December 2000 Archives

do not adjust your browser >>> I’m back. Personal stuff at the end; gonna try to work off my link backlog first.

maybe i am a gun >>> Holiday thought: Lor and I watched A Christmas Story (the “You’ll shoot your eye out” movie) the other day. The past five or six years, various broadcast networks have been flogging the hell out of this story during the holiday season — this year, for instance, TNT showed it continuously for 24 hours. After watching it this year, I realized that it’s really a story about a father buying his son a gun — no wonder it seems so all-American…

do you want to play a game? >>> Morbus drops some thoughts about developing on-line games. Not something I’ve given much thought to, but the points he makes are good.

there’s so much beauty in the world >>> On the list of things I’d buy if I had the scratch: a print of this Nerve photo-of-the-day.

Prude alert: There’s a breast or two behind that link.

save society; encrypt email >>> Fascinating, mind-blowing interview with Eben Moglen, Columbia Law prof and general counsel to the GNU. I tried to find a decent pull-quote, but there’s so many:

MOGLEN: No. What we have here are two different structures of the distribution of cultural product. You have a set of people whose fundamental belief is that cultural products are best distributed when they are owned, and they are attempting to construct a leak proof pipe from production studio to eardrum or eyeball of the consumer. Their goal is to construct a piping system that allows them to distribute completely dephysicalized cultural entities which have zero marginal cost and which in a competitive economy would therefore be priced at zero, but they wish to distribute them at non-zero prices. In the ideal world, they would distribute them at the same prices they get for physical objects which cost a lot of money to make, move and sell, and they would become ferociously profitable. They are prepared to give on price, but at every turn, as with the VCR at the beginning of the last epoch, their principle is any ability of this content to escape their control will bring about the end of civilization.

The interview traverses all over the place, from GPG/PGP to DeCSS to content control and redistribution to how we could have a broadband network with ‘birthright bandwidth’ much like the interstate highway system. Go, read this, and think about how you could you help. Mail me your ideas (encrypted, natch).

PS: Really good for those of you who might be bumming over the election fallout…

obligations >>> Ack! I’m teaching a Perl class in a week and a half! Things I should look at: Picking Up Perl, Edition 0.11, A Freely Redistributable Perl Tutorial Book and the Netizen training materials.

license wonking >>> If you care about this, you probably already knew, but just in case: Newsforge had a preview of the forthcoming revision (v3) of the GNU General Public License.

umm, beer >>> The Post had a winter beer review last week. That reminds me, I need to make a beer store run before the festivities this weekend…

ya emacs21 review >>> This one at LinuxPlanet. Notable because the author actually tracked down the source, built it, and played with it a bit. (Also notable because it completely fails to mention XEmacs.)

blood in the water? >>> How desperate is Network Solutions getting that they need to try something like this? I suppose I should start looking into moving genehack.org to a more reasonable registrar; I expire in September.

strange attractor >>> Things I did not know: There is but one degree of separation between myself and Tom West, central figure of Soul of a New Machine.

yet more stuff to read >>> Paul’s Linux RDBMS Library:

This site is a compilation of the best free online readings about relational databases on Linux. If you’re a Linux RDBMS/database administrator, a database designer/developer, or simply a Linux user with database ambitions, you’ll find links to valuable resources here: articles, papers, and books on various aspects of relational database management. Needless to say, much of this material is more or less applicable to other (UNIX) environments, too.

beaten to the punch >>> In the aftermath of the amihotornot.com blow-up, I had an idea based on the classical definition of pornography: “I can’t tell you what it is, but I know it when I see it”. The basic concept was to have a mix of porn and non-porn images (contributed by users) which would be rated on a porn to not-porn scale by whoever wanted to play. Eventually, after the thing had run for awhile, the results (this picture is porn, this is art, this is crap) would be fed into some sort of expert system that could then generalize rules for discerning whether a particular image was pornographic or not. I guess in some sense I’d be gaining some bad karma for helping to develop such a thing, because if it was successful, it would lead to wider adoption of net filters. However, it looks like some places are going to get those, like it or not, so it would be nice if they were at least effective.

