April 2000 Archives


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Hey, New Order. It’s been a while since I’ve had this disk in the player. One of the nice things about moving is you (re-)find things you’d forgotten about.

The latest in the parade of “My, but Heinlein was right a lot, wudn’t he?”: Companies Swoon Over the Moon.

The next couple of these were nicked from the always excellent rc3.org:

First, news that the governor of Maryland (my new home state) signed UCITA into law, paving the way for this scene in a future Oz:

Large, scary black man: What you in for, man?
Small, scared white man: Um, I bought a computer, and then complained about the OS in a chat room.
Large, scary black man: (smiles a special “Hello, new bitch” smile)
(fade to black)

Of course, the Washington Post had a rather, um, unique take on the story, which was reported under the headline: Glendening Signs Measures Boosting Internet Commerce. Yah, it’ll be a ‘boost’, that’s for sure.

Second, in other “shut up and drink yer Keystone” news, the FedGov is fixing to make linking to sites with drug-related information a felony. Because the past programs that have clamped down on the spread of on-line information has been such huge successes, and they’re starting to get really, really good at it. I expect this sort of thing from Hatch and Ashcroft, but I hope California voters remember Feinstein’s involvement in this mess when it comes re-election time.

Demonstrating that it’s not just this side of the pond, the EU is looking to ban anonymous remailers. Because of the past successes in elimination of undesirable behaviour on the ‘net by meatspace bans, no doubt.

Whew, thought I had more — but maybe it’s good I don’t, as I seem to be getting a bit worked up. If all goes well, the new and improved GeneHack should be rolled out sometime this weekend. Geez, I hope so — I’m so sick of the current look, and feel like I’m getting really stagnant. I need to get some new link sources, put on a fresh face, and kick it back up a few notches. See ya Monday, and hey — be careful out there!

Augh — it’s gonna be a short one today, as I spent far too much time in the sooper sekret off-week #BlogIRC chat. I’ll make it up to you tomorrow.

Salmonella-Resistant Cows: This is so breath-takingly short-sighted that I’m stunned — I mean, how stupid do we have to be? Giving antibiotics to food animals, or to people who don’t actually need them, should be grounds for a medium-class LART-ing — resistance just develops too fast, and I’m pretty sure we’re pulling from a finite space when it comes to developing new ones.

There are some more screen shots of Evolution, the Outlook work-alike that HelixCode is developing for Gnome. I’ll give it a test run when it’s ready, but I’m not sure anything can replace Gnus+BBDB.

This country just gets more and more scary all the time: Mistrial declared after jurors decide conviction with coin toss:

Jury foreman David Melton told The Courier-Journal for Tuesday’s editions that jurors decided to flip a silver dollar to avoid a hung jury. Because all agreed on the coin toss, they thought it was legal, he said.

Mental note: check out this paper, on standardized tests to evaluate genome annotation software. Sounds like things are getting dramatically better from the numbers quoted in the article; they weren’t nearly that good on the last evaluation I read (a couple of years ago).
Nicked from the snowdeal.org bioinfo section, which should already be on your daily rounds if you’re a bio-head.

I wonder if I can get something together in time to go to the Bioinformatics Open Source Conference? I should probably stick to a more biological meeting, at least this year.

In the Crawling Out From Under a Rock section, Salon covers Vigor, the MS Office-ish paper clip for vi. Hmm, it seems like some sites have covered this before

Dan’s out of town, so I’ll point out that today’s Keith Knight addresses that always thorny issue of what kids are wearing to school these days. Aren’t the uniforms supposed to solve this problem?

I’m getting about 10 spams an hour — well, actually, I’m getting about 10 copies of the same spam, because somebody misconfigured their mass mailer. It’s in Chinese, like ~75% of the spam I get. sigh. See ya tomorrow.

Well, the cold finally caught up with me, and I took yesterday off, from ‘blogging and from work. I hate to take sick time so soon after starting a new job, but I didn’t think infecting my co-workers was the best idea, either.

Before I collapsed, I managed to make it to the DC LUG Installfest on Saturday. It was fun; I got to meet quite a few Linux people in the area, and I got to play with some hardware that I was unfamiliar with — older Sun kit. It’s not too bad, either — apparently the University of Maryland has a lot of surplus, so I might have to check that out. I also picked up a small Tux doll, so overall it was quite the day.

Tigert has an older Gimp tutorial up on his site, which gets into the basics of using layers, and some of the other Gimp tools. It also looks like it might be useful for PhotoShop users, if you can translate between the different command sets.

Mike “Larkfarm” Gunderloy has up a page listing software engineering resources, which I’m putting in here so I can find it when I need it.

