July 2000 Archives

Hey, I’m back! Didja miss me? In case the long gap without updates has caused you to forget, I took last week off from the blog to concentrate on BOP, my nascent blog manager/CMS thing. Didn’t get as much done on that front as I wanted to, but I did get some stuff done, and I may have gained a co-developer (more later as that develops), so maybe the rate of progress will start to pick up.

One reason I didn’t get as much done as I wanted to was because I woke up Monday with hives. I’m still not sure why I got them; there doesn’t seem to be a good causal event that Lor or I can identify. Appropriately, it was the day of my seventh wedding anniversary. I never realized that seven-year itch thing was supposed to be taken so literally. Anyway, between the itching (which rendered rational thought pretty much impossible) and the heavy dosing with Benedryl (which stopping the itching but damn near rendered me unconscious), I didn’t get much coding done.

The only other personal event of note during the week off: Lor gave me a cell phone as an anniversary present. (Apparently the pet store was out of leashes in my size. 8^) Just kidding honey!) I don’t think I’m going to broadcast the number, but if there’s some reason you need it, drop me a line.

I did manage to bookmark a few things during the break, however, so let’s see if I still remember how to do this…

CipherSabre looks like an interesting example of grass-roots crypto activism. I haven’t forged one (yet), but I did finally get Mailcrypt and Gnus to play nice with each other. So, in the future I’m going to be GPG signing all my mail and news postings, and using encrypted mail where possible. Just seems like the prudent thing to do.

One of the reasons it seems prudent, of course, is Echelon. For those of you not familiar with this, here’s an overview.

Oh, and my key is over here, or on the public key servers.

Speaking of crypto stuff, cryptome.org has been silent since shortly after the names of two FBI agents were posted there in defiance of a FBI demand to keep them secret. Anybody know what’s up over there?

I’ve been playing around with Galeon a little bit. It’s nice, but the lack of cookies is a real killer, and it’s been on the unstable side. Encompass is another alternative Gnome-based browser. I haven’t built it yet, but I’m going to give it a go later tonight, assuming I don’t just blog until all hours.

Third edition of the Camel is out; anybody had a chance to check out the changes relative to the second edition yet? I know I’ll be buying it, the question is more how long I’m going to put it off.

Hey, all you Visor users out there — anybody upgraded yet? Thumbs up or down?

Odd and/or disturbing search engine queries that hit Genehack last week:

It’s not just that these searches are going on; I’m actually okay with that. My confusion and amazement stems from the fact that in order for me to even know about these things, the searchers are clicking through to Genehack — presumably because they think they’re going to find what they’re looking for here. I just don’t get it.

The release of Debian 2.2 has been dedicated to Joel Klecker.

Here’s another ‘do-good via clickage’ project: Race for the Big Cats. (via Dave, who is web-page-less.)

Hey, speaking of Dave, (seriously belated) thanks to the people who sent him birthday emails. He did indeed freak out. 8^)

Some useful bioinformatics Perl one-liners. I keep meaning to polish up my one-liner skills, but never seem to have the time to do it. It’s usually quicker for me to do a multi-line script that will work the first time, rather than mess around with getting the one-liner right.

Lots of Perl stuff from the indomitable Abigail.

The closure of K5 really sucks. When the guilty party is found, I hope they kick ‘im once for me.

So, last week I mentioned writing a letter to Richard Grant about his ‘UNIX versus Linux for Bioinformatics’ article. Apparently my letter and his response are going to be in The Biochemist at some point, but you can read them now. The exchange also ended up sparking a somewhat lengthy thread over in bionet.software, which has veered into a discussion of source code access and peer review, with numerous side forays into related topics. One of the better Usenet exchanges I’ve been involved in in quite some time.

Some tips on avoiding bad software design. I think I’ve made about half these mistakes, and I’m probably working on making the rest. Maybe I’ll manage to miss one or two of them now.

Jessamyn is trying to take back Vermont — .com guerrilla style, baby! (See this for the explanation.) Good on Jessamyn.

I’m listening to a mp3 of a bootleg of the Get Up Kids doing ‘Better Half’. At one point, before a chorus, the singer shouts out “Sing it with me, Seattle!”, followed by about three bars of no vocals and no audience participation. Cracks me up, every time.

Another legal link from Jay Baylink’ Ashworth: PTO to rein in gene patents. I think the new guidelines still sound a bit looser than I’d like. Here’s a quote:

Companies like Incyte Genomics have isolated, purified, sequenced, and discovered a commercial utility for genes and put them into commercially useful formats for development of drugs and diagnostic tests,” [Randal Scott of Palo Alto, Calif.-based Incyte Genomics Inc.] testified.

