Sunday, July 31, 2005

That Jessica story

Ok, while I am remembering Jessica, as sad and poignant as her death is, remembering this story can still make me laugh.

This happened at the 2003 American Medical Informatics Association Convention in San Antonio. Another grad student--let's call her Amy for the moment, until I find out if she's ok with her part in this story being shared--was crashing in my room, but was not benefiting very much from the talks, because she was working on a project for an undergrad CS course she was taking. Unlike grad courses, undergrad courses aren't flexible about things like conferences, so she still had to get this in on time, even though she was at AMIA.

One night, Amy was up working late on her project, and she was concerned that she was keeping me up, too, so she offered to go down to the hotel lobby and work there. She said she'd be back by midnight, and I went to sleep. I woke about 3:20 AM, and not only was she not there, her bed had clearly not been slept in--there was no evidence that she had ever been back to the room.

So now, I wasn't sure what to do--if she was genuinely missing, I was the only one who knew about it, and I should sound the alarm right away. But if on the other hand, she had only just lost track of time, and was having fun with friends, then it would be overreacting to report her missing.

I went down to the lobby to look for her, and there was no sign of Amy there. I asked the desk clerk, who hadn't noticed anyone working in the lobby. So I went back up to the room still wavering.

I wasn't sure what to do, although I knew if I did wake up the grownups (profs, admins from our group) at this hour, it would instantly escalate. So I was hesitating over what was the right thing to do, when it occurred to me to ask Jessica. Ok, I knew she'd bitch me out for waking her up at that ungodly hour--she had a temper and a mouth on her, I knew that--but more important, I knew that she would come through in a crisis, as when she had taken me to the ER in Utah, and that she could help me decide what to do. If she thought this was an emergency, then I would wake up our profs about this. If not, then I would have awakened her for nothing, but I would spend the rest of the conference doing penance to her, and it would ultimately be all right.

I dialed Jessica's room, and let it ring. The phone rang about 20 times, but there was no answer. This was starting to get really weird, and I was starting to get scared, when I heard a cardkey slide in the door, and Amy walked in.

In relief, I put down the phone. It turned out that she had been in the lobby working on her project all this time, and the moment I had chosen to go down and look for her had been, perversely enough, the time when she had hit a snag and gone around the corner to a phone booth to call another friend for technical assistance. We both had a good laugh over the whole thing, and then went to bed, as it was going to be a busy morning.

Around 10 AM, I ran into Jessica at a bioinformatics talk, and she looked awful. I asked her what the matter was, and she responded irritatedly, "Some ratf***er called my room at 3:30 this morning.".

Oops! I quickly decided against honesty being the best policy in the moment, and instead went with a more "Really? Do tell!" approach.

She continued "I thought it was my 7 AM wake-up call, so I got up and got dressed and put on my makeup without looking at the clock.". One thing I haven't mentioned yet is that she was a Goth, so she went to a lot of trouble with her clothes, hair, and makeup; getting ready meant about an hour and a half in the morning.

Still without looking at the clock, she walked over to the convention center, attributing the morning darkness to the latitude. Only when she tried the door and found it locked, and noticed that absolutely no one else was there, did she look at her watch and learn that it was 5 AM.

By this point in the story, I am feeling absolutely, horrifically, guilty. But this is the story that keeps on giving, so it didn't end there--in an absolutely foul mood, she went back to the desk clerk on duty, and tore him or her a new orifice for messing up her wake-up call.

Much, much later, did I tell her what really happened, and by that time, she was able to laugh at it. So that is the story about the time Jessica called me a ratf***er.

Jessica made me laugh, and she made me cry, and I miss her.

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Jahrzeit für josefinek

Almost exactly a year ago, my friend and colleague Jessica went missing. After people searched frantically for her for days, she was found, having died accidentally and tragically (in the original Greek sense of the word, not in the superficial way it is used promiscuously today).

I am in a very pensive mood today, as I remember her. She was dangerously smart, wickedly funny, and very kind to me, especially during a medical emergency while we were traveling to a conference in Utah, and for the surgery afterwards. She was also complex and mercurial, and there were problems toward the end, which I don't want to either gloss over, nor dwell on, because people I care about got really hurt in the aftermath--but she was also a fiercely loyal friend who stood by me when I most needed it. I am grateful that I got the opportunity to know her, for however short a time it was.

