Older blog entries for jfleck (starting at number 334)

Booties have changed my life. My feet are toasty warm on bike rides now (or at least not painfully cold), and I have a sleek and stylish superhero look as well. Ice monsters bow down before me! I am Bootyman!
Found a handy little script to fill the boxes in my gnuplot bar charts and redid my cycling graphs this afternoon. I'd been doing a whole bunch of stuff by hand to generate them, so I tidied it up and put it all in a shell script that handles everything.

Now I just need to figure out how to extract the data downloaded by my heart monitor into some sort of usable form. The software that came with it leaves a great deal to be desired, but it looks like all the datafiles are plain text, to I ought to be able to gin up something useful of my own. I think about software in a whole new way.
Tracked down a copy today of Watson and Crick's original Nature paper delineating the structure of DNA. The paper's second sentence must be one of the most successful bits of hubris in the canon: "This structure has novel features which are of considerable biological interest."
I blog elsewhere about cloning. (This is another one of those "which blog should I put it in"? things.)
xach: "Creeping batshit insanity" would be a great name for a popular music act. Unfortunately "Bowie" is already taken. (And for what it's worth, I'm convinced Bowie Poag is not real. Couldn't possibly be. Could he?
The luminarias are being readied (that's not my house but you get the idea) and Mom's been cleared to spend an hour up at her apartment tomorrow afternoon to open up Christmas presents. All is now right with the world.

Happy holidays all.
Mom Diaries
Mom's tough. It's a weird sort of toughness that I only recently fully grasped, because it's masked by this sunny "everything's going to be all right" disposition that could be mistaken for a persistent state of denial. But she's fine now. I mean, she's got a steel ball where the head of her femur used to be, and walking is still exquisitely painful, but she's really quite fine. The physical therapist said she'll be able to walk without a walker or even a cane.
Rambled long yesterday, out along the river with no particular destination in mind, just to be away from anyone I had to talk to about anything remotely important. Hooked up with a couple of speedsters for a while in a nice little train, but mostly I was solitary. It was cold and the trails were empty and aside for the inevitable frozen feet it was a delightful ride.

So delightful that I rode outdoors again this morning, never mind the looming snowstorm.

So there's this great quote attributed to Jamie Zawinski:
Some people, when confronted with a problem, think ``I know, I'll use regular expressions.'' Now they have two problems.
Substitute "perl" for "regular expressions" and you'll understand why I was thinking about that Saturday and Sunday while I wrestled perl temporarily to the ground. My problem was to create a reasonably comprehensive listing of "all the documentation in GNOME". (I'll leave the definitional problem to others, and simply say that I defined it as "all the documentation in the directory where I keep my GNOME cvs stuff".) Going through by hand seemed somehow wrong, so I tarted up a bit of perl to prowl the tree looking for things that looked like docs (and their accompanying omf files). I am totally ass at this sort of thing, so it took me far too long and was a thoroughly delightful experience.
blogs and truth
Sitting in the hospital cafeteria with Dad, Lissa and Nora, trying to explain blogs to Dad:
Me: It's like a daily journal, or a diary.
Dad: Do you tell the truth?
Me: (Pause) Well, no. That is to say, I don't lie, but I do leave things out. Is omission a lie?
Mom Diaries
Mom goes home today, sorta, to the health care center attached to the retirement apartments where they live. She'll be there for a couple of weeks doing physical therapy (i.e. learning to walk again with her new hip). It was such a relief to see her last night, still all crippled up in her hospital bed but looking strong anyway.
I had to leave.

A team of three nurses was moving Mom from the emergency room gurney to the bed in her new hospital room, and I knew it was agony. She is a strong woman. She never screamed. But I knew it hurt. Earlier the emergency room nurse had been asking mom for to rate her pain in a scale of one to ten. She said the pain when the moved her from the gurney to the x-ray table and back was "darn near ten".

So I just walked down the hall for a minute until it was over.

Mom fell yesterday morning while she and Dad were walking to Loyola's, a neighborhood restaurant, for breakfast. It's the place the cops hang out, and three of them rushed out, called an ambulance, and covered her with their jackets and stayed with her while she waited to be scooped off of the sidewalk and into the bowels of the medical system. It is remarkable - she broke her hip before 9 a.m., and before 5:30 p.m. they had given her a new one.

So Lissa, Dad and I spent the day in the bowels of the medical system, trying to help Mom cope with unimagineable pain and eating ice cream. And quietly thinking about and tentatively starting to talk about what happens next. People around us in that emergency room were in far worse shape, suffering from things that could end their lives. Mom's problem is closer to being a huge hassle than a threat to her life. Now we have to think through the hassle.
An Elvis number of two.
9 Dec 2002 (updated 9 Dec 2002 at 16:48 UTC) »
Saw a 1907/08 Picasso yesterday afternoon at the Museum of Fine Arts in Boston, a big cubist nude, one of the handful he was working on during that pivotal year when he made Les Demoiselles D'Avignon. Understanding the context and importance of that moment in the push toward modernism a century ago makes the work incredibly moving. It's a beautiful painting, too, but it is tangible contact with its importance that gave me goose bumps.
It is, I suppose, a biologist's parlor trick.