Okay, but why should they be allowed to patent the genes? The therapeutically useful drugs and what not aren’t the genes — they might be the proteins encoded in the genes, or they might be other molecules that interact with the genes, or the protein encoded in the genes, but in most of the cases I’m aware of, the actual DNA is not the therapeutic. So why not patent the actual drug, be it protein or molecule, or whatever? Answer: Because it’s more difficult to get to the point where the drug has been developed, or the protein has been purified, or whatever. It’s difficult to see the attempts to patent gene sequences as anything other than premptive land grabs, designed to prevent competition from other companies.

Cool! Gimp for Newbies. I just turned a co-worker onto the Gimp. (Builds just fine on our Solaris workstations, once you get all the libraries built too.)

Okay, I think that’s it for today. Hopefully I’ll be back tomorrow with more. If you’ve got a spare minute, shoot me some email (jacobs@genehack.org) and stroke my ego by telling me how much you missed me.

It’s my wedding anniversary today; Lor and I have been married for seven years, and together for about eight and a half total. I love her more with each day and would be lost without her. She completes me.

Just to finish up my thread on this, Lance Armstrong won the Tour yesterday. Overall, he had an amazing performance, out-riding Pantini (regarded as the best climber in the world) on the mountain stages and beating Zabel (world time-trial champion) in the last time trial. Expect to see Armstrong picking up a medal or two come Olympics time.

I was busy all weekend — visited the Smithsonian on Saturday, and spent most of Sunday hacking on BOP. I’m going to be taking most of this week off to go head-down on BOP — it’s close to being usable, and I’d like to concentrate that for a while. If you’d like to know when I update again, join the update list.

Busy, busy. The short personal meta stuff normally found here is at the end, cuz it’s a bit longer than usual, and I know some people prefer to skip it.

Upcoming weekend project: put pictures in photoarchive.

Database Mining in the Human Genome Project. Interesting looking white paper, being developed under an ‘open source’ method. I’ll have to print this one out and read it carefully, but at first blush, it might be worthwhile.

The American Society for Microbiology says genetically modified organisms are okay. The statement they released is (IMNSHO) balanced, fair, and above all, refreshingly sane. As such, it’s probably not going to make one whit of difference in shaping public opinion. My favorite section:

Those who resist the advance of biotechnology must address how otherwise to feed and care for the health of a rapidly growing global population forecast to increase at a rate of nearly 90 million people per year.

Perl 6 is going to be a ground-up re-write. This should be fun (and I’m not being sarcastic, for a change). Here’s the official info center, which has the initial announcement.

Miguel de Icaza says “Unix sucks”. One of the primary reasons he cites is the limited amount of code use that occurs in the Unix (and Linux) software world. I’m not going to disagree; I’m simply not qualified. One thing that does puzzle me: it’s generally agreed that computer monocultures lead to (among other problems) greater susceptibility to viruses and other types of exploits. Wouldn’t universal code release take this problem to it’s ultimate extreme? There’s a discussion going on at Advogato; I especially like the point about how use of higher level languages are a form of code re-use.

Speaking of Open Source hacker types, what happened to Mandrake?

Jay ‘Baylink’ Ashworth sent along a link to a story about genetic testing abuses, over on law.com. You’re getting the printer friendly version, because the formating of the regular version is unbelievably god-awful ugly in my browser.

Personal Meta: Those of you here for the genetics, turn back now!

It’s been an odd couple of days. I was feeling a bit down at work, like I wasn’t really pulling my weight, or making the most of the opportunity of being at the NCBI. After a bit of thinking about it, I realize that I’ve been suffering something akin to burn-out — there’s just so much that I need to learn, and do, and there’s no obvious place to start — I just have to jump in and start swimming, which is not exactly my prefered working style. I was also not as excited about the stuff I was working on as I should have been.

Over the last week or so, however, that’s all pretty much changed. I’ve started setting small achievable goals for each day, and I think I’m covering a decent amount of territory (which means it’ll take longer to get anywhere, but that’s the way it goes). I also adjusted the focus of what I’m working on; it’s much more ambitious now, and once we get it built, I think it will be well-received and popular in the community. Of course, the new project is a much larger undertaking; if I was in over my head before, I basically just reached down and strapped on some concrete ankle weights. By any reasonable measure, I should be even more depressed about my situation, but instead I feel pretty good. We’ll see how long I manage to stay on top of everything. 8^)

I also had some minor epiphanies about BOP over the past couple of days. I realized the overall design had some fairly large flaws, and I could accomplish many of the things I’m trying to do in a lot less code, by taking advantage of some implicit inheritance. The win here is not only that the whole system will be easier to use, but also that pages will ‘know’ what they contain — so updating a glossary item or an included bit of HTML will result in all the pages that contain the updated object getting automagically flagged for re-publication. I still need to think about this a bit, and finish writing the documentation — yes, I actually started writing documentation before code — but I think that once that’s done, I’ll be able to get to a usable system much more quickly than I anticipated.