Dino is a molecular structure viewer that reads in quite a few different file formats and then outputs pretty pictures. My boss was looking for something like this the other day, so I might have to point him at it, and see what he thinks. (He knows a lot more structural stuff than I do.)

I don’t remember what ‘blog I saw this on, but this girl’s-eye-view comparing Ferris Bueller and Lloyd Dobler was cool in that rose-tinted nostalgia way. From my perspective, I never wanted to be Ferris Bueller, but Lloyd Dobler — Lloyd was an inspiration.

The Music CD Librarian is a Perl script for indexing your CD collection. You run it, drop each disk in the drive, and the script does a CDDB lookup and stores the results in a MySQL database. Pretty cool, if you’re got the patience to run through all your CDs.

Salon interviewed E. O. Wilson last week. Much interesting content about spirituality and conversation.

This planet is not in physical equilibrium like the other solar planets. It’s in a shimmering disequilibrium that comes from vast arrays of species and plants and animals and microbes living on a thin film.

Salon also has a review of a biography of Kinsey, of Report fame. I hadn’t realized he was such an… um, interesting character.

Feed is running a special issue focusing on DNA, and they stretched the rules enough to include an article on software breeding, where genetics and programming intersect, or cross-pollinate, or something. I’m not sure I buy Danny Hillis not understanding the sort algorithms he’s bred — you could at least do analysis to find out if the different isolates are using similar sets or series of opcodes, for example.

It’s still coming. I’m feeling down, but I’m not sick enough to stay home from work. (Plus, I’d feel guilty about bailing on work on Friday and then going here on Saturday.) Being sick sucks, but actually being able to feel yourself getting sick is worse.

Murphy loves to take down the high and mighty. Okay, actually, nobody’s been “taken down”, but the people in the article are correct; Venter would have slammed anybody else who did this. I wonder if this incident will result in any calls for increased scrutiny when (and if) Celera releases the human sequence?

Hmm, while I’m thinking on that topic: I wonder how it happened? Contamination with vector sequences was a problem, back in the day when large scale (and even small scale) sequencing was first starting, but (IIRC) there are now automated filters that flag sequence that appears vector-like. That’s clearly not what happened here, either — I wonder who screwed up? Also, I wonder how much human sequence was submitted, and what genes it contained, and what impact that will have on their future patent-ability? I smell a due diligence nuisance suit…

I spent most of the day working on a little paper database, to keep track of the papers I’ve read. Nothing fancy (yet), just command line driven Perl talking to MySQL. This intro to DBI at perl.com was quite helpful a couple of times today, so I thought I’d stick it here, so I’ll remember it in the future.

I found that via Perl Monks, which was slashdotted a couple of days ago. It looks like it could grow into a useful resource, and it’s got one of the most interesting “moderation” systems I’ve come across. I’m not going to try to explain it; you’re going to have to look for yourself, but the D&D’ers in the audience will be pleased.

Today’s linkage made possible by the letters P and V, and by Deepleap, which I’ve switched to for my remote bookmarking needs. I do wish they’ve offer an option to directly bookmark a site, without having to hit that save button…might be time for some email feedback…

Vermont’s looking like a nice place to live. Now we just need to get them to recognize polyamory groups, and everybody can be happy.

Have some type of bioinformatics question? Maybe TAMBIS can help. It’s an ambitious looking project; I wish I had the time to play around with it and see how well it works.

Also in the “looks like fun but I really don’t have the time now”, Darwin, an “interpreted computer language for the biosciences”.

Well, part of the message is good, but some of the things Leroy Hood is quoted as saying in this Wired article are a little bit scary:

All of the details that most of us memorize in medical school — you don’t have to learn those things. They’re going to be in your computer.

Makes “Blue Screen of Death” take on a whole new meaning, eh?

As a culture, we’ve been struggling with technology running ahead of the law since, well, forever. Are we going to do any better when the tech is biotech, concerning our own genomes, our own bodies? Some researchers say we’d better.

Ever wonder where the animals on the O’Reilly book covers come from? Here’s a nice article that explains the history, and the process behind the Animal Books.

Thought for the day: I really need to revise the Daily Dose pages — I’m really getting into a rut with my reading habits. I also want to start reading fewer ‘blogs (or maybe the same number of blogs, but less often), and more primary sources, at least for a little bit. Maybe I’ll get to that this weekend…

I wonder if my difficulty with updating the ‘blog is due to the fact that I’ve been spending the majority of the last 3 or 4 days at work trying to build various bits of Gnome as a non-root user on a Solaris machine? (I’ve been mostly successful, but there are a few bits that still aren’t working.)

