Friday, March 31, 2006

Patently non-non-obvious

Paul Graham has an interesting essay on whether, and how much, software patents matter. Snippet:

If you want to patent an algorithm, you have to frame it as a computer system executing it.
Then it's mechanical; phew. The default euphemism for algorithm is "system and method."
Try a patent search for that phrase and see how many results you get

Yup. Guilty as charged. These are issued patents that I was involved in filing for over 5 years ago and pretty much forgot about until a couple of months ago. I guess they finally made it through the labyrinth of the Patent Office and were actually granted. Look, ma, I'm an inventor !

[Just to be clear -- I don't think that the "systems and methods" described in these patents are particularly "non-obvious", but, hey, I was young and needed the money.]

Monday, March 27, 2006

The most fragile machine in the world

... is apparently the escalator at the Downtown Crossing subway stop. About every 2-3 weeks, its innards are laid bare, and serious-looking, grizzled men, Men Who Know How To Use Tools, stand waist-deep in its guts, among gears, chains and other manifestly metallic, oily things, discussing the state of their patient in grave tones.

Why a machine that moves at the stately pace of 2 feet a second should require almost-weekly maintenance whereas another machine that revolves a few thousand times a minute, a machine driven by blowing sh!t up inside it, can go for years on end with no problems is baffling. Sure, I can see parts wearing out and needing to be replaced, but every couple of weeks seems a bit much. Is there a malevolent escalator gremlin that keeps gumming up the works ? Is the underside of the escalator continuously being sprayed with acid ? Is it shoddy workmanship, leading to a continuous case of "what had happened was ..." as the escalator repair company tries to explain the latest breakdown ?

Inquiring minds want to know.

Saturday, March 25, 2006

An update from the experimental trenches

It would seem that I'm being punished for my recent whistle-blowing description of the realities of lab work. Consider: since then, I've wasted a week trying to figure out why a boringly standard PCR reaction [a technique for amplifying DNA, kind of like a copier] wasn't working, only to find out that it was because one of the reagents was contaminated [and of the two tubes containing that reagent, I kept picking the contaminated tube ...]. And I've spent the last week trying to get run-of-the-mill yeast cells to grow in a medium that is the yeast equivalent of nutritional paradise, with no success.

In other words, I'm having trouble even with stuff that should be simpler than falling off a log. This does not bode well for my proposed thesis project, which involves making lots of changes to yeast DNA. On the other hand, maybe I'm just frontloading all the experimental woes and once I get past the startup issues, everything will go swimmingly ... yeah, that's it.

Friday, March 24, 2006

Kickin' like Bruce Lee

After a couple of weeks of false alarms, when Christina could feel the baby moving and kicking but I couldn't, I finally felt him kick. Very cool. Borrowing a turn of phrase that seems to be popular in scientific papers, I think that it's fair to say that "this evidence, taken together with earlier pictorial evidence, argues convincingly for the presence of another human being inside Christina".

That said, I still think the whole person-living-inside-another-person bit is ... strange.
It's one thing to know about the process in an abstract sort of "Oh, yeah, babies grow inside their mother's womb" way, but observing it on a daily basis definitely brings home the reality.

Friday, March 17, 2006

Creation of fire by unnatural means

From a Driftglass rant [thanks to Tozier for the link]:

"Blame everyone who was screaming “Fire!” while the coming conflagration -- that you created by briskly rubbing stupid ideas together -- was containable"

Awesome imagery. And here's the appropriate soundtrack, courtesy of Beavis and Butthead.

Wednesday, March 08, 2006

Alternative uses of nuclear power

As a big fan of comic books, I whole-heartedly agree with TJ Prima.

Sunday, March 05, 2006

Panic-inducing, somewhat arbitrary, classifications

Sometimes, the phrase "high risk", it does not mean what you think it means.

Case in point: standard prenatal testing usually involves an ultrasound at 12 weeks that measures things like the nuchal translucency of the baby, plus a maternal blood test that looks at the levels of various hormones and proteins. Passing this data, plus the mother's age, through the diagnostic meat grinder results in a number that tells you the risk of the baby having Down's Syndrome. This number is generally conveyed to you by your doctor/ob-gyn/midwife/initiate-in-the-healing-arts-of-your-choice.