My Dad called me tonight, which is unusual. There’s no big family horror story there — quite the opposite. We see each other about once or twice a year, and we talk then; we’re just not big phone people. When I call home, I just usually end up talking to my mom. Anyway, Dad called with some info we’d asked for earlier in the week, and I ended up having a nice conversation with him. My parents are coming out for a visit in the fall, and I’m quite excited about that — I think on some level I’m finally starting to feel ‘grown-up’ since I finished school, and I want them to see that.

I guess I’d like to think I’m over that kind of parental approval-seeking — but I’m not sure anybody gets over that. I admire my father (Mom too, but this isn’t about her right now), but more than that, I actually like him as a person. The older I get, the more of him I see in me, and the less upset I am about seeing that. Recognizing this and dealing with it isn’t easy for me — my family isn’t really overtly affectionate; instead, we tend to express affection and respect via jibes and digs — something I still tend to do, and something that’s off-putting to people who’ve just met me. Ultimately, I guess I’m trying to say I love my father — I just hope I’m able to tell him that, one of these days.

Whew. Hopefully that wasn’t too heavy for y’all, on a Friday and all. I realize it wasn’t 24 useless facts, but you’ve probably had your fill of that elsewhere. Hope everybody has a nice weekend, and I’ll see you back here on Monday.

Somebody called me their hero on Usenet today. Just thought I’d share.

Here’s a tutorial on using crypto in Web-based apps that I’ll probably find useful at one point or another.

There was a little piece in The Biochemist about choosing Linux versus UNIX for bioinformatics workstations. I only found this article because my Linux page is referenced in the article. I’ve contacted the author about some of the inaccuracies in the article — see the email I sent here. I know some readers are probably better defenders of the Linux Way than I am — if you’ve got any suggestions as to things I missed, or could say better, please mail me.

By the way, there are several interesting looking articles in the CyberBiochemist section of The Biochemist; expect to see some links in that direction in the future.

I played around with Galeon a little bit this weekend. It’s a bare bones browser based on just the Gecko HTML engine part of Mozilla. For me, it misses the target in the opposite direction from Mozilla — there’s not quite enough there, yet. Nevertheless, it’s the best graphical browser I’ve used in a quite, and I’m considering dumping Netscape for it. LinuxPlanet had a review of it today, in case you’re looking to ditch Netscape too.

The Foresight Exchange is open for trading, for people who want to speculate on a different sort of futures.

In the continuing spam fight saga, I found samspade.org, which has some tools that help you track down the sources of the spam you get.

Well, given the voyeur mania and the breakdown of privacy in our culture, I suppose this was somewhat inevitable: the Maricopa Country Jail (in Phoenix, AZ) is webcasting the area where inmates are booked.

Researchers note that doctors can track (in a loose way) if patients are taking their medication by talking to pharmacists, to make sure ‘scripts get refilled. While it’s an invasion of privacy in many cases, there are situations where society needs to track this sort of information. I’m not sure the phone is needed, though — all of this info is computerized, so much of this could happen automatically. It’s also not going to stop the determined — they’ll just fill the ‘script and not take the pills.

Review of a book about forensic entomology — using data about insects found in corpses to determine time of death and other details about murder victims. At the blogger gathering Friday, Mike yelled at me about talking about vomit while he was eating — so this book probably isn’t for him, but the strong of stomach might find it interesting.

Lance Armstrong is starting to talk some smack about Marco Pantini, one of his rivals in the Tour. What the article doesn’t explain is that “Elephantino”, the nickname Armstrong is using to refer to Pantini, is actually equivalent to “Dumbo” — and once you’ve seen Pantini’s ears (look at the picture on the linked page), you’ll understand why it’s appropriate.

Still on the Tour, the Post had a nice editorial today about the lack of praise for Armstrong in the American press.

Salon did a piece on Advogato today; I’m with Rafe in thinking this is probably less than good. I just hope they don’t cover kuro5hin.org next.

Speaking of kuro5hin, there was an interesting story posted there today, about a Hotline sysop who was shut down by the FBI because of copyright infringement issues. I’m not sure how much ground the guy has to stand on, but the story is at least a useful reminder of how quickly and easily community sites can be shutdown.

Air traffic controllers at O’Hare are staging a slowdown. Apparently this has been the worst summer on record for air travel, in terms of delays and cancellations. Lor’s made 3 or 4 business trips in the last couple months, and has run into delays on each one — very frustrating.

Wow, and I almost didn’t update today, because I didn’t think I had anything to say…see you tommorow.

Either I’ve developed some new allergies during my years in the Southwest, or I’m getting a cold. Burning eyes leaking tears down to over-full sinuses, which are in turn dripping down my throat — it’s not healthy time in John land.

