excellent, and recommended. The reason I’m mentioning it right after the above link is a scene towards the end of the movie. Without giving away too much, the movie is about a Jewish family in the 1950s, and how they relate to white Protestants and middle class and lower class blacks. Anyway, in this scene, Bebe Neuwirth (who you may know as Lilith) refers to “Indian summer” — an implicitly racist usage, related to “Indian giver”. In both cases, “Indian” == “false”. What bothers me is that I can’t decide if this was intentional on the part of Levinson — anybody care to comment?

Okay, time for me to get ready to go to work — gonna be a long day, I fear. Have a good one, and keep your head down.

I’m home from work this morning, waiting for our new couch to be delivered. So, morning update for you folks while I wait…
Update: The couch is here! Comfy goodness.

First up, I got a request last week from a college buddy (sort of) that I point out this weekend’s Iowa/KSU football game. Haven’t really been following the Hawkeyes much, especially given the past couple of relatively disappointing years, but if I get a chance, I’m going to see if I can’t find the game on some back channel. No prediction, cuz it’d just be bluffing.

I used to have fights all time with a grad school classmate about anti-aliased text. He’ll be glad to know that Joel says he was right.

Yesterday’s meme lives! It lives!

Great — there’s leishmania in New York. This parasitic disease is normally only found in tropical areas, and nobody knows how it ended up on the East Coast. First West Nile, now this — what’s up with all the odd diseases hitting the Mid-Atlantic states?

In the “can you have negative credibility?” department, TRUSTe was collecting surfer info, at least up until yesterday. Reading the article, it doesn’t sound like a particularly bad privacy violation, but you’d really like a group like TRUSTe to be completely beyond reproach — and that’s just not the case anymore.

Note to self: Download and install new HTML helper mode for XEmacs.

Billy Bob’s Cow Tipping Simulator. Ya know, I’m from a small town in the Mid-West, and I hadn’t ever heard of this cow tipping thing until I went to college. And then, it was people from Chicago telling me about it — I think this might be an urban legend. Any of you ever tip a cow?

Fun at your next group meeting! The nuclear blast simulator lets you map the effect of a ground or air warhead detonation onto a map of your area (via Mapblast). Make your co-workers think you’re even more dangerously unstable than you actually are!

Sure, everybody’s pointing at the LEGO desk. I dug a bit, and it turns out the guy has done some other sculptures — including a globe, R2D2, and Tux the Linux mascot. Pretty cool!

Check out the Readymade site. Ignore the obnoxious popup. Download the “The Block Alone” mp3. Groove. Be happy.

Last week’s Nerve photo collection featured a nicely tattooed couple — see some sleeve style tattoos, or a nice full back butterfly. Usually the all-black ‘tribal’ style tats (like the butterfly) are strong abstract shapes. Seeing one depicting a butterfly makes for a nice contrast. Not so wild about the star on the ass, but it’s not my body, now is it?

Hey, I’m a nodalpoint admin! I’m pretty excited about this — expect to see some of the bioinfo stuff from here to either get duplicated over there, or (more likely) to just move over there. But, I need your help too — get over there, get an account, if you haven’t got one already, and start some threads! Get to talking, people!

A couple weeks ago, Mikki Halprin, author of The Geek Handbook, graciously sent Lor and I an autographed copy. It’s a pretty fun read, and if you’re a non-geek it might help you gain some insight. If you are a geek, you will recognize yourself in the examples quite a bit. I didn’t realize it until I read the author bio, but Mikki was co-author of the smash Girl’s Guide to Geek Guys. Anyway, thanks again Mikki!

Okay, I guess now that the couch has arrived, I should go to work. Have a good weekend, y’all!

Been working hard over the past couple days, so no time to blog. Am going to try to at least post a short update, however — otherwise, I forget to say things I want to say.

Today, we’re going to try to start a meme. (Well, I’m going to try; I hope some of you decide to help.) First, a bit of backstory: Yesterday, I was sitting at work doing a bit of early morning surfing (before it all hit the fan later — but that’s another story) and I saw the Sony/Napster thing go ‘cross /. Thought, “I should blog this…”, realized I had no way to do that from work, and fired off a mail to Dave over at Scripting News, on the off chance he’d miss it. Link got posted, probably had nothing to do with me, but that’s okay. Last night, I was trying to decide whether to blog it here too. Thinking about that caused this meme to be born, and now I’m releasing it into the world:

The music industry is a drug dealer. Napster is drug legalization.

