a.k.a. “We really have no idea how we still are in business, but it shouldn’t last much longer…”

When it comes to services and subscriptions (cellphone, ISP, banks, heroin dealer…), I am a company’s wet dream customer: one that never leaves for a competitor. Not that I develop any particularly fuzzy feeling for whatever nameless corporation happened to have a branch on the right street-corner on the right day, but when it comes to going through endless paperwork again, moving my account data, updating everything: I just. can’t. be. arsed.

Which is why I have been a faithful customer of AU for over 5 years: not because they are great (Docomo is cheaper, Softbank has better phones…) but because I will always endure a sizable share of customer abuse and groundless fees, rather than having to track all my friends and acquaintances to send them my new contact info (and when you think of it: these things have a price too, so I am not doing it all out of pure apathy).

Why won’t I be a customer of theirs for another 5 years, then? Well, read on and learn how a company loses a customer without even noticing it.

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The end keeps nearing. Last weekend in Berlin. Feeling ever so slightly gloomy, for all sorts of reasons. Luckily I have the thought of warm Spring days ahead, plus many exciting plans for the months to come, to keep me from thinking about it too much. Also: it is about time that I resume working on that thing they call a PhD.

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…

Berlin, 7am.
I have more ink on my wrist than… a… erm…

Too soon?

On the program for this month, we have so far: two operas, three official Berlinale screenings, two music recitals and a couple exhibits.

Sometimes I do work too.

Now you know why updates are scarce around here…

Thanks to some exceptionally warm weather day this week (where temperatures nearly went over zero for one hour, around noon), a frozen hand sticking out of the snow on the side of a street, holding what looked like a note, was sighted by passer-by. Although the thawing did not last long enough to consider excavating the body before the end of Winter, the note was recovered and is faithfully transcribed below.

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.

It eventually happened.

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.

Sorry for the abrupt end of communication, earlier this month: past two weeks were spent far from civilisation and internet access. But snowy mountains, skiing and delicious local food more than made up for it.

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

Today, the entire 3-month research stipend covering the cost of my stay in Berlin (living expenses, plane ticket etc), was deposited on my bank account. All at once.

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?

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 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.

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Note to Self of Two Weeks Ago: Great foresight on that massive batch of bolognese sauce in the freezer! Should consider storing more Saturday-morning emergency food around the house.

Note to Self of Yesterday Night: Maybe not so heavy on the distilled sweet potato juice, next time. Should consider picking a recreational heroin habit instead.

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 are 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:

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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. [↩]

In order to prepare for my upcoming 3-month stay in Berlin, I have started brushing up on my terminally rusty German: buying a couple books and checking out online newspapers somewhat regularly (more than just once every three months when I am curious to know the Frankfurter Allgemeine’s position on some European issue).

Much to my surprise, I not only still remember a sizable chunk of German despite over 10 years with zero practice, but my level has in fact improved since then. That is to say, I am nowhere near fluent, nor able to remember half the vocabulary I once knew. However: turns of phrases and idiomatic expressions that I know would have me staring painfully for minutes on end back in high school, now seem perfectly natural to me… Most phrases hit the comprehension part of my brain directly, without going through the lengthy “decoding word-by-word and digging up through memory for idiomatic equivalent” phase. In some way I have magically become more “fluent” than I was, when last I studied ten years ago.

At first, I just assumed my memories were being overly modest and that, maybe, I was not the teutonic classroom failure I remembered being. Then I thought back of the long evenings laboriously spent stringing together 20 lines of homework, endless hours of classroom procrastination, barely coasting by, year after year, and the extremely mediocre A-level — or French equivalent thereof — grade that ensued. There is ample objective evidence that I really sucked as a high school student of German and it appears that I suck ever so slightly less, now that I am resuming ten years later… Which goes squarely against the widely accepted notion that foreign language acquisition skills decrease with age.

In proper logic-obsessed OCD fashion, I tortured my brain for days, trying to come up with a rational explanation for this, which did not involve being abducted, probed and experimented on, by German-speaking aliens.

And I think I found it…

The better half of the years spent studying German, were when I lived in Paris. I therefore studied in French. Grammar explanations, bilingual vocabulary lists, chatting with classmates, thinking about the ongoing lesson, were all done in French.