This guide to choosing a Perl book is also filled with small useful hints to help you get into and understand Perl Culture.
Found at Fozbaca.

A tool that might prove useful once I get GnuPG talking to Gnus: Secret-Agent.

Now that the human genome is ‘finished’, things can start to get really interesting. As an example, Harvard, which recently signed on as a subscriber to Celera’s database service, is planning on using that service as part of their plan to distribute gene samples. They’ll be providing this material free to academic scientists. The twist here is that this directly competes with one of the ways Celera is planning on making money. Expect some freaky licensing agreements on those cDNA clones.

One more tidbit from that article. The director the human genome center at Washington University is quoted as saying:

“Celera’s current business plan seems to be to produce resources similar to those that are freely available,” he said. “I don’t see how they can do that profitably.”

That’s pretty much the prototypical Open Source business plan getting slammed there — seems like if it’ll play in one space, it should play in another. Of course, that would require consistent behavior from investors, so I’ll probably be wrong on this one too. (I’m ignoring the whole ‘profitably’ red herring — we all know profit isn’t important anymore, right?)

Anybody else see this news and think about bread and circuses?

In other rather depressing news, 31% of Americans surveyed said “a group should not be allowed to hold a rally for a cause or an issue if it offends others in the community.” See the press release or the full survey. (The later is only available in PDF, which is ironic considering a free speech group did the study.)

Speaking of irony, you can expect to see stories about the recent NSF study reporting that “well-informed” Americans are a minority linked heavily in BlogWorld over the next couple of days.

Bacteria is not a dirty word.

Celera is looking to move into proteomics. Shouldn’t they finish the genome sequence first?
(Yes, that was a cheap shot. Wanna make something of it?)

The Killfile Dungeon, where net.k00ks are rehabilated into productive Usenet citizens.

This was a good weekend. The blogger Brickskeller gathering went well, aside from our inadvertently hiding from Kevin ‘Ghost in the Machine’ Murphy. As unofficial organizer, I feel somewhat responsible for not setting things up a little better — Kevin, first round’s on me, next time.

Other than that mishap, things went well. All I’ve got to add to Mike’s summary is that we learned that Mike doesn’t just have a little frat boy in ‘im, he’s got a lot of frat boy in ‘im — something that, really, comes as no surprise to those who’ve met him. Plans are underway for a repeat engagement of some sort in August, when Steve actually moves here for good.

People thinking about ditching Windows for Linux might want to start here.

Odd search referal of the week: “decss dvd erotic down load”, via the German language version of Google. I’ll note, without further comment, that Genehack appears to be the only site indexed by Google that matchs that particular combination of search terms.

In contrast, many sites match a Yahoo search for “pictures of obscene hand gestures”, but Genehack is number two. I feel so, umm, proud. Or something.

I finally got my Visor’s USB cradle working again this weekend, and so I was finally able to give Sitescooper a go. In case you don’t know, Sitescooper is a Perl-based app that lets you download various sites for later reading on your Visor or Palm handheld. It’s very cool, and I can already tell I’ll be using it as part of my daily routine.

That’s it for today — didn’t get much surfing done this weekend. Too many social gatherings; too much BOP hacking. It’ll be better tomorrow, I hope.

I over-slept this morning; ended up getting up about an hour late. All day, I’ve felt like I was running after that one hour. Never caught up, either.

Linux.com has an interview with the Ian of Debian.

Are Bert and Ernie gay?. From 1994, if you can believe it.

Question for my oh-so-knowledge-able audience: Anybody know of software that will load man/texinfo/pod documentation into a Palm? I know I could just take the text and pipe it into a .doc; I’m looking for something that will preserve some of the formatting.

Here’s a cool bit of Palm software: a Harry Potter Sorting Hat. Find out what house you’d be in, if you weren’t a hopeless Muggle.

Yet another band that makes my head bounce: Mirah. (Source of today’s title.)

Well, I can see how it would come to this: An Iowa man, upset over sewer problems, took a bucket of human waste to a city council meeting, and some of it splattered the council. The article makes it sound almost accidental — I mean, it’s not like the guy tossed the stuff at them, or anything…

More ‘Carnivore’ news: The ACLU is getting into it. Personally, I’m with — well, damn, I can’t find it now — I’m with the weblogger who mentioned modifying his .sig to indicate that encrypted mail was preferred. Weekend project: Get Gnus and GPG to play nicely together…

Speaking of encryption, this page has some pictures of people with RSA-in-three-lines-of-Perl tattoos — which, legally speaking, makes their bodies munitions that can’t be legally exported out of the US.