That’s it. Who has the most to fear from drug legalization? Drug dealers. Why? Because drug legalization will reduce profits for them. The drug dealer is a drug addict too — but their drug is called money. Just like any other addict, they’re willing to do whatever they have to to keep the drug coming. They also need more and more of the drug to get the same effect.

Do I think this is actually a valid way to think about the situation? Well, sure it’s a bit cutesy and over-the-top, but yes, I do. I think the Sony VP’s comments about Napster were surprising to quite a few people — but if you think about Sony as money-addicted drug pushers, it all makes sense: the drug dealer doesn’t care about laws, what’s right, or wrong, or any of that stuff. He just wants to get his product to you in the way that makes him the most money — especially since money is the drug dealer’s drug. Considered in that light, the “we will firewall you on the beaches” speech isn’t surprising at all.

Ok, that’s it — let’s see how this plays: little meme, I set you free. It’s a dangerous world out there, so be careful…

Lor’s off again, another early morning flight, which means I was up about two hours earlier than normal. I sort of like these early morning updates — aside from all the pain caused by lack of sleep, that is.

Here’s one for you paranoids: Read this story, which summarizes some of the recent left-wing protest activity, and trots out some of the standard “this movement has no center” memes. Consider, historically, what happens when you combine large groups of passionately dissatisfied yet unfocused citizens with a charismatic leader. Extrapolate.

Children of the Kernel talks about the need to teach newcomers to the Free Software movement some manners:

If the Linux community is to survive, it must educate these new users in etiquette. They must be taught to appreciate the fact that much of the software they take for granted came to them for free. Just as are forefathers sacrificed for our freedom, new Linux users need to be reminded that thousands of man-hours were spent perfecting the software they are now using; they should thank Linus Torvalds, Alan Cox, Richard Stallman et al in their /etc/cron.daily prayers.

In a related vein, expect to see a revival of the “Linus is a sellout” meme as Transmeta gears up for its IPO.

Round three of the “It does kill, no it doesn’t” BT corn/Monarch butterfly thing goes to the “it kills” side. I haven’t actually read any of the papers, and I’m certainly not a botanist, so I’ll save my opinion on the research. I will say that this quote:

Novartis defended the safety of its Bt corn, saying the new study did not duplicate real-world conditions.

“Research conducted outdoors doesn’t indicate what happens in a field environment,” said Novartis spokesman Rich Lotstein.

makes it sound like something fishy is going on, doesn’t it?

Note to myself #1: Add Remembrance Agent to the list of things to play with.

Note to myself #2: Follow through on that promise you made to yourself, that once you got out of grad school and started making some money, that you would give some of it to the EFF.

Note to myself #3: Add The Super Friendz to the “To Buy” list, cuz Karate Man rocks.

In the “God I’m glad I live in the US” file: Buy a used car, get a free rifle (plus water guns for the kiddies! yah!).

New studies suggest left-handed people don’t die sooner than righties (at least as long as they’re not in the military).

That’s about the only good medical news I’ve had in a while — over the past couple weeks, I’ve been going through the rigamarole of the first really comprehensive physical I’ve had in, well, ever. Somewhat depressing, in the “jesus I’m getting old” category. However, I had a nice long talk with my dad last night, and it turns out that most everything I’ve got, he’s had too, for the past 15 or 20 years. So, I guess I won’t be keeling over right away, or anything. Oh, and that story Mom used to tell about the postman must be false!

Okay, time to run off to work — code, code, code! I slacked on mail last night, so I’ll be getting back with you, you, and especially you later on tonight. Have a good one, everybody!

Minor meta: Corrected the date of yesterday’s entry.

Lor and I took in the Woody Guthrie exhibit at the Smithsonian on Saturday. It was really pretty amazing; prior to this, I hadn’t known very much at all about his life. As one very minor example, I didn’t realize that This Land Is Your Land was written as a sort of DIY/punk rebuttal to God Bless America. The exhibit is going on the road in about a month, so if you’re in DC check it out soon — if you’re not in DC, look for it at a museum near you.