Unfortunately, it’s all for naught, cuz somebody else has the obvious domain name, and they’re doing the obvious thing with it (i.e., don’t click that link if you’re at work).

ya gotta love somebody who attempts to be definitive >>> On my ever-growing TODO list: setting up all the keyboards in my life according to this manifesto (scroll down a bit). Explains some of the mysteries behind the differences between BackSpace and Delete (and how to fix them), and doesn’t pull a lot of punches:

We type 8-bit characters with the Compose key: this is the universal method for typing 8-bit characters of any character set. National keyboards can burn in hell. Everyone should use american QWERTY. I have suffered enough from these AZERTY stupidities (which don’t even have all the necessary keys to type French correctly on them, actually).

(Italics, spelling, and capitalization as in original.)

Also on the list: figuring out if I should use XHTML and reading about XML and relational databases in Perl, which could impact BOP development at some future point.

yet another meeting >>> DIMACS Workshop on Whole Genome Comparison. Don’t think I’ll make this one, but you never know — it’s close to home, and it’s pretty cheap.

you are what you eat >>> Dru Oja Jay passed along a pointer to a Monkeyfist interview with Ann Clark, a plant argiculturalist and critic of the idea of genetically modified organisms (GMOs) as foodstuffs. Some interesting points get made; some I agree with, some I could quibble about (but won’t), and some I don’t have enough data to have an opinion about.

I agree with Clark’s points about corporate funding of academic research and about the ‘owning’ of genes. I also found the comparison between GMO release into a ecosystem and the introduction of an ‘exotic invader’ into an ecosystem to be intriguing. People sometimes have trouble understanding some of the risks, but the ability to break it down to a comparison between the English swallow and kudzu is a useful way to clue them in.

One of the quibble-able points I have is where Clark says the genes don’t act alone. That’s not strictly true — many genes do have extensive effects when they are the sole introduced change in an organism. She might have meant to say that genes don’t act in a vacuum — that there are many other factors which need to be absent, or present in the right amount or at the right time in order for the introduced gene to have an effect, but that’s not really the same thing.

I still think the best reason against patenting genes is due to the lack of actual discovery. Sequencing a stretch of DNA doesn’t really involve any creative work; figuring out the function of the protein encoded by that DNA does take a bit of work, but it’s mostly formulaic. The real creative step, and one that’s essential for any commercial application, is in the development of a large-scale purification process for the protein. That process you should be able to patent.

Finally, the thing I don’t have enough data to really argue about is with regard to the comparison between organic farming and large-scale commercial agriculture. When asked “Is organic farming a viable alternative to extensive industrial farming on a large scale?”, Clark replied “Yes, unquestionably.”. On the face of it, that’s a bit hard for me to swallow, and so I’d really like to see some data or citations to back up that claim. The part that I’m really finding difficult to believe is that organic farming would be competitive on a person-hours worked per people feed per unit time level versus large-scale agriculture as currently practiced. However, she’s the agriculture person; I’m just somebody who knows a bit of molecular biology.

(Oh yah, since I haven’t put it in the footer yet: the above opinions are mine, and don’t represent how NCBI, NIH, the FedGov, Clinton, Gore, Bush (either one), or my mom feel about anything. So there.)

personal stuff >>> Survived the meeting I went to. Not going to talk about that too much, as I’m writing a review of it — I’ll post a link when that’s up.

Survived Xmas. Still have to do a bit of gift purchasing, for the parents and Dave, my gradual school buddy.

Did okay in the personal swag department. My home box got the RAM upgrade I mentioned earlier, as well as a Voodoo3 3000 (impulse purchase at Best Buy ‘cuz it was cheap). Lor and I gave ourselves a TiVo. Everything everybody says about these things is true — they’re fantastic, and if you watch more than five or ten hours of television a week, you should probably look into getting one. It’s also making our cable bill seem a bit more palatable too, because we’re watching many more movies than we would have before.

Other than that, it’s been mostly recovery-oriented activities around here — a bit of reading, a bit of holiday partying, a bit of work on BOP, a moderate amount of TiVo-ing, and a lot of sleeping. Hope yours has been the same.

seriously minus on minutes >>> I’m leaving for Durham, NC in a couple of hours, for the CAMDA ‘00 Conference. Hopefully it’ll be a good time, and hopefully I’ll learn a thing or two. I think everything is good to go, although I’m being haunted by that “you’ve forgotten something” feeling, and there’s a thing or two I wish I had dumped to the printer before leaving work on Friday…

Anyway, I’m going to be off the grid for the next two or three days. Luckily, the holiday break will let me get caught up (yah, right!)