And speaking of mail, I mentioned a couple days ago that I’d started using gnus-junk.el to try to reduce the amount of spam I get. I’ve managed to kill 3 accounts, and was late to the party on 2 others. I’ve also gotten about 20 bounce messages — leading me to formulate my new mail policy: If I send mail to abuse@foo.com and it bounces, that’s it — you’re on John’s Not-So-Realtime Shitcan List — any and all mail from that domain is routed to /dev/null. Once I get my act together a bit, I’ll put the list up on a page here, just so everyone can see who the lusers are.

HIV may make you more horny, at least during the initial stages of infection. The benefits to the virus, of course, are obvious. Viruses that alter human behavior are somewhat scary and very cool to think about.

LiveJournal looks like a Blogger-like service.

Hey, if you’re in the DC area, and don’t have any plans for tomorrow night, why not swing by the welcome party for Lyn?

Revisionist Meta: Fixed the date on the last entry — it was for the 12th, not the 11th.

Four hours of sleep does not make thinking about statistical models a very productive way to spend your day.

In the Cathedral and the Bizarre, a Mac developer deconstructs ESR’s recent MacHack keynote. A valid point or two is made, but the whole thing feels off, somehow. I think it’s the focus on the user as customer — because, fundamentally, in the Open Source world, the customer is the developer, not the user — it’s a self-serve world, and it all gets back to the ‘scratching your own itch’ motivation behind developing software and giving it away. I’m doing a poor job of explaining this, I think — perhaps I should think on this some more…

Memoware has scads of e-text for your Palm or Visor.

(By the way, my Visor is free of the 8 MB memory problem. Yay! On the downside, I’ve been struggling with getting USB to work properly, and I think I’m just going to fall back to the serial cradle for the time being.)

Here’s another BBC article on Lake Vostok.

The repressive Taliban regime just arrested a US citizen. Said citizen happens to be a woman who was in Afghanistan trying to help poor families and widows. I hope this is resolved quickly and peacefully, but also hope that the Powers That Be won’t hesitate to use appropriate force if other avenues fail.

After-market spun aluminum replacement cases for the Palm III series. Start your drooling here.

Continuing yesterday’s music stuff: I’ve been head nodding to Barcelona quite a bit — I’ll have to pick this one up if I see it.

Continuing yesterday’s Big Brother stuff: The FBI has a new tool they call Carnivore. Sounds like a glorified packet filter to me — basically, they get a wire tap warrant against you, then plug this box into your ISPs internal network, and hover up all your email. The only problem is, they have to scan all the email to find out what’s yours. Here’s a question for the lawyers in the audience: generally, evidence of other crimes uncovered by wiretap is admissible in court, right? (For example, if you wire-tap me because I’m a drug dealer, and you record me ordering a hit on a rival, I get sent up for that as well — even though there was no reasonable cause to suspect me without the wiretap.) So, what’s to stop some bright boy or girl from adding a little word-recognition to Carnivore, such that other email, not explicitly covered by the tap, is scanned for things like ‘bomb’,’murder’, or ‘PICKYOURWORD’?

This picture made me laugh out loud today.

This would certainly put a different spin on things: the LAPD is threatening to protest the Democratic national convention.

Rafe, I see your RMS, and raise you one JWZ and one ESR. Interpreting the significance of the number and level of certifications is left as an exercise for the reader.

Hey! I’m done updating, and it’s still early! Maybe I can reduce the email backlog a bit… I’m taking tomorrow off; it’s Pint Night with the NCBI Systems Crew. See you back here on (probably) Friday.

Argh. Lor’s off again on another round of business travel. She had an early flight, meaning a very early airport shuttle pickup, meaning an ungodly wake-up time. So, I’m doing this update about six hours late, or 18 hours early, depending on how you look at it.

I caught the Freaks and Geeks marathon/finale/what-have-you on Saturday. It was nice to be able to see the last shows in the series, but also depressing. Especially so when you compared them to the crap NBC was advertising for next season. Fresh Hell points out that the Fox Family channel has picked up the show, but it’s not clear if any new episodes will be produced.

Speaking of TV, if you’re not watching the Tour de France, you’re missing out. The Tour is the only sports event I actually make an effort to follow, and this year’s is definitely a classic. Lots of confusion and excitement in the early flat-land stages, and yesterday, in the first mountain stage, Lance Armstrong positively decimated the field with a second-place finish that put him back in the yellow jersey. If he continues to dominate in this fashion, it should put an end to the nay-sayers who like to point out that his win last year was against a relatively under-powered field.

One of the other things I did this weekend was give Mozilla another try — something I continue to do periodically, despite past experience. This time was no exception — the damn thing is still way too slow, both to start and to run. Maybe I’ll give Opera a go…

I get a lot of spam — much of it in Chinese. (I guess I’m on a “No, he’s really a Chinese guy hiding behind that Anderson name nonsense” list, or something.) When I say ‘a lot’, I’m talking over 5% of my daily incoming mail is spam — and I get over 200 mails a day, what with various lists and my fabulous social life. I finally got fed up enough to do something about it — I grabbed gnus-junk.el, which lets me send a complaint to the relevant addresses with a single keystroke (plus a bit of address munging). I’ve been doing this for three days, and I’ve gotten two accounts shut down. Hopefully if I keep doing this aggressively, my name will move over to the ‘spamkiller’ lists.

ibooks.com is offering e-versions of O’Reilly titles — for a fee, of course. Too bad the site keeps killing my browser.