Godspeed, Josefine K.

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Saturday, July 30, 2005

A moral tale

So I missed a whole day of work this week due to cat seizures (story to follow), and I needed to make up work this weekend anyway. Friday I called the bike store and they said my bike was ready, so I decided to leave work an hour early, swing by the bike store and get my bike, and just make up one additional hour of work this weekend.

The bus is pulling out, when some guy runs out in front of it and blocks it. He gets on, and he and the driver start threatening to punch each other (when two passengers are fighting, you get the driver, but when the driver's involved in the fight, I'm not sure what the protocol is). About then, I get out my cell phone, unlock the keyboard, and set it to the entry for 911, just to be ready if necessary.

The argument continues until the guy gives up, goes to the back of the bus, and lights up his crack pipe. As someone who wouldn't even dare drink a Coke under the No Eating/Drinking/Smoking sign, I have to admit, that's chutzpah!

In the meantime, a buzzer starts going off loudly and a red light flashes on the dashboard. To me, that would mean pull over, but the driver just ignores it and keeps going down the highway. I'm hoping the engine doesn't explode, and the woman next to me observes "This ride just keeps getting better and better.".

Finally, the driver is forced to pull over by the fact that the bus isn't running anymore. So there we are in the middle of nowhere, just standing around in the heat. A little entertainment is provided when the driver decides to call 911 on Crack Guy, but he's had time to dispose of his stash, so although 3 police cars show up, nothing happens. His protestations of injured innocence were, however, quite well performed; he was lying, and everyone knew he was lying, but with no evidence, he got away with the virgin act. At least that bit of dinner theater killed about 20 minutes, as the Transportation Authority couldn't be bothered to send out an extra bus, so we had a lot of free time on our hands.

We had to wait for the next bus an hour later, plus the 40 minutes late that it was, just on top of that. As it ended up, I got to the bike store at exactly the same time I would have if I'd left work on time, and now I have an hour of work to make up this weekend.

Moral: that'll teach me to leave work early.

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Bad blogger!

Blogborygmi's got my number; actually, several of them. (and isn't that a clever name?)

I've got several posts in the works, but I've been busy at the new job, and Philadelphia's got more things to do than Seattle (no offense, Seattle!). Plus, that old tropical malaise set in here, with all the heat and humidity (don't let the latitude trick you; Philadelphia used to have malaria, yellow fever, and dengue fever back in the day). But enough excuses; I'm missing blogging, and tonight's a good night to get back to it.

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This is sad

Orac links to a story on how poachers taking tusked elephants out of the gene pool is causing the percentage of tuskless elephants to rise.

Still, that is a classic example of how natural selection works in response to a selection pressure--and maybe if this makes fewer elephants targets for poachers, it's a good thing in disguise.

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Monday, July 11, 2005


This movie was on over the July 4th holiday weekend, and the History Channel seems to like to play it a lot, too. I never get tired of watching it, though I think I've seen it through from beginning to end only once--usually, I just flip in in the middle, and then stick with it.

It's not a profound film, and it is very violent; my mother-in-law saw it once, and barely made it through it at that. But it is a war film, and it is a buddy movie, and it does that job well--and most important, it highlights an aspect of history that remained buried for a long time after WWII, although it is more talked about and better-known today.

The Navajo Code Talkers were instrumental in the defeat of the Japanese in WWII, and more and more people are hearing about that today. But some other important things are not as well known, although they should be. I learned this from my professor, Dr. Gary Witherspoon, who taught Navajo language, culture, and history.

After the Long Walk, where Kit Carson pursued his anti-Navajo campaign by killing the animals and destroying the crops of the Navajo, and forcing them to abandon their homes and march far away from their land, the Navajos eventually were able to return to their home. But governmental policies to protect US markets led to more massive killings of Navajo livestock in the early 20th century. As an outsider, I cannot talk with authority on how the Navajos feel about their animals--I can only say that it was a tremendous tragedy on both an economic and a personal level for them. They had every right to be bitter about it, and to tell the US to take a hike when they came looking for help to defeat the Japanese. That they did not, despite the grievances the American government had visited on them, and that they were able to put together such a decisive effort to defeat the Japanese, speaks far more highly to their patriotism and bravery than I can do justice to.