Now, here's the way you don't want that person to start the conversation: "I'm afraid that you're at high risk of having a child with Down's Syndrome." [which is how the conversation started for us]


That's the sound of our jaws and hearts hitting the floor. After the initial "Wha' happen ?" reaction, and a flurry of agitated questioning, it turned out that our kid apparently had a 1 in 130 chance of having Down's and the midwife suggested we go see a genetic counsellor to talk about what to do next. Needless to say, we were fixated on the "high risk" bit and dragged ourselves out of the door in a somewhat dejected manner.

About 30 minutes later, when my brain started working again, I realized "Wait a sec ... 1 in 130 ... that's less than 1% ... that's 0.8% ... that means the chances of the child not having Down's Syndrome are 99.2% ... sh!t, those are better chances than just about anything in life." Actually thinking about the numbers like that made us both breathe much easier.

It turns out that the phrase "high risk" means "greater than 1 in 250", and that cutoff is chosen because the risk of inducing a miscarriage by having amniocentesis, which can tell you for sure whether or not the child has Down's syndrome [as well as other chromosomal abnormalities] is about 1 in 250. In other words, the high-vrs-low risk classification is based on a cutoff that nobody without a screaming case of the OCD heebie-jeebies would consider "high risk", even taking into account the increased risk sensitivity induced by the thought of bringing a new person into the world.

You would think that part of the training given to people dealing with already on-edge parents-to-be would include helping them to see these sorts of diagnostic numbers in context. I mean, contrast a conversation that starts with

"Your child has a 99.2% chance of being OK, which is a bit lower than the 99.6% we usually like to see, so let's talk about what you might want to do"

with one that begins

"You're at high risk of having a child with Down's Syndrome."

It's hard to imagine a harsher start than the second one, other than maybe something like "Based on our tests, your child is doomed to a lifetime of pain and suffering -- an eagle will feast on his liver daily, he will be made to push a boulder uphill in perpetuity and, oh, let's see, it says here that ... every two days or so, he'll have to dive into a pile of razor blades, after which he'll be sprayed with salt dissolved in lemon juice. Any questions ?"

In any case, we opted to have amniocentesis to get rid of that niggling 0.8% of uncertainty and the child is fine and definitely a boy.

The moral of the story: when you hear a fuzzy phrase like "high risk", ask what the precise definition of that is before you get all wound around the axle.

Saturday, March 04, 2006


We had an initial inkling based on ultrasound pics that were just a bit too early to be definitive, but it's now been confirmed: we're having a boy. And each time I think "I'm going to have a son", it stops my train of thought in its tracks because a first-born son has such ... mythical associations.


Sweating the little things isn't always bad

Arts and Letters Daily has links to two articles that debate the effectiveness of the "broken windows" approach to crime fighting, which is based on having the police pay more attention to misdemeanors, such as "loud parties, unleashed dogs, public drinking, and even littering".

I have no idea how effective this approach is in reducing serious crime. However, I think it's not a bad idea for the simple reason that it might make people more civil. And that's something that's sorely needed in Boston, where the pendulum of individual rights vrs communal obligation has definitely swung a bit too far to the "It's a free country and I can do what I want" side. Actually, it may not even have as much to do with people explicitly asserting their liberties as it has with them just being oblivious to the fact that, oh, dropping trash in the middle of the street when there's a garbage can 10 feet away, or singing [badly and loudly] on a crowded commuter train might just be, y'know, not very "considerate of other people".

I never knew I was such a "people suck" curmudgeon until I moved to Boston. At least I think of it in terms of "Back in Seattle ..." instead of "Back in my day ...".

Thursday, March 02, 2006

Whole numbers in the range 1-10 only, please

First object lesson in being a teaching assistant: do not make up a homework problem whose solution involves a lot of fiddly arithmetic with numbers that have to be accurate up to 4 decimal places. Or else you'll end up having to check that fiddly arithmetic for 60+ problem sets. And that's no fun for anyone.

Words worth a thousand words

Every once in a while, you hear a new word or phrase that is so obviously le mot juste that it is immediately absorbed into your vocabulary. Here are two recent acquisitions of mine:

- If you've ever wanted a perfect way to describe the look that comes from kids wearing sweatshirts with the hood up, or a beanie/skull cap/knit hat, and their pants around their knees, forget "gangsta". A much more evocative term, courtesy of Christina: urban gnomes. It's brilliant. I mean, compare this and that and you'll see what I mean. I'll never be able to look at these kids again without giggling.

- If you want to convey how earnest you are, appropriate use of the word sinceriously will make your sentiments perfectly clear. Again, from Christina, but not one she coined; it was generated by somebody she works with for whom English is a second language.