As usual, way behind in the note-keeping business, but a few random tidbits instead:

• Gotta love a city where catching an afternoon performance of Mahler’s Third by the Staatskapelle Berlin conducted by Daniel Barenboim (brilliantly filling in for James Levine), is as simple as: picking Nino fresh off her plane at Alexanderplatz, walking over to Staatsoper and buying three (very cheap) last minute-tickets.
• Used the excuse of miscellaneous out-of-town visitors to check a few of the more touristy items off my Berlin list.
• For an artist squat long past its underground heydays and part of even the most casual touristic tours of Berlin, Tacheles was still surprisingly fresh and unassuming: with some cool art, a relaxed atmosphere and a funky bar to grab a drink at in the middle of the night. You can also buy “Kultur kann man nicht kaufen” postcards for 1.30€ there.
• I apparently look very fetching in a tiara. A comforting thought, in case I finally quit research to pursue my lifelong dream of becoming a pretty princess.
• Only major piece left missing to our Berlin nightclub collection, Berghain was actually sort of a letdown: not bad, but definitely nowhere near what the legend gave it as. Perhaps just that particular night. Had fun anyway.
• Also caught Jazzanova (or a two people subset thereof) at Icon. Rather unimpressive DJing skills (at least before the 5th Vodka mit Red Bull), but some damn awesome blend of everything Latin, Jazzy and Danceable (from Calypso to Cumbia, with your fair share of random house beats in the middle). Funnily enough, threw the same Led Zep nod as Theo Parrish at Yellow, a couple years back: except they played Whole Lotta Love, not Kashmir…

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More Random Comments and Appreciation: a Berlin Wrap-Up

Too soon?

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Back from the Clubs…

1. You get shocked, touching your own desk.
2. You get shocked, touching the metal doorknob to your office.
3. You get shocked, washing your hands (not touching the faucet, mind you).
4. All of the above.
5. All of the above, over a 20 minute timespan.

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Electrostatic Research

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The end is near…

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More random sights of Berlin life…

… at 4 terabytes…

… per user.

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You know you are in a Bioinformatics lab when…

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A Night at the Museum

• Despite my impression of the past few years that Japanese cinema was losing ground to more daring, less formulaic Korean filmmakers such as Park Chan-wook, Japanese movies were particularly well represented at the Berlinale and fared pretty well.
• Of the three screening we attended, Korean movie Ki-chin was definitely the weakest: beautiful photography, unfortunately undermined by a contrived plot and the least engaging depictions of food I have ever seen in a food-oriented movie (not to mention terminally inept subtitling work, which made it difficult to follow even basic dialogues).
• Yoji Yamada’s films were of a much higher grade. Friday’s première screening of Kyoto Uzumasa Monogatari was a nice prelude to the more involved Ototo, on Sunday. Both had a rather typical Japanese vibe of quiet everyday life events mixed with deeper topics that never take themselves too seriously. Still not convinced about the Japanese conception of slapstick physical humour as the height of comic relief, but overall good movies.
• Thanks to Berlin’s opulence in Opera venues, we obtained last minute tickets for a representation of my all-time favourite (my undying love of Verdi’s works, over any Bellini, Wagner or even Mozart, is a clear reflection of my mundane operatic tastes, sure, but I stand by it).
• Musical happiness.
• Small aside: people who can’t help loudly coughing, right in the middle of Violetta’s dying aria, deserve to be put to a slow and painful death. I don’t care how much your throat itches: put a lid on it or stay home. And while we are at it: do not clap at the end of every single fucking scene. Keep it limited to the overture, the end of each act and at most a few noteworthy arias and find something else to keep your hands and cerebral-motor cortex busy.

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Random Comments and Appreciation

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Busy Week…

Sometimes I do work too.

Now you know why updates are scarce around here…

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This month’s ticket purchases…

Liebes Diary,

It has now been 15 days that the great yellow star has vanished from the sky. Ancient ones have prophecised that it shall return one day if we make the proper sacrifices to the gods. Then again, ancient ones will say anything for a chance at skinning a dozen virgins, while getting high on mystical plants. According to German news, such a dark spell had not occured since 1964. I liked it much better back when meteorological records involved “longest dry spell ever recorded on a rainy season” or “warmest autumn since the invention of thermometers”. Now that we have successfully debunked the liberal global warming hoax, can we go back to abnormally mild winters, exquisitely hot summers and dangerously rising sea levels? That Siberian datcha I bought last year is not gonna become a waterfront on its own.