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Être et avoir

This was a funny, sweet little documentary that I just saw about child-centered teaching in rural France. No big plot points, just a lot of character development, a lot of great modeling behavior (and some not so good :), and clearly a man who loves children and loves teaching them. I wish I could have had a teacher like M. Lopez.

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Just saw this film the other night--I can't get over the contrast between the heroism of Jean Dominique, a man who spent his life fighting to bring truth (and paid dearly for it), versus the media we have nowadays.

A stirring, tragic film--I highly recommend it, but prepare to be disturbed.

I also have a much higher opinion of Jonathan Demme for bringing out this film--not that it was ever low, just that I never gave him much thought before this. Apparently, he is very involved in Haitian social justice issues. His assistant calls this film a "hagiography", and yeah, it kind of is--but that does not detract from its essential truth.

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Giving up the yellow jersey

"We don't need the yellow jersey," Armstrong said. "We don't need to keep it through the Alps. We need to have it at the end. I felt like today might be the day when the jersey was given away, and that's how it turned out."

I agree that this is a good strategy--defending the jersey at this point would have been a distraction. I expect Lance to retake it in the later mountain stages, when it counts more than now.

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Baby panda!

Mei Xiang had a baby while I was traveling, and this is the first I heard of it!

Bear pregnancies are often difficult to diagnose in advance; their cycles are not fully understood, and they have pseudopregnancies, which complicate the picture even more. I'm not sure when they determined she was pregnant, although they have been monitoring her behavior and hormones for a while. But this is great news--another baby panda in the world!

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Saturday, July 09, 2005


The French verb rester (to stay) is a regular -er verb. It is conjugated in the usual way:

je reste---I stay

tu restes---you (familiar, singular) stay

il/elle reste---he/she/it stays

nous restons---we stay

vous restez---you (formal, plural) stay

ils/elles restent---they stay

The French proposition avec means "with". So "rester avec quelqu'un" means in English "to stay with someone". That is the denotation of the term.

The Kreyol language of Haiti has an enormous amount of French influence, but it is not strictly derived only from French--many African languages as well as English have influenced the vocabulary and the grammar. Still, there is a great deal of overlap between Kreyol and French, and Haitians still study French in school as well. So it is not surprising to find many of the same words in French and in Kreyol.

"Connotation" is different from "denotation", in much the same way that "term" is different from "concept". The denotation of a term is its dictionary meaning: the denotation for "dog", for example, is "a member of the species Canis familiaris". "Connotation" includes the emotional and other psychological layers invested in a term, thus going beyond the simple denotation. A person who has been attacked by a dog may think of dogs not only in their dictionary meaning, but as "a vicious animal"--for him or her, that is the connotation that "dog" holds.

The French "reste avec" (spelled "restavèk" in Kreyol) thus denotes that [someone] stays with [someone]. However, the reality (connotation) of "restavèk" is child slavery. A child is sent away from his or her family to "stay with" a host family.

These children act as live-in domestic servants and rarely are sent to school, receive new clothing, are allowed to play or visit their families; are often verbally, physically or sexually abused, and are nearly always exploited beyond the limits of national and international standards for the rights of children.

Often, they die young.

Some sites for learning more about the problem of restavèks and what is being done to help them are here, here, here, here, here, and here.

Je reste avec ma famille.

Tu restes avec les tiens.

L'enfant reste avec qui?


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Friday, July 08, 2005

Goodbye Seattle, hello Philadelphia!

Blogging has been even lighter than the norm lately, due to traveling across the country and limited access to the Internet. But that should pick up over the weekend, as I get settled into my new (temporary) life.

I now have lots of threads outstanding, and will soon have time to get back to them (beaver cloacae, anyone?). So I'll be blogging on new Philadelphia stuff, as well as tying up loose ends.

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Tuesday, July 05, 2005

Lance in the lead

Étape 4: Tours > Blois

Lance regained the yellow jersey in this stage.

Lance Armstrong first, George Hincapie second, and Jens Voigt third. David Zabriskie had a crash today; it remains to be seen how this will affect the rest of the Tour for him.

Lance Armstong has the yellow jersey, Tom Boonen the green, Erik Dekker the polka-dot, and Yaroslav Popovych the white.