Otherwise than our museum jaunt, it was a pretty uneventful weekend. Watched some tee-vee; read some books. Got caught up on the pile of miscellaneous paper-work that was piled up on my desk. Yay. Oh, and I tweaked out something in my back, and I can’t look to the right now unless I swivel my whole torso. Double yay.

Search engine query of the week: “nude pictures of ladies in suspenders”. (#14, and the first non-sex site to boot!)

Okay, so the 2600 gang lost the first round of the DeCSS case — unfortunate, but not surprising. Hopefully this will bounce to the Supreme Court soon, so that the more stinky parts of the DMCA will get booted to the curb. In the meantime, never fear — linking to the DeCSS code may be illegal, but linking to links to the DeCSS code is still a-oh-kay, near as I can tell. Therefore, this link => Put that in yer pipe and smoke it, MPAA.

Ohh, good mp3 player — The KLF’s “3 AM Eternal” just came up in the rotation. (It stands for Kopyright Liberation Front, in case you’re not down with the Mu-Mu.)

Via Jay ‘Baylink’ Ashworth, Wired News has a bit on IBM getting into the bioinformatics arena.

In this BBC story, Napster’s lawyer says:

“If users are not themselves infringing, then we are not liable for contributory infringement,” Napster lawyer Jonathan Schiller said on Friday after filing a written defence in the latest stage of the company’s court battle.

And when if they are infringing? This seems like a very stupid place to draw a line in the dirt, but IANAL and all that…

Initial reaction: Study says Americans worried about privacy on the ‘net, but too stupid and/or lazy to do anything about it. After reading more closely, however, it appears that somebody along the line missed some stats classes. Based on my reading of the data they present, the alternative explanation of two distinct populations (one concerned about protecting info and aware of how to do that; the other unaware and not too worried) also looks valid. Of course, I can’t be arsed to chase down the original study to find out…

A few home-grown PCR tips for Dan (offered in public in case anybody else is planning on playing along). I haven’t seen the particular book Dan mentioned, but I have seen some other short guides, intended for use by high-school biology teachers. For the gel electrophoresis step, you don’t need to bother with buying agarose — it’ll set you back a bit. Low-grade agar is fine, and I’ve even seen a protocol that used Jello (unfortunately, I don’t recall details for that one). Be careful on the visualization step — anything that stains DNA in a gel stains it in your fingers just as well, and is therefore likely to be mutagenic as all get-out. Ditto for the UV light that’s often used in visualization. Use a full-face shield if at all possible to avoid a ‘raccoon-eye’ sunburn — a welder’s face shield works well. The record player should work for a shaker, but you might be able to scrape by without the blenders. I’ve seen people use a modified stationary bike system for centrifuging (hint: most DNA extraction protocols have spins 2-3 times as long as they need to be. optimizing this step might be good if you intend to do this a lot.); you also don’t really need a vortexer. just hold you tube near the top (firmly) and then rapidly tap the bottom of the tube. If you’re doing it right, you’ll get a vortex (a ‘whirlpool’) forming in the tube. Have fun, and put up the gel pictures, if and when.

In the ‘blog-rolling category, warm wishes and a good thought in Fred’s direction.

Since I feel like a bit of a slug for not having done more this weekend (hell, I don’t really even have good links…), I offer up a short photo-essay about my recent shaving:

with the beard
(sorry about the flash)

(one of the reasons i hate shaving)

without the beard
(who the hell is this?)

Okay kids, see you back here tomorrow…

Lor’s up in the loft, and she’s got the Beautiful Girls soundtrack playing, and we’re singing along…

Minor Rant: Last night, at the weekly ‘Get Drunk with the Systems Crew’ gathering, I ended up agreeing to take over some responsibility for the Fellows Committee website, because one of the people who had been carrying that bag is leaving for greener pastures. The site is moving from it’s previous location on an FTP site to a real hosting environment, but there’s been some confusion between the people doing the work and the part of NIH that’s doing the hosting. Long story short, I ended up on the phone today with a person who works in the hosting section. It’s really a bad sign when they’ve turned off FTP out of security concerns, but they’ve never heard of SSH or scp. It’s a bad sign when the ‘recommended’ way to move files to the site is via SMB shares, and the person has never heard of Samba. It’s a bad sign when I ask where the raw log files are, and the guy doesn’t know, and can’t understand why I’d want them in the first place. I’m pretty sure this person is pulling down a lot more money than I am; why am I the one with the knowledge? Why did I take the time to explain what SSH is, and what Samba is, to this obviously Clue-challenged person? Probably the same reason I keep answering my co-workers’ questions about shell scripts. sigh Oh, and after all the “FTP isn’t secure because it transmits the password in cleartext” crap, how do they send me the user id and password? Unencrypted email. I’m clearly in the wrong line of work or something.