Perl Web Utilities — I need to have a look at this and see if there’s anything I can ‘borrow’ for BOP.

US teens having less sex, with more condoms. Yah, or they’re getting better at giving researchers the ‘right’ answers.

Oh geez! Apparently, being left-handed makes you gay. No word on whether forcing children to use their right hand by tying the left to a chair arm keeps them straight. There’s also no word (yet) on calls from religious groups for left-handers to abandon their Godless lifestyle choice.
For the record, I’m left-handed, mostly.

Reading this at work? Wave to Big Brother for me, ‘kay? (Just use your right hand, for the love of Pete — or who knows what might happen!) Here’s a scary thought — companies are pulling this crap in a time of (reported) shortages of qualified ‘high-tech’/IT workers. Imagine how bad it’ll get if the economy tanks.

Dan Gillmor is taking on RIP, a proposed new UK law that regulates all sorts of electronic activity. I especially like the provision of jail time for people who refuse to turn over encryption keys on police demand — it makes dealing with difficult cow-orkers so much easier. Why? Well, it’s difficult to prove that you don’t actually have the key to that encrypted mail with a Subject line of “Getcher free child porn sample”, see…

(Please, please, please, let the quoted text string in the paragraph above never, ever result in a referral to this site. Please.)

Big happy birthday shoutout to my buddy Dave — one day late. Dave and I were in gradual school together, and one of the more difficult adjustments with moving cross-country to NCBI has been not having him around — something summed up quite effectively by Amanda’s 10 July entry about Lyn.

If you’d like to do me a favor, drop Dave a mail at dcs@u.arizona.edu, and tell him ‘Happy Birthday’. Don’t tell him I told you to do this, of course — if I know Dave, he’ll completely freak out at all this mail from strangers. That’ll teach him to not read this page…

Good weekend in the Genehack Compound; got some stuff done, got some relaxing time in, and I must have done some coding, ‘cuz my wrists hurt. Hope yours was mostly the same, minus the pain, unless that’s your thing. Now, strap yourselves in, because this is going to be a biggie — I really should have updated on Saturday, but I never got around to it, so today’s going to be extra-jumbo-large.

A link I need to pass around at work: CLEAVER : analyzing microarray data using known biological categories.
Transcribed from snowdeal.org’s bio-info section.

Inessential and Scripting News have been talking Napster and mp3s all last week. It’s been a musical weekend here too — while I was doing my BOP coding this weekend, I generally had a disc in the drive, ripping to mp3. In fact, I’m listening to some of the stuff I ripped as I write this. Hey, the Pixie’s Diggin’ for Fire just came on — I love this song. It goes deeper than that too: today’s title is from a Magnetic Fields song that’s been stuck in my head since Friday, when I heard it on indiepopradio.com, which I generally have on when I’m at work. I don’t usually really listen to the music; it just drowns out the din from the other fattening pens^W^Wcubicles. (I’ve got the same headphones as Jason, in case you care — they rock.) Anyway, he said, winding up the long digression: I can always tell when I’m going to like a song — I start nodding my head to the beat, to the point where I break out of the work ‘zone’ and become aware of the music — which is when I reload the playlist, to see what I’m hearing. I’ve got mp3’s shuffle-playing as I write this — maybe I’ll just note when a song breaks me out of writing mode…

Wired News had a tidbit about SNPs last week. Single nucleotide polymorphisms are places in genes where individuals differ by a single base, and they’re likely to be the key to some of the more profitable results of the human genome sequencing projects, things like pharmacogenetics — adapting medical treatment to individuals based on their genotype.

Just when the Vermont civil union stuff was making me think the country was starting to grow up a bit, Louisiana has to go and ruin it all.

Cool! The crystal structure of a transposase:transposon complex has been solved. More popularly known as ‘jumping genes’, transposons are behind the horizontal gene transfer that I mentioned a while back, and they’re also related to proteins involved in the propagation of retroviruses, like HIV.

Well, somebody had to advocate it — the people behind the cloning of Dolly have come out in favor of human cloning. It’s just a matter of time, folks — we can either talk about ways to do it ethically now, or we can play catch-up.

Giant squid washes up on beach. No word on whether or not the locals were planning to blow it up.

More crypto-zoology news: A possible Bigfoot sighting?

(Music moment: Forgive and Forget, The Get Up Kids.)