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Monday, July 04, 2005

Catching up on the Tour

This is all second-hand, as I've missed the Tour for the last two days--too busy! So here are the results, without any interpretation.

Étape 2 - Challans > Les Essarts 181.5 km

Tom Boonen of Belgium won the stage, followed by Thor Hushovd of Norway and Robbie McEwen of Australia. There was a crash, but apparently all the riders were able to get back in the race. David Zabriskie keeps the yellow jersey. The green goes to Tom Boonen, the polka-dot to Thomas Voeckler, and Fabian Cancellara keeps the white.

Étape 3 - La Châtaigneraie > Tours 212.5 km

Tom Boonen won the third stage as well, followed by Peter Wrolich. Robbie McEwen finished 3rd, but was ruled to have interfered with Stuart O'Grady's line at the finish, so third place went to O'Grady, and McEwen went to 186th (last) of the main peloton.

David Zabriskie keeps the yellow jersey, Tom Boonen keeps the green, Erik Dekker takes the polka-dot, and Fabian Cancellara keeps the white.

I hope I can catch more of the Tour before I leave on the 7th; we'll see if that's possible.

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The fireworks show over Lake Union had some nice pyrotechnics this year, but dear Buddha, the music! Did they decide to save money by replacing the musical director with an iPod shuffle this year? Although there were some nice fireworks, like cubes and volvox-like effects, the music really detracted from them.

Later in the show, they did some appropriate pieces--"R-O-C-K in the USA", and the "Viking Kittens" song (I'll have to look up the real name in a minute. UPDATE: "Immigrant Song" by Led Zeppelin; I always want to call it "Valhalla", and I know that's not right)--but they started off so lackluster. "Smoke on the Water" is a cliché by now, and "Unforgettable"? At least they didn't do the posthumous version with Natalie Cole and her father.

The worst, though, was the segue from "True Colors" to "Ride of the Valkyries"--that was just embarrassingly bad. As Iain said, he never thought he'd be hoping to hear "Carmina Burana" with fireworks again, but there you are. It picked up after the Wagner for a while--the big band piece worked ok, although there were better ones they could have used--but then bobbled a bit, although the Kate Smith "God Bless America" finale was strong.

This "jack" radio format just doesn't work for these kinds of fireworks shows. Please, One Reel, hire your music director back--please don't let an iPod coordinate the music for the fireworks show next year! Otherwise, I might just as well turn down the sound and play my own soundtrack instead. And believe me, you won't like my soundtrack...

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Saturday, July 02, 2005

"Parrot" makes its debut


I'm pleased with it for a first project, but I do see some things I would do differently.

I can't photograph them very well; I need different lighting, and/or a lens that can fit the whole thing in without messing up the perspective, or both. But these rough photos will at least provide an idea of what I'm getting at.

The first photo of the piece hanging on the wall has an awkward flash in it, but it does do a good job of showing the texture of each kind of glass. So you can see that the sky is kind of striated, the blue feathers are kind of pebbled, etc. The beveled panels all around are a nice touch; they weren't my idea, but a suggestion that really worked out.

The second piece is taken with the piece on a light box, so it is illuminated uniformly from behind. All the texture is flattened out, and the contrast between the transparent yellow and the translucent or opaque other colors disappears--but you can see details here that you can't in the first photo.

I am pleased with the red that runs through the brown in the tree branch, which you can see better in this photo. Something I'm not quite so proud of is the gap between the parrot's large blue wing and its yellow body; it is the small white spot above the lead came in the blue wing.

Most of this design was pretty forgiving (unlike the Necker cubes I wrote about below); this is an example of where I needed to be more precise. For a hanging, not such a big deal (especially for a first project); if this were an exterior window, on the other hand, that would have to be redone.

I am pleased and impressed with our teachers John and Rumi, and their pushing us to do a project right away. I thought we were just going to do rectangles or something; when I saw what they had in mind, I did wonder what I had gotten myself into. But it worked out well.

I will not have an opportunity to finish the copper goldfish until I get back from Philadelphia, but it's ok. I already know what I want to do for my third project--a sun bear! and both the goldfish and sun bear will still be here when I return in November.