For all you high schoolers thinking about where to go to college, the top party school list is out.

There’s been a successful pig cloning. Big news, because pigs are the primary candidate species for xenotransplantation — putting organs from other species into humans. As a nod to this, the clone’s name is Xena.

All is not rosy in the xenotransplantation world, however. A study suggests that pigs might harbor retroviruses, which would definitely put the kibosh on any transplant efforts.

Things are starting to get ugly in the Verizon phone worker strike. Two union members from New York ended up in the hospital after cutting an electric line. They thought it was a phone cable, see…

There’s going to be a proteomics conference in DC in the near future. I might have to look into going to this.

Couple of new Open Source content management systems: Webmake (from Justin ‘Sitescooper’ Mason) and eGrail. The latter looks like overkill for my needs, but the former might have some ideas or code that I can steal^Wborrow.

Speaking of CMSs, I’ve not been doing too much on BOP, and I need to get back into that. I’ve just been so strapped for time, and that was the first thing to get sacrificed. I had another look tonight, to try and figure out what I need to do next, and I think it’s time to start using it, and flesh out the skeleton in that way. I suppose I should make an effort to do the BOP site, and maybe write some documentation, and then figure out what I need to do next. Of course, any of you out there are encouraged to download and give feedback too — just make sure to get the CVS sources; the tarball is totally out of date.

It’s looking like there might be a small DC-area blogger gathering to see the Guthrie exhibit at the Smithsonian tomorrow — if anybody out there wants to tag along, give a holler.

Hope you all have a good weekend, and I’ll see you back here on Monday, if not before.

Bringing you an early morning update today; listening to the Mirah disk I ordered the other day. As expected, it’s good — recommended, if you’re into that indiepop stuff.

Now that I’ve found nodalpoint, I know what to do with all that comment posting energy that’s been seeking an outlet since K5 closed. (Actually, I didn’t find it, the site’s founder contacted me, but you see what I mean.) If nothing else, you should go and get an account, cuz just maybe this is the new K5, and this is your chance to get one of those all-important low-numbered user IDs.

Webcam at the Debian booth at Linuxworld Expo.

Blah, blah, blah, Linuxworld Expo, blah, blah, Gnome everywhere, blah, blah. Maybe this means I’ll be able to get it to build on the Ultra at work.

Cool: crystal structure of Ebola virus shell protein solved. Not cool: no picture.

Protesters had a CriticalMass in LA yesterday night. I’m of two minds; I sympathize with the message, but I know I’d be pretty pissed if I couldn’t get home after work. OTOH, if one of these happened in the morning, I’d be much less pissed about missing work

Observation: whoever came up with the name ‘ecstasy’ was an untapped marketing genius. I’ve never taken any, but, come on — who doesn’t want a bit of ecstasy in their life? I predict future drugs with names like nirvana and bliss.

Bored by the possibilities of extremophiles from hot springs? Or, more likely, are those organisms now too encumbered with various patents to be worth chasing? Look to the dirt.

A panel of ‘expert’ UK scientists has come out in favor of limited cloning of humans. By ‘limited’, they mean therapeutic cloning (stuff for the purposes of medical/research uses), as opposed to reproductive cloning (i.e. Mini-Me).

As I think I’ve mentioned, I run Junkbuster to filter banner ads and unwanted cookies and such. Occasionally, I get to see something interesting (~250 kb jpg).

Okay, time to rush off to work — probably won’t be an update tonight/tomorrow, so I’ll plan on seeing you back here Friday.

