Personal Health Update

I wasn’t exactly handed a winning ticket at the Genetic Lottery. As a kid, it would have taken less time to list the parts that did work as they should have. But things got under control and I am generally fine these days1.

However, God personally hates me and wants to make sure I know it. Which is why I belong to the statistically improbable demographic of young people with recurring kidney stone problems despite relatively healthy dietary habits2.

On a nearly regular basis, about once every two years, I get to enjoy the pain of childbirth, minus naming process and postpartum hormones rush.

On the plus side, with the years, the routine has started to take the edge off (or I am developing a much higher tolerance to pain): when a stone episode strikes, nowadays, I just casually recoil in a fetal position for a couple hours at a time while waiting for it to pass after a week or so; years ago: I would longingly stare at a kitchen knife while considering my options for self-surgery on the spot.

The other good thing is that I have learned to recognise early symptoms (as well as the time they are likely to occur: mine always happen in Winter, for no reason any specialist has ever been able to explain satisfyingly), which helps preventing me from making bad decisions… such as embarking on a 15 hour trip home to San Francisco from Paris via London (aka: the Story of my First Stone). Testament to the good old pre-911 days: when some security guy at Heathrow noticed the sweaty, grimacing guy waiting for his plane, went and asked “Sir, I must ask you: have you been consuming any drugs?” and got a near-hysterical answer of “No, but if you have any, I’ll take them!” through gritted teeth… he just walked away as he came.

These days, once the chest pain shows up, I would know better than trying to lob it with, for sole comfort, 2 aspirins and a cup of boiling hot tea purchased on the Eurostar.

Three days into the current episode, I finally went for a consultation at my nearby hospital: a CT scan confirmed the obvious and I was sent on my way with the usual advices and a couple prescription drugs.

Incidentally: I paid ¥5,000 (less than $50) for a full consultation and a CT scan, both of which took a grand total of 40 minutes, from the moment I stepped into my neighbourhood clinic. The actual cost, pre-universal-coverage, was ¥19,000, or about $200 (for that money, a US CT technician won’t even spit on you): dear US readers, aren’t you glad you live in a country gloriously free of such pesky Universal Healthcare and reasonable health costs.

Anyway, all that to say that I am slightly incapacitated at the moment, and lagging on communication (although oddly productive on whatever I manage to put my mind to, in between two bouts of holding my abdomen, wondering if downing a bottle of Draino might help). It will get better and I’ll catch up on email and everything, soon (i.e. anywhere from next week to next year).

That’s it for the immediate personal health update. Everybody with a normally working pair of kidneys and zero interest in the practice of hobbyist medicine at home can (and should) stop reading right now. Trust me, there’s nothing interesting under the fold.

  1. beside that violent twitching on the left side of my face and the regular furball coughing, that is []
  2. people in their twenties who barely drink a can of coke a month aren’t supposed to get kidney stones, let alone chronic ones []

Japanese girl at local bar: Do your prefer Japanese girls or foreign girls?

Dave: Err… huh… dunno… Country doesn’t have much to do with it…

Japanese girl: Aaah, of course… It does not matter…

Dave: Indeed.

[…]

Japanese girl: Ok, so… Which type of girl do you prefer: long straight black hair or blonde with blue eyes?

After keeping it on the back burner for way too long, I felt I should finally make this project public, no matter how unpolished:

KanjiStory.com is a website geared towards people studying Japanese kanji (and, I guess, to a lesser extent, Chinese… but it probably needs some tuning for that). It provides a simple yet powerful interface for people to write kanji mnemonics in the form of a simple story.

The best way to see what I mean is to go register (10 seconds, one click), read a few stories and finally: take a stab at writing your own. Allowing users to contribute stories is at least 90% of the point of this website at this stage, so please do not just go, check out the dozen sample stories and call it a day without trying the editor.

The current version of the website, although quite spiffy code-wise, needs a huge amount of work to be called a proper beta. And then, there are two million cool features just waiting to be added. However, given my very limited time resources, I figured I would first check to see how much interest (and active participation) in the project I can raise, before committing any more time working on it.

Do not hesitate to post your comments and suggestions below, but keep in mind that this is all very early-stage development and that many new features will come, once (if) this ever takes off the ground as a community project.

As an aside, if you are a reasonably experienced PHP dev with an interest in contributing to this project: get in touch (use the address: “zedrdave” at Google’s mail).

If you want to be kept informed of future KanjiStory-related news, easiest way for now is to sign-up as a fan on the facebook page (until I set up a proper forum and RSS feed on the website).

As a hobbyist translator and someone with a general interest in languages, I always enjoy a good mistranslation roundup. Not just nitpicking on what idiom best conveys some tricky expression in another language, but plain outright mistranslations (French faux amis, for example).