Laura went to New Orleans last week for a meeting, and brought back a nasty cold. She was here for four days, was sick as a dog for the first two of them, and has now gone off again (to Chicago this time), but she did manage to pass on her germs to me — I can feel a tickle at the back of my throat, and I’m sure it’s only going to get worse. Lor, if you’re reading this, thanks bunches!

The window manager formerly known as sawmill has had a name space collision with a httpd log analyzer. Jump on over to sawmill.themes.org and vote in the poll to pick a new name.

While I’m on computer stuff, I’ll point to the Debian Diary, which is a ‘blog-ish system log cum journal chock full of useful info about configuring Debian installs. When I get my DSL installed, I’m sure the iptables info will be helpful.

Feed magazine is doing a special DNA issue, apparently because of Celera’s recent (widely misinterpreted) announcement. I haven’t had time to look at the whole thing, but this article by Jeff Howe hits on quite a few of the interesting issues being raised in the wake of the sequencing efforts.

Okay, I think I’m going to try to catch up on email (yes, still). Tomorrow night is BlogIRC night — hopefully I’ll remember to show up this time! See y’all later.


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very time I think I’ve got a handle on things, something else pops up.

We went out Saturday and paid a visit to Ikea, to replace some of the furniture that was broken in the move. That night, I assembled some of the stuff we brought home with us, and most of the rest after it was delivered on Sunday. I think there’s still one bookcase left to put together, but that won’t take too long, as I am now an Ikea master-builder. We didn’t get that much stuff; but I was working slowly, so the final product would look decent, and after I built each piece, we had to move things around so that there was room to assemble the next. Hopefully we now have enough places to put things that we can put most of our things someplace, so we don’t have to keep stumbling over them.

I was also very excited to find out that the Potomac Mills outlet mall has a Lego outlet store — my desk now features a Star Wars land-speeder built out of Lego, complete with Luke and Obi-Wan minifigs. That pretty much made my whole weekend.

I had been planning on going down to the protests on Sunday, but I had to wait for the delivery of the furniture, so I wasn’t able to go. I think I just officially became a member of the bourgeoisie — I can see the conversation now —
“Gran’pa, weren’t you in Washington during the Protest of 2000?”
“Why, yes, I was”
“What did you do? Did you get arrested?”
“No, I was too busy assembling pre-fab Swedish furniture to go to the protests — but I had them on CSPAN the whole time!”
“You’re lame, Gran’pa!”

Why can’t I get to Running Tally anymore?

I think this ad campaign can be judged a success. The only potential cultural artifact remaining is an alt.dollar-amount.dollar-amount.dollar-amount.priceless newsgroup.

Okay, that’s it for now — I’ve got more organizing and unpacking to do (yes, still). I just wanted y’all to know that I’m still out here, and planning on getting back into gear Real Soon Now, so keep checking back — there will be a real update one day…


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So much for that whole “back in the saddle”,”updating every day” nonsense, eh? Still way too much going on with getting in the groove at work, and getting things set up here. As Jessamyn notes, three moves does equal one fire. Maybe a fire and a half if the moving company breaks a bunch of your stuff.

Things should start to settle down a little bit; I’m all set up at work, and we’ve gotten ~90% of all the personal paperwork stuff done (car, insurance, etc.) Maybe I’ll actually have time to finish the content management stuff I was working on, and redesign this site. I’m getting really tired of olive green.

If you care at all about personal privacy, libertarianism, cryptography, or the nature of the social contract, you should go read this Salon article. I’m not going to attempt to summarize it, and I’m not even sure what I think about it — still too early. The author does seem to have picked up a libertarianism == voluntary hermitage meme somewhere, and I don’t think that’s all that accurate, which is making it difficult for me to analyze the rest of the commentary.

The cphack case continues to develop. (See the links at the bottom of that page for history, if you don’t recall what this is about.) I’m still confused about this — Mattel seems to be hammering on the point that cphack allows people to bypass the filters. So, why doesn’t somebody take the code, remove that ability (while preserving the decrypting ability), and then release cphackLite? IANALawyer, but it seems like that should be entirely permissible under the terms of the GPL.

Wendel left me out. Sniff. I feel so small now.

The weblog eGroup is no more, but long live Weblogs_reborn. Ah crap, that reminds me, I missed another BlogIRC — and this time it was just because I out and out forgot. Damn.

Couple of European meetings coming up: Genome Based Gene Structure Determination in June, and the 15th German Conference on Bioinformatics in October.

Sigh. Still haven’t caught up on the email, either. And this desk I’ve been forced into using is way too high, which is killing my wrists. Hopefully I’ll be able to get out this weekend and get a big table to use as a worksurface, and then I’ll be able to rip right through those mails, and write that code, and, and…

Anyway, I’ll see you kids back here ‘round Monday or so. Thanks for sticking around during the rather sorry interlude of the past couple of months.