As predicted last month to easily amazed Japanese friends, our German flat comes with such marvels of 19th century technology as central heating and double-windows. Unfortunately it also features 10ft high ceilings, which sorta defeats the purpose. Something is not quite right when the longest dimension of your bedroom is height. I assume, however, than my no doubt imminent transformation into a blood-sucking creature of the night will solve this issue by making “upside down, hanging from the ceiling”, a perfectly natural sleeping position.

Although technically “in” Berlin, my laboratorium sits in the middle of the German tundra. Access requires usage of the entire bahn alphabet, followed by a vivifying walk through neighbouring parks and forests. I spotted a couple wolves in the distance, on my way home yesterday night. They fortunately seemed too busy fighting over the remains of some unlucky coworker to notice me. I did notify the lab secretary this morning that I did not think Hans was staying home with the flu, as was initially assumed.

My German is slowly crawling back to the satisfyingly mediocre level of my high school years. I still tend to answer all questions with “sou desu ne“.

The Fall of the Berlin Wall, German reunification and ensuing economic and sociological challenges of the early 90s, are expectedly way less popular a conversation topic than may have been implied by 7 years of high school language classes relentlessly covering the subject. Had Frau Wagner spent just a little less time obsessing about Wiedervereinigung, Ossis, Wessis and balloons coming in easily roundable numbers, I might actually know how to say useful everyday things. As it is, I am now known in my social group as the guy with a surprisingly rich German vocabulary pertaining to the plight of disenfranchised and politically disillusioned East German workers confronted to consumerist and individualist values inherent to the capitalistic system of the West. Also known as: that guy with the tedious conversation who can barely order for himself at the restaurant. Fuck you Frau Wagner.

Linguistic limitations aside, and despite the equally unsurprising lack of opportunities for congratulating one’s interlocutor about the cuteness of their monkey in casual bar conversations (“Was fur ein süße Affe!” — year 1, lesson 1), people are friendly and fun to hang out with. Sadly, my considerable repertoire of Hitler jokes remains largely unappreciated, strangely enough.

I have an increasingly hard time repressing the urge to punch newly met acquaintances who mention how great and enjoyable Summer in Berlin is. Which they never fail to do. Preferably shortly after it has been announced that the negative double-digit temperature is likely to last until at least the end of February (“When did you say you were leaving again? Oh… I see… sorry”).

I must now step out to go replenish our survival chocolate supply at the store across the street. It looks like there’s yet another small snow storm outside. Where did I put the damn polar bear gun.

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Deutsch Chroniken, Teil 1

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Walking on Thin Ice

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How cold, you ask?

It took a while, but I think I finally know how it feels to be the ancient one, sitting helplessly while the younger ones try to operate antiquated machinery from another era… say, a turntable.

Picture if you will: a standard Berlin bar, two cheerful yet terminally hopeless barmaids, a pair of standard-issue decks, a [presumably rather cheesy German] record to be played…

It went a little bit like this:

1. Barmaid places record on deck, tries to play it for 2 minutes before realising said deck has no needle (stylus or cartridge, for that matter).
2. Barmaid repeatedly tries to spot the beginning of some track she is presumably looking for, using a lighter for sole light source. Gets ever so slightly pissy when yours truly points [as gently as possible] toward the button to enable the dedicated target light that comes standard on all SL-1200.
3. Barmaid #2 [unsuccessfully] tries to fit a raw stylus into the standard needle connector, apparently oblivious to the obvious size/shape difference.
4. Barmaids have stroke of genius and finally decide to switch the entire deck with the other deck (changing cables and all), yet again failing to notice that simply switching the cartridge, would have been a considerably easier endeavour.
5. After finally plugging the new deck in, barmaids enter long struggle to figure the on/off dial on the new deck. Get increasingly pissy at any attempt to point them in the right direction… Finally give up in frustration and put a CD instead.

Seriously: now I know exactly how old-timers feel, when they see condescending-yet-clueless youngsters trying to operate a 1930s radio… and miserably failing at it, as if it was some alien technology.

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The Youth of Today…

The only question is: does either go up to 11?

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Stronger or Strongest?

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Max Planck in Berlin

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New Year’s Eve in Paris

In Paris for New Year’s Eve (and a few more days after that), before going back to Berlin until the end of Winter.

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Snowy Winter Break

If your talk lasts 25 minutes and goes into the minutiae of protein-protein interactions with regard to oncogenic pathways, maybe spending half of it convincing an audience of biologists and bioinformaticians that cancer is a bad thing that needs curing is not the best use of presentation time.