Okay, I’ve got some things I’d like to say tonight, but I’m also still really behind on email. So, I’m going to deal with my backlog, and then update here if it’s not too late. For reference, it’s now 10:21 PM, and I’m starting in on the mail bag…and it’s now 11:35, and I’ve finished. Well, mostly — there are still a couple, but I’ll get those tomorrow. I spend way too much time writing email — I seem to feel the need to make sure each one is perfect, or something. (Right now, my regular correspondents are saying, “Yah, right!”) Re-read the mail, write the response, re-read the mail and the response, spell check, and sign, so that’s easily 10-15 minutes per mail. I am enjoying the 3 or 4 long-running threads I’ve got going with different people, however.

Like everybody else, I thought Legal Tips for your ‘Sucks’ site made for interesting reading. The only times I’ve really been tempted to start a “FOO Sucks” site, the domain names were already taken — US West in one case, ABF in another. If I’d known that redirected to the main ABF site, I would have been much more cautious about trusting them with my money or my stuff, which would have been a good thing. I mean, I can see registering the domain name, just to get it out of circulation, but redirecting it to your main site? Please.

NewsForge looks interesting, as does Transhuman.

MonkeyFist has a nice rant about the criminalization of political dissent in America. Certainly, reports in the aftermath of the Philadelphia protests don’t sound good. We’re headed down a dangerous road here; when people feel their voice has been taken away, we’re going to start to have real problems.

New bio-journal: EMBO Reports.

Here’s an unfortunately dystopian overview of Vernor Vinge and his ‘singularity’ hypothesis. I find the singularity concept intellectually attractive, but I’m not sure whether I want to be around to see it happen.

potato is out. And there was much rejoicing in Debian land…

I was going to stick my nose in somewhere it really doesn’t belong, but upon further reflection, I’ll just keep quiet. Ultimately, all I’d accomplish is pissing off one or more people, and I don’t really want to do that. I will say that I think Steve and Mike have pretty much pounded the whole military readiness issue into the ground, broken it off, and set fire to the remaining stub, and I sorta wish they’d get back to talking about other things. But that’s just me, wanting to be entertained.

itch fest

| No Comments | No TrackBacks

Lor and I went to a barbeque this weekend — and now my legs are covered in bites. I’ve even resorted to cortisone cream, which is unusual with me. The ones on my legs I can ignore most of the time, but the ones on the backs of my hands aren’t making this typing any easier…

This weekend, the 100th annual hobo convention was held in Britt, Iowa. Anybody think there’s going to be a 100th weblogger convention?

Reliability of Statistical Procedures in Excel. One-line summary pullquote:

Excel’s statistics add-on pack is riddled with potential disaster areas, and since it has been subjected to the best analysis available in the world and found to be wholly lacking, the only applicable words are ‘avoid’ and ‘plague’.

Attracted to Gnus, but can’t stand using one of the emacsen? Give VINE (Vim Integrated News and Email) a go.

Don’t forget to vote for your choices in Linux Journal’s Readers’ Choice Awards.

Okay — that’s it for tonight. I’m terribly behind on email, so if you’re waiting for something from me, try to be patient. I’m getting to your mail as fast as I can…

Pretty standard couple of days — nothing to exciting of personal note. On to the links…

A couple things for my wife:

First, a computer glitch at Northeastern has lead to an incoming class 600 students larger than expected.

Second, Lor and I were discussing the upcoming election the other night, and she was expressing a fear that not voting for Gore could lead to a Bush victory, and the subsequent erosion of some rights we both believe in, like the right to choose to have an abortion. So, I think she’ll find Feminists for Nader an interesting read — and you probably will too.

There’s going to be a structural biology meeting in Fredrick in September, for all you bio types in the area.

And speaking of which — I’m pretty much an idiot when it comes to looking at protein structures, but some of them are quite pretty. I especially like the domain alignment in the background; this is outstanding information presentation, especially considering the standard of the field.

I discovered Genome Biology today — it’s a new journal affiliated with the BioMedNet portal. The first issue had some decent stuff, including this excellent article by Andrew Murray talking about the changes genomics is going to bring to the field of biology.

Joel’s Guerrilla Guide to Interviewing. People in academia don’t really do these extensive sorts of interviews, so this was quite eye-opening for me. I wonder if bio-tech industry job interviews are this focused and purposeful — anybody care to comment?