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Stage 1: Fromentine > Noirmoutier en l’ile

Wow--the Tour is off to an exciting start!

I had some doubt yesterday about whether Lance's head was in the race enough for a seventh win; today went a long way to convincing me (although Mr. Raven never agreed with my analysis anyway; he says it's not the way athletes think. Since I only follow sports once a year, and he does year-round, he may just be right.).

Despite slipping out of his right clip on setting out (at least it was on the upstroke, not the downstroke, where it could have been much worse because of the force applied), Lance caught, then passed, his rival Jan Ullrich, and came within 2 seconds of winning the stage, which finally went to David Zabriskie. Until he came in after Zabriskie, there was some talk of his being the first rider to dominate every stage since 1934, but I'm actually relieved that that's not the case--it would have been a distraction, when Lance needs to concentrate on the mountain game ahead.

Today he was primed--making good time, yet not looking like he was straining as he climbed the bridge at the beginning of the route,

while Jan Ullrich was working hard. Lance just kept going, until he overtook him, and continued to gain time while leaving Ullrich in his tracks. In fairness, Ullrich did have a crash yesterday while reconnoitering the route, a fact which Lance acknowledged in the post-stage interview, and which probably affected Ullrich's performance. Still, Lance often holds back until the mountain stages--for him to come on so strong in the preliminary stages, where his rivals are looking to gain capital, has got to be a psychological edge.

Results after Stage 1:

1. ZABRISKIE (USA, CSC), 20’51’’
2. ARMSTRONG (USA, DSC), 2 seconds later
3. VINOKOUROV (KAZ, TMO), 53 seconds later
4. HINCAPIE (USA, DSC), 56 seconds later
5. BODROGI (HUN, C.A), 59 seconds later

At the end of the first stage, the jerseys are:

  • yellow (highest overall standings): David Zabriskie
  • green (highest point standings): David Zabriskie, worn by Lance Armstrong
  • white (highest in young rider standings): Fabian Cancellara

This was an easy (relatively!) day: 19 km. Tomorrow, Stage 2: Challans > Les Essarts, will be a more grueling 181.5 km.

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Best. Cover. Ever.

"Hurt", by Johnny Cash.

In fairness, had I been the record exec it had been pitched to, it would probably never have been made. Good thing whoever's idea this was had more imagination than I did, because it is absolutely great.

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Cat culture

One of the traditional (note I did not say "true", just "traditional") criteria for demarcating humans from animals has been the assertion that animals act only out of instinct, while humans can decide to act out of other than pure instinct, and can transmit that kind of action to other humans, through teaching. In that way, certain practices become cultural.

A troupe of macaques in Koshima, Japan gave that assertion the lie when researchers watched one monkey take her sweet potatoes down to the ocean for washing. Other monkeys observed her, and began doing the same, finally transmitting this "cultural" behavior across generations. In my home, there is a similar phenomenon. Somewhere along the line, many years ago, my cat Momo began tapping or poking my hand when she wanted to be petted.

Momo is long gone now, but all the cats who knew Momo do the same--and even some who never knew Momo. I'll be lying on my side, and Cleo will come up behind me. Poke, poke, poke--non-stop, until I roll over and pet her. And if I stop before she's sated, she'll start poking again. Same with Bear and Diana (except they give up more easily than Cleo does). Only they understand the concept of "Soft paws, please!" (no claws) better than my little semi-feral rescue Cleo.

It's not as if it's the most profoundly abstract connection any animal ever made--they're simply demo'ing the behavior they want carried out. So it could possibly be a simple case of independent invention--but in 100% of the post-Momo cats up until now? It seems unlikely, though I have no idea how I'd figure out the p-value for that one.

Iain recently brought home a new cat, Andy, who is settling in just fine. I hypothesize that within a year of watching them poke or tap me to get a pet, he will be doing the same--they will have taught him what passes for culture in our little cat society.

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Well, another rainy weekend in Seattle--not a big surprise, even in July. It could go either way for the Fourth; let's hope it clears up for the holiday.

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Friday, July 01, 2005

Fire ants

After a long conversation over on Pharyngula about fire ants, I just learned that there are over 200 species of fire ants in the group of "fire ants", plus others--also called fire ants--in other groups. That's the best example of the difference between referent and term that I've seen in some time.

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