On the seriously off chance that any Genehack readers are going to be there, give a shout-out. I’m the pony-tailed guy with a beard in the green Tux the penguin hat who looks sorta like this.

I’ve got a load of linkage to deposit upon y’all, but it’s going to have to wait — I’ve got just enough time to grab some lunch, pick up my cow-orker Wataru, and then it’s off to Durham in the trusty Saturn SL2. See ya when I get back.

personal meta >>> Woo boy! Busy weekend, followed by a busy Monday. We picked up a Christmas tree this weekend, and Lor spent most of Sunday trimming it, and putting out the Christmas decoration stuff. I managed to fall into a bookstore on the tree acquiring expedition, emerging with Damian Conway’s Object Oriented Perl (excellent through the first two chapters), Joe Celko’s SQL for Smarties (haven’t really got into it yet) and Allen Steele’s new collection Sex and Violence in Zero-G (finished this on Sunday; choice stuff). Ordered some RAM, too, which means I’ve basically finished my Christmas shopping for myself 8^)=. RAM is ridiculously cheap right now; I paid about $65 for a 128 MB PC100 DIMM, and I didn’t really comparison shop that aggressively, choosing instead to go with the (probably illusionary) safety of Crucial, Micron’s retail arm.

Things are probably going to stay a bit quieter than normal around here as we head into the holidays; I’m trying to push hard on a thing or two at work, and the BOP project is still slowly re-awakening from hibernation now that Magick has started to help out (I hope to have a revised design spec posted to the mailing list this week). Anyway, it could get a bit quiet, as I said, or it might start to resemble an Advogato diary for a while, but that’ll pass.

more celera >>> Reaction about the Celera/Science deal continues. Sean Eddy had some excellent comments over on /. Sean and Ewan Birny, (one of the heads of the Bioperl project) sent out a mailing to the Bio* lists (archived at bioinformatics.org) urging people to contact Science and ask them to reconsider their decision, or at least make it known (politely) how poorly the decision is being received in the community. Genome Web also got in on the fun for that one. (There’s a spot for a rant here about how dead tree publishing has out-lived its useful life span, and how we ought to be doing everything on-line in community-run and reviewed public archives, but I’ll save it for another day.) Finally, the lads over at Nodalpoint have started a thread to discuss the issues associated with the whole thing — get over there and comment.

Oh, and while I’m on the topic, I was reminded at work on Friday that I should really have some sort of disclaimer on this site. I’m too lazy to frob the template right now, but just keep in mind that the opinions and other material on this site are mine, and in no way represent the NCBI, the NIH, the FedGov, or anybody else.

But you already knew that, right?

while we’re on the subject >>> New Scientist had a bit about gene patents last week. Little new info, but summarizes some of the problems, and talks about the current backlog in various European patent offices.

Wait, I know! They can get around that backlog the same way the US PTO has — by just approving every damn thing that comes through the door!

what is the sound of one helix winding? >>> Find out at the Nucleic Acid Database Musical Atlas.

keep an eye on this >>> Ben Lewin, founder and former editor of Cell, has a new start-up called ergito.com. Some of the stuff they’re talking about doing looks cool, but I’m a bit worried about the design of the website — maybe I’m just gunshy, I don’t know.

avoidably detained >>> Sorry about the lack of new stuff this week; I’ve been in a bit of a work funk since Thanksgiving, and I finally started to come out of it, resulting in a lack of blog time. On the work tip, however, things look like they’re starting to click again: I got about seven solid hours of hacking in today, finishing up the refactoring of the Perl libraries for one of my two projects. Reduced the code size by about 25%, but totally FUBARed the interfaces, so the next task is to rewrite all the CGIs that use those libraries.