Later this month, we’re likely to be able to see a new comet with our naked eyes. I wonder if the religious wackos will make a big deal of a comet in 2000? Surely not… 8^)=

Here’s another story about the efforts to clone the extinct Tasmanian tiger.

(Another music moment: Hallelujah Jordan, the Hothouse Flowers.)

This article raises (but unfortunately doesn’t discuss at length) an interesting question: How much of our world can be modeled by a Universal Machine?

Stolen from somewhere: Natural language principles in Perl. It’s not an accident it looks like a mess; it’s that way on purpose. 8^)=

Here’s an interesting way to think about the “Linux is only free as long as your time is worthless” problem: like free sex.

CNN did a bit of a puff piece on Jon Katz’s Geeks, but there’s some follow-up on Jesse, one of the kids in the book. The book was okay, if you can ignore the broad brush Katz applies when deciding who is and who isn’t a geek. I was disappointed in the short shrift that Eric, the other kid, got in the book. It’s too bad that that’s continued in this story.

The UK is fixing to crack down on cyber-criminals. Of course, the only concrete example of so-called cyber-crime given in the article wouldn’t be a crime in the US — and I’m not even sure it’s a crime in the UK. Any reader feed-back on this?

(Music: Grey Cell Green, Ned’s Atomic Dustbin.)

Workers at Rosetta Inpharmatics (sweet name, BTW) have combined gene expression profiles and computational analysis to accomplish an impressive feat: identifying a previously uncharacterized gene product as a drug target.

Tests of Bt corn under field conditions show no adverse effects on swallowtail butterfly larvae. This contradicts earlier lab research that showed that monarch butterfly larvae were affected.

Why we need Debian. Genehack is produced on a Debian box, and served from a Debian box, in the unlikely event that you care.

A RISKS Digest post says NASA wants everybody to know that a hacker didn’t endanger astronauts, as an article I linked last week reported. Moreover, the author of the RISKS post claims that mission-critical information didn’t flow over the public ‘net, which was something I questioned at the time, as I recall.

A draft assembly of the human genome sequence is available at UCSC. Here’s a story about how that came about.

Info on HipCrime, an entity or entities involved in rogue Usenet cancels. An entity dubbed HipClone was pulling this garbage last week, but has been shut down, according to traffic in the Scary Devil Monastery.

Why Perl is bad for you. (From a comp.lang.lisp posting, so consider the source.)

Intro to XHTML.
Nicked from CamWorld.

Salon covers Pottermania. When I was in $LARGECHAINBOOKSTORE this weekend, I grabbed the first Potter book, just to see what the fuss is about. (Plus it was cheap — US$7 for a trade paperback, at 30% off, ended up below US$5 before tax.) I tore through the book in a couple hours this afternoon — it was decent. I’ll probably read the others in the series, but I can’t see shelling out for hard-covers.

Here’s a comparison of MySQL and PostgreSQL, two free relational database management systems. I think I’ll be sticking with MySQL…

iMacLinux might be useful for LinuxPPC people — or for people having trouble with LinuxPPC.

Hey, all you DC area bloggers — think we should have some sort of party/gathering/happening to welcome Lyn to town?

Seems like there was something else I was going to write about, but I’ll be swelped if I can remember what, and this thing is already probably too long for a Monday — most people probably gave up back at the Grey Cell Green reference. See ya tomorrow…

Wow, where did today go? (And how come I didn’t get anything done?) Ah well, at least the weekend is almost here — I’m sure I’ll get a bunch of stuff done then. </sarcasm>

Couple of people wrote about the “is your DNA yours” question yesterday; I’ll be getting back to them this weekend. Magick put his response up. Some good points and questions; I’ll be getting back to ya soon…

Remember about a year ago, when Echelon seemed like a really bad nightmare brought on by too much X-Files and Cheez Doodles? Well, now things are getting real.

In related news, various parts of the FedGov are thinking about nixing a buyout of Verio by Nippon Telegraph & Telephone, because they’re worried about their continuing ability to wiretap Verio’s network infrastructure.

Linked because I’m sure I’ll want it at some point: the GNU coding standards. Useful not because I’m going to follow them, or anything (can’t stand naked braces, personally), but because of the reasoning explaining some of the practices, and as an example of the detail required in a usable coding standard.

Nature has started a Genome Gateway, sort of a proto-weblog of genomics resources.

We spent the Fourth at the home of a high school classmate who happens to live in the DC area (somewhat odd that we’re in the same area, considering that I only have 25 classmates from high school). We watched the Bowie fireworks celebration from their backyard, and today I noticed that I have about 10 insect bites on my lower legs. Mosquitoes have always found me more tasty than average, and that’s why this plan makes me just a wee bit nervous.