Here’s a review of the new Mirah disk. I’ve heard three or four songs off this on, and really liked all of them, so I went ahead and ordered it.

What job is right for you? Top five for me: doctor, engineer, geneticist, lawyer, researcher.
Via Fresh Hell.

Hope everybody has a good weekend; I’ll see you back here on Monday.

Today’s update is actually being done in the morning, before I dash off to work, and is consequently a bit less verbose than normal…

Emacs CSS mode. Here’s some documentation.

There’s a new issue of the BioInformer up. Some interesting stuff there that I might come back to later.

The BBC has an article about a technique for using a digital movie camera to print microarray chips. This is pretty old news — I gave a talk on this paper back in January or February of this year. Still pretty cool, and potentially could make microarrys much more usable, by greatly reducing the price.

Okay, off to work now — see ya tomorrow.

Had to go to the doctor today, to get a ‘new patient physical’ for my new insurance coverage. I have to say, there’s really no better way to start a Monday morning than having a stranger wearing rubber gloves grab your wibbly bits and tell you to turn your head and cough. At the very least, you can be pretty sure it’s going to be uphill for the rest of the day…

Oh, I want one of these: “curb ‘door-to-door disciples’ in your neighborhood” with this sticker.

Steve’s searing slams about recent political events here in America pretty much nail shut the coffin for anything I’d be saying, so I’ll just save you the time, and point to him instead. I think Mike is probably going to be the anchor man for the other side, but he’s rooting for somebody I’m not even considering, so it’s harder for me to get into what he has to say.

I’ve been on a big Woody Guthrie jag since Mermaid Avenue came out, so this interview with Billy Bragg, discussing the history of the project, was a must read. The exhibit at the Smithsonian should be back open now; any DC area bloggers want to check it out this weekend?
(Copped from Looka.)

Congrats to Graham on the new digs.

Contrarian view of the ‘golden rice’ issue. While there’s nothing I can really argue with in the broad issues raised, there are a couple nits I’ll pick:

The fundamental problem with genetic engineering from the very beginning has been the absence of anything like an ecological approach. Genes are not the unilateral “controllers” of the cell’s “mechanisms”. Rather, genes enter into a vast and as yet scarcely monitored conversation with each other and with all the other parts of the cell. Who it is that speaks through the whole of this conversation — what unity expresses itself through the entire organism — is a question the genetic engineers have not yet even raised, let alone begun to answer.

This is simply not true — while we haven’t ‘begun to answer’ the question, it’s certainly being raised — that’s the whole point of genomics and proteomics. Figuring out how genetic networks are perturbed by the introduction of new genes is a critical question, and lots of effort is going to devoted over the next decade or two figuring out what the rules are (or if there are generalizable rules at all).

But without an awareness of the organism as a whole, we can hardly guess the consequences of the most “innocent” genetic modification. The analogy with ecological studies is a close one. Change one element of the complex balance — in an ecological setting or within an organism — and you change everything.

Not quite true — you don’t actually change everything; you potentially change everything. This is actually worse, because the problem is that many or most of these potential changes are very small and not terribly important to the big picture — but some of them are. Figuring out which is which, and how to fix them (or not introduce them in the first place) is the Big Question.

And then there are the other Big Questions: will the use of the ‘golden rice’ help more people than it hurts? Even if we’re pretty sure that the long-term effects of the use will be negative, does that justify blocking this use altogether, thus (potentially) eliminating some short-term positive effects? Finally, does our (presumed) greater understanding of the technology and the consequences of using it give us any right to tell Asian people whether or not they should use it?

(I nicked the original link from Rebecca’s Pocket, BTW.)

Here’s a Scientific American article on a different type of gold: The Bioinformatics Gold Rush. I really like the closing quote:

Systematic improvements will help, but progress—and ultimately profit—still relies on the ingenuity of the end user, according to David J. Lipman, director of NCBI. “It’s about brainware,” he says, “not hardware or software.”

A couple of meeting announcements for the bioinfo people in the crowd: RECOMB 2001 and Transcriptome 2000.

Jay ‘Baylink’ Ashworth sent along a link to his ePinion of Spider’s latest, which I mentioned yesterday. His opinion is basically the same as mine, with the exception that I don’t tear up at the end of To Sail Beyond the Sunset, but rather at the end of The Moon is a Harsh Mistress.