I also shot my mouth off one too many times about how good a language Perl is, with the end result being that I’m leading a Perl study group. I’m hoping it won’t be too much extra work, and I do have an ulterior motive: after I’ve build up a group that has some good basic skills, I hope to start an advanced Perl study group to read and talk about things I’m interested in. In the meantime, if anybody out there has advice about leading a medium size group (~70 people in ~25 person chunks) through the Llama, I’m all ears.

bigger and badder >>> There’s been lots of news recently about Emacs21, which should be released sometime in the new year. It’s going to feature a whole slew of new features, like a GTK GUI. You can see some screenshots with accompanying commentary over at userlocal.com, or others over at alpha.gnu.org. I’m quite impressed (in a ‘boy that looks pretty but I could never work that way’ way) with this one.

If you run Debian, you can pick up some sooper-sekrit Emacs21 .debs, if you know where to look. Be warned, however, that they just core-dump for me, so it might not be worth the bandwidth.

speaking of emacsen >>> Recent nice article about reading mail in Emacs, which also pretty much applies to my editor of choice, XEmacs. It might seem silly at first to read your email in your text editor, but writing email is basically all about manipulating chunks of text, so why bother learning a second app just for mail reading? Odds are, you’ve already got an editor that you know how to use, and prefer.

what’s this white stuff? >>> Since it’s supposed to snow any day here, and since I gather that DC is pretty wimpy about shutting things down when that happens, I’ll probably need to remember that government closures are announced at the Office of Personnel Management, specifically on this page.

in the unlikely event… >>> …that you need to move SQL-ish things to and fro on your PalmOS device, SQLpilot might come in useful.

not that i’m mentioning this for selfish reasons >>> If you’ve got a geek on your shopping list this holiday season, you could do worse than something from copyleft.net. This ‘got DeCSS?’ shirt, for example, is quite fetching.

a+ idea; b- execution >>> Maynerd Olsen’s latest idea is trying to get the biomedical research complex (specifically the drug development part) to stop focusing on finding genes that make people sick, and instead to look for genes that keep people from getting sick. Excellent idea; the issue is how to find them. Basically, you’d need a situation where somebody should have gotten sick, but didn’t, and you’d need a way to be reasonably sure that it wasn’t just chance. Ideally (speaking utterly without regard to morality or ethics), you’d like to see a region with two mostly (but not completely) distinct, largely inbred populations — Icelanders and Pacific Islanders, for example. Then you’d like to see the introduction of some sort of nastiness that killed off or sickened people of one background, but not the other. Then you’d take the people with ancestry from both populations and try to correlate some gene(s) with the susceptibility to $BAD_THING.

Of course, if these types of test conditions were plentiful, somebody else would probably have come up with this idea by now…

a bargain at twice the price >>> If you’ve ever wanted your own personal MCSE (Microsoft Certified Service Engineer) around, to answer your Windows tech support questions and whatnot, wait no more — your prayers have been answered by Virtual MCSE

odd brit stuff number one >>> Wednesday, a woman in Newcastle was convicted of biting off her friend’s husband’s testicle. (Got that? Not her friend’s testicle, not her husband’s testicle, but her friend’s husband’s testicle.)

I was boggling at the headline, but then I read this:

“The defendant was not aware that she had bitten his testicle until after the incident,” prosecutor Stephen Duffield said.

As if that makes it better? And then this:

It was only after police arrived at the house in Gateshead, near Newcastle, that the missing testicle was discovered under a picture frame in the sitting room.

My mind exploded at this point, and I was unable to carry on.

odd brit stuff number two >>> I recently learned, via the miracle of foreign cow-orkers, that the word ‘fanny’ in British (as opposed to Merkin) is not a mildly archaic word for ‘butt’, but rather a current and fairly crude word for ‘cunt’.

Use of this knowledge to shock or startle the Brits in your life is not only allowed, but encouraged.

we’re a corporation; those rules don’t apply >>> As they crow about in this press release, Celera has submitted a draft paper describing the sequence of the human genome to Science, one of the top journals in the bioscience field. Normally, this would mean that they had deposited the sequence(s) being discussed in the paper (i.e., the human genome) to GenBank, which is the public repository for all sequence data, and the standard place to send your sequences prior to publication. In fact, that’s what Science’s Information for Contributors page instructs, under ‘Conditions of Acceptance’:

Archival data sets (such as sequence and structural data) must be deposited with the appropriate data bank and the identifier code should be sent to Science for inclusion in the published manuscript (coordinates must be released at the time of publication).

(Bolding mine.)