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Bioinformatics Conference Pro Tip

Although it could probably go lighter on the whole Mission: Impossible antics (unfortunately, it seems you just can’t sell a documentary nowadays if it doesn’t feature endless gratuitous action montages), the scenes it captures are captivating and hard to ignore. Beyond the expected money shot of an expanse of ocean literally red with dolphin blood, the investigative work offers some fascinating insights into the cynical political maneuvering that goes on to ensure the fishing doesn’t stop.

The vast farce that is the International Whaling Commission and a long tradition of Japan’s bribing third world island countries for votes, gets the bashing it deserves: I don’t care what your opinions on the whaling issue are, if you seriously believe in the “scientific whaling” argument, you are very misinformed or a moron.

Casual observers of Japanese modern history do not need to be told of its infamous propensity to always side with industries against public welfare, when environmental or public health scandals strike. Others will probably think that the recount of Minamata disease’s infamous cover-up is exaggerated… After all, while Western countries routinely poison locals in remote third-world countries and get away with it, it is quite a rare thing for a country to let companies do it on its own soil and unfalteringly support them when things go awry (and long after that). Long-time residents will also enjoy the nod to Japan’s sub-par criminal justice system, delight in spotting the usual cast of Japanese administration characters (the blatantly corrupt – yet utterly polite – cop on local business’ payroll, the roboticized bureaucratic talking-head, the government “scientist” spouting pseudo-science etc. etc.), without, unfortunately, escaping the usual trite clichés (is there a single japanese story that cannot be illustrated with a nail and a hammer?).

This documentary is not without its faults and I honestly have my doubt about the efficiency of the “Us vs. Them” brand of activism, when confronted to Japanese culture. But regardless of which side of the Blubber Hamburger / Cute Smiling Cetacean debate you stand on, there are a couple items worth pondering in there.

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The Cove: Japan’s Delicious Dolphin Burger Industry

Guess them all and win a bunch of iTunes coupons for free installs of KanjiBox for iPhone (along with my undying respect for your extensive musical culture).

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Think you know Japanese music?

Am I a bad person for even wondering how many years I could live off that, were I to accidentally end up on some remote beach island instead of Berlin’s Max Planck Institute for Molekular Genetics?

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So many zeros…

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 days (beside that violent twitching on the left side of my face and the regular furball coughing, that is).

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 habits (people in their twenties who barely drink a can of coke a month aren’t supposed to get kidney stones, let alone chronic ones). 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; 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 2 aspirins and a cup of boiling hot tea purchased on the Eurostar for sole comfort.

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 payed ¥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.

Kidney Stones remedies

Like anybody confronted to their 4th or 5th stone in a decade, I have collected a good deal of empirical knowledge on the issue. It also helped that the first two episodes happened outside of the realm of modern medical medicine: the magic of timing, transatlantic flights and insurrance-less lulls between [proper] jobs in the land of proudly unaffordable healthcare (needless to say: in between years of fully covered, perfect health… try to tell me God doesn’t have it in for me, after that).

Googling and webbing of all stone-related issues tends to yield a mix of obvious, factual and completely moronic/batshit insane advices. With a recurring theme being the product-pushing agenda of the websites giving said advice. In light of this, I figured I would compile a few of my anecdotal findings on the matter, for the sake of the odd Google seeker who may end up here.

Note that:

1. I am not a doctor (unless you count that honorary degree in Love Potion and Curse Healing from Kinshasa’s University of Black Magic). I shouldn’t even have to tell you to consult with a professional, before anything else (frankly, if you hadn’t figured that for yourself, you shouldn’t have the IQ required to operate a computer). Once you have seen a physician, received a diagnostic, commiserating pat on the head, painkiller prescription (and little useful else): feel free to come back here.

2. These aren’t tips to prevent reoccurrence of stones. I’ll let you google/consult for these. Although, they may not always do the trick (take it from somebody who’s been drinking liters of water a day and depriving himself of chocolate for the past few years, and yet is currently contemplating removing the coating from his painkillers to try and snort them for faster absorption).

3. The focus here is on things that will help you deal with pain (and, possibly, but with absolutely no guarantee, help pass the stone faster… on the assumption that not wriggling in pain and spams, helps smooth the descent).

4. Any [already questionable] advice contained here applies only to calcium oxalate crystals (you know, the cool spiky-looking ones that seem designed to tear your insides while clawing their way out). Some might work for other types of stones, but no guarantee here.