Okay, so I said above that I was going to stay out of the politics thing, but I do want to note one interesting thing. Over at (where, umm, I only go to read the articles. Really. Ahem.) Sharkey notes that Lieberman, Gore’s new running mate, was the leading force behind some recent efforts to ban various video games, in the name of ‘anti-violence’. I’m also sure I won’t have to remind too many people of my generation that Tipper Gore, Al’s wife, was one of the leaders of the PMRC effort of the 80’s — another attempt to get media banned in the name of ‘decency’. Interesting coincidence, or sinister plot? Meanwhile, on the other side, we’ve got Bush, who apparently used to like to party a bit, and Cheney, who has an openly gay daughter who will be helping with her father’s campaign. What the hell is going on here? I think that both parties, in their mad-cap rush to the so-called ‘center’ of American politics, have over-shot, and ended up in enemy territory. Got that? Black is white, bad is good, down is up, cats and dogs, living together…sorry, lost it there for a minute. Anyway, what I’m trying to say is that the coming election appears to have been scripted by Hunter S. Thompson, on one of his less together days, and more frighteningly, nobody seems to have noticed, or to care.

So, what am I going to do? Personally, I’m leaning pretty hard towards Jorn’s advice. It’ll make for a nice change from (a) holding my nose and voting Democrat or (b) voting for good ol’ Hopeless Harry Brown.

Okay, that’s it for politics for awhile — pinky swear. See y’all tomorrow…

Very minimal update today, and journal-y at that, I’m afraid. Not so much surfing time this weekend…

I did finally do some BOP coding. It’s pretty close to what I was aiming at for a 0.1 version. I just need to do some code clean-up, some doc writing, and then redo the BOP site using the tool, and I’ll release. (I know the wait has been killing all 2 of you out there…) Maybe then I can re-design this site…

I also went book shopping this week-end, and picked up the third Camel, which looks like it should be fun to blast through and Spider Robinson’s latest, Callahan’s Key. Most of yesterday was spent tearing through it; it was a pretty good yarn. If you’re a Spider fan, you’re going to buy it anyway, and if you’re not a Spider fan, this is not the one to start with, anyway, so I’m not going to go into it any more than that.

I’ve been sitting here for 10 minutes trying to come up with another paragraph or two of pithy and/or humorous text, but it just ain’t happenin’. Come back tomorrow; it’ll be better.

Hey, what happened to my week? I really did mean to update a bit more often… Plus, BOP hasn’t been getting the attention it needs, either. When Lor’s traveling, I have to shift my wake-up time an hour or so forward, and that just really seems to kill everything except work. I guess I should just make the shift all the time, but it’s not really what my body wants to do.

This press release describes the testimony of one of the EFF’s witnesses on the last day of the recent DeCSS trial. Cam linked to the actual transcript last week, which was a pretty good read, but this press release does a nice job of summing it up. Basically, the line between ‘expressive’ or protected speech and computer code is pretty darn thin — which is something that most code writers seem to grasp, but seems to be poorly understood by the judicial people reviewing cases of this nature.

MSN sites barf for me, because I’m running the Internet Junkbuster, a personal ad-filtering proxy. I’m not even blocking things all that aggressively — which makes this all the more annoying. I suppose I could track down the offending line(s) in my config files, but I think I’ll just quit linking to MSN stories instead.

The Post had an excellent article this morning about genetically engineered trees.

This series of photos from the recent Open Source/Perl Conference is awesome. Really nice uses of perspective tricks to capture some amazing images of Big Names and ordinary folk.

In the ‘unintended consequences’ column, bootleggers are using assistive devices intended for the deaf to produce high-quality recordings of live shows. In the long run, this could be bad, especially if it results in the devices becoming unavailable. That said, the geeky side of me is pretty impressed — this is a cool hack.