Translators working on closely related language pairs such as French and English (as opposed to more distant ones, like Japanese and English) have a tendency to be writers first, translators second. Their actual mastery of the source language is sometimes surprisingly low, but (for good or bad reasons) editors seem to think that the quality of their written production in the target language can make up for their weakness. This is an especially common occurrence in English to French translations, where French speakers barely English-fluent have been known to translate major English literary works (not a new practice either: Baudelaire‘s famous translation of Edgar Allan Poe, while delightfully written, is so incredibly riddled with errors that it could be a new work in its own right).

The smug pleasure of pointing out errors in the work of so-called professional translators can only be beat by one thing: the even smugger pleasure of pointing out errors in said corrections…

In a recent Guardian article, Germaine Greer plays on a rather trite cultural tropism: “Why do people gush over Proust? I’d rather visit a demented relative“.

Yes, we get it: Proust’s writing is long, convoluted and not exactly packed with action. I am far from his greatest fan and would not even put him in my personal top ten of French authors, but criticising his style on length and paragraph count is about as subtle as calling Picasso’s paintings a bunch of kid scribbles by a guy who couldn’t draw a normal face.

The translation comment, however, is what grabbed my attention. Ms Greer chose to illustrate the poor quality of Proust’s English translations with a sentence drawn from the fifth volume (La Prisonnière, aka The Captive):

And we are back on the slow crawl toward eventually explaining what I do, out here in the darker recesses of my lab tucked in the remote Kansai countryside.

Aside from breeding deadly mutant monkeys to serve in my army of evil minions when I kickstart the world-domination part of my plot, that is.

Before I go any further, let me remind the casual reader that: 1) it is most likely nice and sunny out there where you live and you would be considerably better off looking at squirrels running through the trees 2) if you have even the slightest inkling of formal mathematical/computer science training, you will be better served foregoing this edulcorated version in favour of one of the 10 million tutorials and entries on bioinformatics available throughout the internets (Wikipedia being a good place to start). The entry written henceforth is geared at some hypothetical grandparents who would care to know what the fuss with modern Science is all about (for instance mine, were they not already perfectly content in the sole knowledge that the good Lord has put all these tiny amino-acids together in the best possible way of all worlds and that modern genetics is the work of the Devil1).

In last month’s episode, we laboriously learnt that Biology abounds with really, really, tough problems. Two major points were:

1. For all practical matters, NP-Complete problems are all in the same bag: finding a way to solve one efficiently would mean you can solve any other in roughly the same order of time.

2. Once you have proved that a problem is NP-Complete, trying to find an exact solution for a real-life set of data, is about as meaningful as trying to take down the Everest with a toothpick. There are however plenty of ways to find an approximate solution. Proving NP-Completeness is your cue to start looking for approximation algorithms; and thus the fun begins.

Today, instead of going straight onto the myriad fun ways in which mathematicians solve biology problems, and which one of those I am actually connected to, another digression and an illustration everyone has heard of: genome sequencing.

Full genome sequencing (mapping the entire DNA of a given organism) is one of the earliest application of modern bioinformatics techniques, a seminal example: it starts off as a rather straightforward bio-chemistry problem, soon runs into pesky matters of size, complexity and intractability, goes through a difficult phase of alcohol and substance abuse, but is ultimately saved by the power of Love and Mathematics.

Before I go into the gory details, allow me to dissipate a common misconception about DNA sequencing: it is nowhere as easy as you might have been led to believe by your TV (most people’s preferred source of Science™ facts). Hearing of “DNA tests”, “DNA crime database” and other everyday life DNA-related techniques might make it sound like sequencing is as easy as sending your saliva swab to the lab and waiting a couple days for the results. In reality, despite serious advances, actual full genome sequencing is still a multi-year, multi-million-dollar affair. When people talk about DNA in a forensics or medical context, they are usually looking at a single base nucleotide, located at a precise location on one gene, out of the entire genome. Even cases that require a larger sample of such observations (e.g. DNA matching, when it actually uses sequencing altogether) are still somewhere in the lower hundreds (if that). That’s a mere 100 bases to look at, against 100+ million for the first organism fully sequenced, 10 years ago (make that 3 billions for humans). Quite a difference in scale. And, of course, this is one of those problems where solving twice the size requires much more than twice the time (hopefully by now, this does not surprise you, otherwise you might want to go back and read episode 1 again).

OK, let’s start:

  1. I know: one is not supposed to capitalise the name of God’s evil nemesis, but I am going on the assumption that Satan is a vindictive bastard and one can never be too prudent in courting the good graces of major players of the afterworld. []