First day at work went okay. Got the Ultra10 late in the day; should have the Mac (a/k/a the typewriter) tomorrow. Got most of the running around and paperwork type stuff out of the way too — just the health insurance stuff remains, and that’s getting taken care of tomorrow. Now I just have to truck all my stuff into my cube…

Forgot to mention that I watched Forces of Nature Sunday night. It came on right as I was sitting down to eat dinner, and it was good enough that I watched the whole thing, even when I shouldn’t have. Nice, light, romantic comedy fare.

New apartment thought of the day: Having a dishwasher is good!

I don’t recall where I spotted this URL — could have been in an ad in the Post, or possibly on TV — but I of course had to have a look: whybiotech.com. Nothing too exciting. Somebody please tell me I’m not the only one who gets immediately turned off by a site that has ?s instead of ‘s…

Okay, all you people taking the shark cartiledge pills can give it a rest! Turns out that sharks do get cancer, even cancers that occur specifically in cartilegenous tissues.

Taking the polyA/polyT tails off of cDNAs before doing subtractive hybridization results in increased yields of low abundance expressed sequences. How long until the patent is awarded? (I’m sure the application has already been filed…) Bonus points for guessing what name Perkin Elmer will slap onto the kit.

Francis Collins took some of the wind out of Celera’s sails today:

You should not take at face value any claim by any group for at least two years that says ‘we have finished sequencing a human genome sequence.’ It will not be true,” Collins said prior to a conference in Vancouver, Canada, on Sunday.

The BBC also has a version of the same story, featuring the same Collins quotes, but perhaps a bit more balance in the overall tone. The point that Collins is making is an important one: when dealing with sequencing projects (and especially shotgun sequencing projects), saying the sequence is “done” has very little information content.

Hmm, lets see if I can’t clear out some of the links from the recesses of my bookmarks file…

Emacs Package of the Week. Ahh, I can see it now: emacs.themes.org…

So You Want to Run Your Own Server is part of Philip and Alex’s Guide to Web Publishing, which looks well worth working through. Once I get my DSL line, I’m planning on doing so serving, perhaps even moving genehack.org to a machine on my home network, so I guess I should start to look into these types of issues…

The life and times of GnuCash. Anybody out there seriously using this? I’d like a Quicken replacement, but don’t want to invest time in switching over if the program isn’t up to spec.

Savings Bond Redemption Calculator. I’ve still got some Series EE bonds stashed away, so I should save this link.

Apologies to those of you whom I owe mail to; a recent Debian upgrade broke mail sending in Gnus, so I’ve had to switch to mutt for mail composing, and it’s slowing me down. I am catching up, slowly.

Whew! It’s been quite a long week! I’ll spare you most of the personal stuff; we’re mostly moved in, although the loss of the two desks (see below) is turning into a real PITA — it’s hard to work when there’s no surface to work on. I’ll be faxing the claim report to ABF tomorrow or Tuesday — we should be done unpacking by then — and I’ll let you know what I hear.

Tomorrow (it’s still Sunday night as I write this) is my first day at NCBI, my new workplace. I’m pretty excited about finally starting, seeing where I’ll be working, getting my computers set up, and all the other cool new job stuff. More about that tomorrow probably.

I used the RideGuide to figure out what bus to take to the train station tomorrow — it looks like a fairly useful site for public transportation users in the metro DC area, so I’m noting it for later.

Wow, what happened to all the stuff I thought I had bookmarked? Looks like it might be a short day…

Eric “snowdeal.org” Snowdeal sent in a link to a Wired news article about Lincoln Stein, Napster, and data sharing in large-scale sequencing projects. Most of you know probably know Lincoln Stein as the Perl CGI.pm author, but he’s also a fairly famous molecular biologist/bioinformatician. If I say anything more, I’ll sound like a slavering fanboy, so I won’t. But go read the article; it’s cool in a cyberpunky/”the street finds its own uses for things” kind of way.

Robert A. Heinlein: A Reader’s Companion has finally been released. Bit pricey at US$24 for a softcover version (US$32 for the hardcover), but that’s to be expected for small press runs, I guess. If anybody could point me to a (online) review, I’d be grateful — and I wouldn’t cry big tears if a review copy turned up in my mailbox, either… 8^)=

Okay, that’s going to do it. I’m going to try real hard to write something every day this week, to get back into the groove. Tonight, however, I should try to get some sleep, as tomorrow is a big day. See y’all later…

PS: An apology to members of the update list; I attempted to send notice of the last update (see below), but it bounced due to some mail client mess-up on my end, and I didn’t discover that until earlier today.