After all the “Mozilla sucks”/”No it doesn’t” hoopla over the past week or so, I decided to give the lizard another chance. The Debian packages aren’t working for me at the moment, so I grabbed the M16 tarball and built my own. I’ve done this before, but I must have done something different this time — what I’ve got is much more stable, faster, and has a smaller memory footprint than the past times I’ve tried it out. I think I’m going to switch to using it full-time. This is a pretty big jump, however, because I’m really, really bad at remembering site passwords and stuff, so re-registering for things is probably going to be a major pain. It seems like it’ll be worth it, however — it’s faster than the Netscape I’m using, and on the strictly eye-candy tip, it supports a lot of the nifty CSS stuff that Netscape doesn’t. For instance, until tonight, I didn’t realize that that box on the left side of did that nice roll-over light up trick.

Stim looks somewhat interesting. What does it say about me that, given a choice between the “ultimate men’s magazine” and the “ultimate women’s magazine”, I initially choose the latter, and only check out the former as an afterthought?

Kris is swimming around again.

Okay, that’s probably it for this week — if all goes as planned, I’m going to get BOP to a usable place this weekend, and start using it for this site as a bug-busting move. This might even result in (gasp!) a re-design. It hasn’t been easy, being green, and I’m pretty sick of it. That’s good — it’s motivation to code. See y’all on Monday.

Lor's leaving on another business trip. Her flight out of BWI is at 7 am, so her shuttle pickup is at 5 am, so she got up at 4 am, so I got up at 4 am, and now I'm writing this. Woo.

Slashdot: Why Bother? Why indeed. Near as I can tell, every web-based discussion board is attempting to re-create Usenet, for an audience that (for what ever reasons) can't handle actually participating in Usenet. Not only that, but they're doing it badly, and failing, to boot.

In an intentional juxtaposition, has anybody noticed a lot of negativity in the Open Source/Free Software/Linux communities lately? Mozilla's getting slammed by all and sundry, the above article, lots of flames on kernel-traffic. Maybe it's just a self-evaluation phase everybody is going into at the same time -- that would put the Perl 6 stuff in this same phenomenon as well.

It would be really nice if Advogato had some way of tracking certain diary pages, so you'd know when people updated. For example, I'd really like to know when Ewan Birney puts up a new entry. I suppose I could just set up some sort of spy... Oh! Or, if some kind soul wanted to, they could write a generic Sitescooper frame-work that you could plug a user name into.

From the latest RISKS digest, MSIE is re-writing HTML source to remove various non-kosher Microsoft-isms like the use of '\' in path names. The problem is, it's re-written even when you do 'View Source'. This is exactly the type of thing that (a) makes spec-minded techies foam at the mouth and rave uncontrollably and (b) gets your company broken up by anti-trust regulators. On the other hand, I suppose it's nice of MicroSoft to keep reminding us why they should be disassembled. has a tutorial on CVS.

Polymorphic resume (hit reload...)

If you've been to Ikea, you should find Mandrake's 7.31 entry fairly funny. If you haven't been -- well, pretty much everything's accurate. Except he left out the mind-numbing effect of caused by over-exposure to Danish modern design, and the hangover-like cognitive static that occurs when you stumble back out into the world, and are forced to deal with objects that haven't been designed by a team composed of half Finnish architects and half Swedish semioticians.

Incyte is trying to get into the BSP business (that's bioinformatics service provider, in case you didn't know). The hook is that basic things are free; I guess they think people will then be willing to pony up for increased access. It'll be interesting to see if this plays; I think this is the move that Celera should have been making for quite some time. (Watch out for pointless Flash intro on the Incyte page, BTW.)

Spam report HOWTO. I've been getting a lot less spam since I started reporting it back to abuse@FOO and postmaster@FOO. Oh, and black-holing the domains that bounce mail to those addresses.

Bookmarking for later use: the U. of Iowa alumni finder. Are these types of services getting to be pretty universal, or do people just not lose touch anymore? I'm only in touch with a couple of people from my college days, and I think one of the reasons is that email and 'Net access didn't really start to peak until the year after I graduated. If you knew me when I was at the UI, drop me a line.

Too cool! Mutant bacteria from space that live off of human waste products (skin flecks, exhaled moisture) and other substrates found in space habitats, like quartz glass and enamel-coated titanium.

For later reference: " is a Yahoo-like Webdirectory for bioinformatics."

The RIAA doesn't want you to have those mp3 files, so maybe you should just give 'em back.

Boy o boy, is it going to be a long day -- see y'all back here tomorrow...