Nowadays: I live in Kyoto and there is very little French language in my life. Lots of Japanese, of course, but I would venture that well over 90% of my thoughts and interactions occur in English. When I read up a text in German, that voice in the back of my head, trying to make sense of what I am reading, is speaking English, not French.

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Yesterday night’s program included ample (and unexpected) display of full female topless nudity in a public place. For the second time in less than a week.

I must obviously be doing something right. (or very wrong, depending on which side of the ‘gratuitous boobage action’ moral debate you sit on).

Two months and countless draft embryos after initially promising it, here is the first part of an unfathomably long rant describing my field of research. I honestly don’t expect anybody to subject themselves to that read, but at least now I have a place to send those who foolishly ask me about it at cocktail parties.

The short answer is that I do research in Bioinformatics, which is where Mathematics (along with Computer Science and a dozen other disciplines) meet with Biology and Genetics in a dark back-alley, and do all sorts of indescribable things to each other in the hope of: creating a better world, curing cancer, breeding the next race of eugenic übermenschen or making a few bucks for Big Pharma… whichever comes first.

But that sort of answer, while technically correct, does not really tell you why such an unnatural coupling of disciplines was warranted in the first place. Allow me to start at the beginning. Way at the beginning.

[open long semi-relevant digression that can be advantageously replaced by a thorough read on Complexity Theory, if you feel up for the more sciencey and truthy version of things]

The scientific problems of this world tend to fall in either of two categories: those you might eventually solve with a good computer and some time… and those you will never solve exactly, no matter how much crazy sci-fi supercomputing power you throw at them.

This “solvable” vs. “not solvable” demarcation might sound like a tautology, until you understand the full meaning of “never” in the above statement: these, are not problems that might be solved one day, when science progresses far enough or computers get ten, a hundred or a million times faster. These are problems whose solutions require calculation of a complexity that is proven to be beyond the reach of any conventional means of computation in any foreseeable future (“unconventional means” would begin with the discovery of heretofore unknown laws of Physics: in other words, unlikely in your lifetime. at best).

By and large, the mathematical complexity of a problem, is the order of time (or computing power) it will take to solve it, relative to its size.

Without calculating the result of a certain task, it is often possible to predict whether producing this result could or could not be done in a reasonable amount of time (where “reasonable” usually means “in less than the age of the universe, assuming the use of every single computer on earth”, or somesuch).

There are countless examples of tasks falling in the first category, “easy” tasks that can be solved quickly, regardless of how big they are. For example, anybody past kindergarten age can presumably add two numbers of practically any size with a piece of paper and a pen. You just add each digit one by one (and, yes, carry the one) and adding two 100-digit numbers will take barely more time than adding two 3-digit numbers.

Now consider a different task: say you are a traveling salesman who needs to plan their next sales route. You have a map of the region, with the towns you must visit and all the distances between them, given in kilometers. How do you find the absolute shortest route that will take you to each city at least once without wasting gas or time?

More to the point: how difficult do you think finding that route will be?

Sure, it sounds easy enough: pick a starting point, follow every roads that go from that city to another one, then onto the next etc. Keep the shortest distance you’ve found. Can’t be that tough, right?

Let’s say there are five cities: you pick a city to start from, then check all remaining four, and from each four, go onto one of the remaining three etc. etc. In total, that’s 5×4x3×2x1 = 120 different paths to compare (that product can also be written using the factorial function: n! = n x (n-1) x … x 3 x 2 x 1. e.g. 5! = 5×4x3×2x1). Not so bad.

What if there are a few more cities… for instance, two times more: 10 cities. That’s 10! = 10×9x8×7x6×5x4×3x2×1 = 3,628,800 paths to look at. Huh, that might take a bit longer to do by hand. No worries: somebody will write a computer program that gives you the answer in a couple seconds.

Except that, you guessed it, each time I double the number of cities, the difficulty does way more than just double.

For 20 cities, the number of paths to look at is: 20! = 2,432,902,008,176,640,000.

For 70, cities, there are 70! (that’s factorial of 70: 70×69x68x…x3×2x1) possible paths to check one by one. That number has exactly 100 digits. This is (very) roughly the number of particles in the entire universe. Assuming you were to put every single computer in the world to work on this, you likely would not be done by the time the Sun explodes.

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You know what is worse than waking up to a water-heater that refuses to work when you go for your morning shower?

[...]

Having the fucking thing finally work, after you finished taking your cold shower.

There’s a poltergeist in my house, and it has a really stupid sense of humour.