Actually, I attended a talk recently which featured some mention of gengineering mosquitoes to be more resistant to the malaria virus — eliminating the disease by eliminating the vector. I’m actually in favor of a slightly different tack — I’d just like to wipe the little biting buggers out, which should accomplish the same thing, and make me a lot happier in the summer.

Condolences and a positive thought go out to Debra and her family in their time of loss.

Ta, Graham. And the weblogging manifesto echoes some recent thoughts I’ve been having about why Genehack continues to be a priority for me despite some recent negative feedback. Maybe all webloggers should be required to summarize their reasons for continuing on every six months or so…

Have a good weekend, y’all. I’m going to be laying low, hacking on BOP, and trying to catch up on the email front. See ya back here on Monday.

Man, does that middle-of-the-week holiday thing mess up the routine, or what? I’m not sure what day of the week it is anymore…

In the “we’re living science fiction” department, conservationists are calling for a worldwide network of DNA banks, to hold the genetic information from endangered species.

In the “is the DNA in your cells really yours?” department, the Scottish firm that attracted attention for cloning the sheep Dolly is getting some new attention. Turns out they inserted a woman’s DNA into some transgenic sheep without her permission. This, of course, raises all kinds of interesting and thorny questions, but the big one (for me) is whether you own your own DNA, or just hold it in trust for the species. For example, if testing revealed that a person’s DNA contained the sequence for a protein that could cure most cancers, but that person was opposed to genetic engineering (for religious reasons, say), could that person stop the development of a medicine that could save many, many people’s lives? Any thoughts?

In a not-completely-unrelated vein, some evolutionary psychologists are suggesting that rape is a male strategy designed to get around lack of access to fertile females (because other men are monopolizing them). Haven’t seen the data, but I instinctively suspect that the numbers of reported rapes are still dwarfed by non-reports, and furthermore, that children of rape are even more under-reported — all of which could undermine the conclusions of this report. And that’s not even getting into the sociological dimensions of this…which I kinda hope someone better qualified will remark on.

Just like Wes and Cam, I’ve joined Advogato. I held off mentioning it, because I didn’t want to seem like I was trolling for certifications, but someone has independently certified me, so now I feel free to spill the beans. There’s some interesting stuff going on over there, if you’re into that whole Open Source development thing…

In the “Boy, remember when McCain seemed reasonable” category, everybody’s favorite Arizona senator is a co-sponsor of a new bill that would require all media to be labelled on the basis of violence. First amendment? We don’t need no steekin’ first amendment…

I started a mailing list for BOP; if you’re at all interested in a database-backed Perl-driven web content management system, come hang out. I’d love to hear from people who’ve given the not-quite-alpha release a go, but anybody is welcome. This is your chance to drive feature development towards things you’d like to see…


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It’s been a real odd weekend — Sunday felt like Saturday, and there was a whole three-day weekend vibe going on. Since I have to work Monday, like most of you, I imagine, this was a bit disconcerting.

Breaching the Web has submerged, at least for the time being. Have a nice break, Kris. And while I’m blog rolling, I’ll point out the Pursed Lips is back. Heya, Debra! I was starting to miss ya; glad to see you back in action.

The FSF has a page up on why we must fight UCITA. Good info to point people at when they ask why they should care. It’s too late for the state I live in, but it might not be too late for yours.

Oh, and speaking of efforts to screw over the consumer, the new ‘digital’ signature bill might not be what you think. I get an exceptional dark thrill out of the ability of merchants to charge a fee for withdrawal of consent — not only are you not getting a refund for the copy of Windows you don’t use, but you owe Microsoft $49.99 for asking about it!

For all you Visor owners who think we missed out on the Palm 8 MB memory bug, think again. There’s a test app on Handspring’s site. I’ll be checking mine at work tomorrow; gonna be pretty pissed if it’s defective.

I spent most of Saturday reading. I finished Allen Steele’s OceanSpace (quick fun read, not as good as his space stuff) and John Barnes’s Candle (again, okay; not as ultraviolent as Kaleidescope Century; ending was a bit abrupt). Now I’m down to only 1.5 linear feet of books to read…

Probably going to be all over the place tomorrow: NASA says a 1997 crack of their network put the lives of astronauts at risk. No mention of why mission critical data was being sent over public networks, of course.

Also in the “what the hell does secure mean, anyway” column: the recent Love Bug virus made it’s way into “four classified military systems”. Real secret network, guys — sending mail across public networks, running an OS with more security holes than you can shake a stick at, and using a mail client with a known exploit, which had already been used in a highly publicized attack. Geez.

Finally, the much talked about content management system thing has been released — see bop.sourceforge.net. Not too functional just yet, but I’m working on it. If you’ve got the time, download it, play with it, give me some feedback.

Hope all the Murkins out there have a safe and pleasant Fourth; I’ll see you back here maybe tomorrow, or maybe later in the week.