That being said, and before going into things that work, let’s start with:

Things that don’t work

Cranberry juice and all other bullshit herbal grandma remedies. Not because they are bullshit herbal grandma remedies with usually zero evidence-based medical results, but because they all apply to a completely unrelated issue. Kidney stones (calcium oxalate ones, that is) aren’t UTI, nor even caused by UTI and rarely have anything to do with UTI. Whatever anecdotal health benefit cranberry juice (and dozens other Flower Power remedies) may have, are entirely geared at UTIs. Drinking cranberry juice while passing a stone has been proved to help, only insofar as drinking any fluid helps. So feel free to replace cranberry juice by gallons of gin&tonic and call it a family remedy: your chances are the same.

Things that work

Water goes without saying. Gallons and gallons of it. All the time, all day long. That stone isn’t gonna carry itself down (that being said, if/when your kidney shows sign of excessive straining on echo or CT scans, lots of water might no longer be a good idea: that’s what your doctor’s advices are for).

Painkillers obviously work. Although if you have tried, you already know that even the strongest painkillers have a very limited effect, in time and in strength. Dosage increases will barely help. And unless you fancy a life of addiction to opiates, they are rarely a good idea. NSAID are the standard fare (also: they are easier to keep on the stomach than opiates, which helps if you aren’t hooked to an IV feed). I have found antispasmodics to be more helpful in the long term (less direct pain relief, but less cramping, which is precisely the point).
Anyway, no real point discussing pharmaceuticals here: you will need a prescription (or a very good dealer), that, again, is what your family doctor is for.

Cannabis. Yep, herbal remedies aren’t completely useless after all. Surprisingly enough, medical cannabis isn’t just a hoax pulled by aging Californian hippies trying to ensure good-quality supplies at cheap price: there’s a reason cancer patients are told to smoke some reefer.
In addition to being a powerful analgesic, cannabinoids have antispasmodic and muscle-relaxant properties, which is precisely what your strained tubes need (less spasm/constriction = less friction = less pain). Trust me (err, I mean: trust my good friend who tried once, officer), it works well. And if it doesn’t, you can always just put on some Bob Marley records and bob your head to it until you forget all your troubles (just kidding).

Of course, were you to choose the weedy path of natural remedies, you should probably avoid living in a country where possession of any drugs (that are not tobacco or alcohol) is a crime on par with killing kittens or having sex with underage schoolgirls (just kidding, of course: the latter is perfectly OK and barely frowned upon by Japanese society, provided you are a well-off middle-aged businessman who doesn’t mind buying them Hello Kitty toys in return).

Which leaves you with:

Heating pads. No joke.
Heating pads (preferably the strong, chemical kind, universally available in Japan, where they are known as ‘kairo’) are a real life-saver. Staying warm is key: keeping one or two strong heating pads over your lower abdomen at all time, greatly helps with the background pain and seems to lower the recurrence of acute pain episodes. During last year’s episode, I was able to be nearly functional for three weeks, including a (very sober) New Year’s Eve party, patiently waiting for my two stones to go down their merry way (or, more exactly: until a very nasty surgical device was inserted to bring them out once it was realised they wouldn’t come out on their own, but that’s beside the point).
If you live in Japan (or another country where these awesome little pads are easily available), go to your nearest pharmacy and buy a few hundreds. If you don’t:

Hot baths are an obvious piece of advice. But just in case you had not noticed yet: dipping into near-boiling water at regular intervals will do miracles to subdue the pain. Just make sure not to get cold chills when you get out.

Things that Might Work

For pain management, the doctor at my local Japanese clinic only prescribed antispasmodics and told me to come back if I needed stronger (which didn’t bother me much, considering how little effect stronger meds usually have anyway).

Along with the antispasmodics, was a prescription for a slightly stranger medication called Urocalun, which turned out to be a rather Japan-specific drug, based on some plant extract (yes: another herbal remedy, but this one comes with somewhat scientific studies attached, rather than your crazy grandmother’s aunt recommendation). Most salient research papers I could find on the topic are in Japanese and only appeared in domestic publications (as is unfortunately typical of a vast amount of Japanese research) where methodologies are, ahem, not always of the highest scientific grade, or sometimes feature downright bizarre ideas (rope jumping as a way to pass stones, anybody?). More importantly, it is not always clear whether Urocalun is only effective as a preventive treatment or can also help during acute episodes.

But at least, there seems to be some scientific basis going for it (which is more than lots of pseudoscientific remedies like homeopathy ever had) and is the first I ever hear of a widely distributed drug treatment for kidney stones (other than palliative, that is). I have the tablets and will be taking them religiously for the next few weeks, we’ll see if it helps.

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Kidney Stones: A Beginner’s Guide…

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?

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The Art of Subtle Rephrasing

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).

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Kanji Stories…