In the lab at MIT Saturday afternoon learning some basic experimental techniques, and we had some down time while the DNA samples we were "studying" when through the gel electrophoresis reaction we were doing. Clare, the tech who was helping us, gave us each a little vial of salt water and told us to swish it around in our mouths for 30 seconds and spit it back into the vial. She added a chemical to break down the lipids in the cell walls to the vial (essentially soap) and the solution became viscous. Then she added alcohol to denature it and these little filaments began to appear - long strands of my own DNA. You could scoop it out and keep it if you wanted, which I did.
consumption and free software
Clive Thompson yesterday blogged his Washington Post review of a book called "The Support Economy" that argues that in modern industrialized, consumerized societies our identity is defined by our consumption. Mac zealotry is a great example of this. It occurs to me that one of the great attractions of free software is that one can also help create that which one consumes.
The Open Source Mouse
I had the intution, but cannot claim credit for the phrase "open source mouse". That credit goes to Annalee Newitz, who seemed to flash on the idea about the same time I did. We were sitting in the auditorium yesterday afternoon at the Whitehead Institute, listening to Tyler Jacks talk about his woes in working with oncogenic mice.

Jacks works with mice genetically engineered to have tumors, which is a useful model for cancer research (since introducing tumors in a mouse has fewer downsides than introducing tumors in humans). This is a limited but useful research technique, but it has one big drawback. For historical reasons involving work done at Harvard back in the 1980s, DuPont owns the patent to the idea of the oncomouse. Not any particular implementation, but the general idea.

Jacks doesn't have an agreement with DuPont - he just uses oncogenic mice. This is apparently common in the university research community. You can see the potential for mischief here, which is already playing itself out.

Free/open software offers another model for all this. Actually, to be fair, what free software is doing is conceptually borrowed from academia, where the "products" of research are freely shared and one builds on the work of one's predecessors. Perhaps the mouse people should get together and open-source their critters.
The postmodern is sorta like pornography - difficult to define with precision, but one knows it when one sees it. Here goes: a real bar, I'll call it the "Bull and Finch", serves as backdrop for a wildly popular television series - I'll call it "Cheers". Then the real bar is renamed "Cheers". The TV series runs its course, but the real bar stays named "Cheers" and becomes some sort of tourist destination.

I stumbled on Cheers this evening while walking 'round Boston in the snow. I did not go in.
One of my colleagues had a great line in the newspaper Wednesday : "Thanksgiving never really looked like that Norman Rockwell illustration, the one that shows an apron-draped grandma serving a gigantic turkey to Caucasian kin aglow with beatific light." We've been manufacturing our own family T-Day traditions now for a while, embodying some of the Norman Rockwell goal but drifting pleasantly away.

I ran my 10th consecutive Albuquerque Turkey race this year, in my 43rd year, thankful that I still have 5k in my legs. It's an incredible affair, run by a kinda goofy running shop owner, winding through the country club neighborhood and then out by the river. I don't race much any more - the turkey is the only race I've done the last couple of years. I keep a log of every race, and the times become a record of my aging. This year's was the slowest 5k I've run, and I take pleasure in the gentle aging that implies. There were some really old people out there still doing it, a good set of role models.

Mom and Dad came over late morning, and we ate some of the most fabulous cheese for lunch, then cleared off the table and started the puzzle.

The puzzle is a more recent tradition - a big all-day jigsaw puzzle fest. This year we did a map of LA, where we'd all spent decades of our lives. It was a hoot, finding the places in isolation, then figuring out how to assemble them. Lissa did the San Fernando Valley, Mom, cheerfully proud that her fading eyesight still let her do the puzzle, did San Bernardino, Dad did the mountains and I marched up and down the Pacific Coast Highway, past the Santa Monica Pier and down to the beaches of Laguna that I love so much. Only Nora was left out, too young when we left LA to remember any of that.

We went with the nice linens, but none of us are so into feasting that it was really that big a deal - a small turkey, some lovely rice stuffing and Dad baked me a sugar-free apple pie.

After dinner, the four of them played word games while I bowed out to do some packing for my trip.

It was a gentle day, no longer freighted with expectations, just filled with an easy rhythm.
Back to school next week. I'm off to the Whitehead Institute at MIT for a week of intensive academic exposure to people much smarter than me, who will attempt to teach me and a handful of other science writers about the genes and the revolution in biochemistry. I am very excited about this. (And bonus stuff - I get to sandwich in a couple of days with my sister, Lisa, and her husband, Tom, at the beginning and end of the trip.)

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