However, as this LA Times story reports, that’s not what’s happening. Instead, Celera is going to hold on to the sequence themselves, and is apparently planning on requiring people to agree to not use it for commercial purposes before allowing them to view it. Read the LA Times story; there’s lots of good reaction from leading people in the field. I’ll just include the quote from David Lipman, head of NCBI, and my boss’s boss:

“For two decades, the policy of requiring submission of sequence data to Genbank has been a tremendous success and has been critical for much of the progress we’ve seen in genomics,” said David Lipman, director of the National Center for Biotechnology Information, which manages Genbank.

I had a spirited discussion about this issue with a cow-orker earlier tonight. He was arguing that this was an acceptable compromise, which allowed Celera to get the data out there without having to take the major step of attempting to patent it all. I (unsurprisingly) disagree. I’m not against Celera making some money back on their large investment in obtaining and annotating the sequence. However, if they want to do that, they shouldn’t be attempting to publish the data, in any form. If they are going to publish, they need to follow the rules that have been established by this section of the scientific community, just like everybody else.

My colleague argued that if they didn’t publish, they would run the risk of other firms beating them to the punch on desirable products derived from the sequence. My response to that? “Life is hard.” Business is risk, and by attempting to beat other firms in the product development race, Celera is taking a risk that they might get beat.

Ultimately, I’m not surprised that Celera hatched this deal. From their point of view, it’s really the best thing to do — they get the best of all worlds: protection from competition by other companies, the chance of some measure of good will in the academic and public communities, and the ability to argue prior art on anything other companies try to produce.

I am, however, completely disgusted with the editorial board of Science. By rolling over for Celera, they’ve lowered the bar for future publications from drug companies, and they’ve made life more complicated for thousands of academic researchers. Science is published by the AAAS, the American Association for the Advancement of Science. This decision doesn’t advance Science, and it doesn’t do a whole lot for the American public either. About the only thing being advanced here is Celera’s opportunities for profit. I’m not, nor have I ever been a member of the AAAS. After this mess, I’m not sure I ever will be.

more beer >>> Thanks for the kind word, Steve (and thanks for the continuing top-notch reporting — you’re really going above and beyond “weblogging” with what you do).

However, I do have full Anchor Xmas’s from ‘98 and ‘99 (1 bottle and 5 bottles, respectively). Some day a bit closer to the 25th, I’m planning on starting out with the ‘98, moving into the ‘99 for a bottle or two, and then finishing off with the 2000.

Oh, and the beard is fully back (why, yes, I am a hairy lad!). It seems to have stopped at its usual one to two inch length. I’m thinking about giving it a mild trim to see if I can encourage further growth…

weekend >>> Yet another weekend come and gone and I’m not sure where it went. I did manage to finally track down a beer store worthy of the name (Montgomery County, where I live, is appallingly lacking in decent liquor stores, apparently due to some combination of state and local laws). Anyway, Saturday night I bopped on over to Chevy Chase Beverage, located just over the District boundary, and picked up a little of this, a little of that, and a case of the 2000 Anchor Christmas brew. Verdict: it’s good, per usual, but not startlingly so. I wish that Anchor would do something a bit more radical in terms of the spices and such that they use, but who am I to bitch?

There’s a story behind the Anchor — Lor and I have a bottle from every year since we started dating; a remenant of the ‘beer wall’ from my college group house. Currently, we’re at ten bottles; here in another decade or so, we’re going to have quite the collection.

Aside from the Anchor and the beer store finding, I didn’t accomplish all that much this weekend. Caught up on mail, caught up on websites, and caught up on sleep…

more stuff i don’t have time to read >>> Part two of the Perl/GNOME tutorial is up.

dww followup >>> As usual, I came out of DWW with mixed feelings — I could get into it, but I’ll just add a big “me too!” to Graham’s 12.02 entry.

good deals done dirt cheap >>> I’ve got links to some ‘do-good’ websites (sites that contribute to some sort of charity or good cause in return for a click) on the Daily Dose, but I often just don’t get around to clicking on them. Luckily, Steven Sachs has come to the rescue of lazy gits like myself with a script called charities.cron. Download it, add a cron job to run it once a day, and relax, knowing you’re doing your part for income redistribution in the name of Good.

My DWW page is archived.