Tuesday, May 29, 2012

Long Time No See

Things are settling down a bit around here. As I thought I haven't had the energy to write anything longish, but I did post the occasional short tidbit over on Google+. Just to get things going here again, here's links to some of them.

A 3D space tracking input device that promises high tracking resolution, compatibility across all platforms and expected to cost less than a weekend dinner and drinks for two at a decent restaurant. Of course, with our luck it'll get bought out, patented to death and removed from the market, guaranteeing that an open, usefully hackable device will never see the light of day.

Ed Young has a good story on IR-tracking beetles that actively search out forest fires. Sometimes I wish schools would focus more on all the odd exceptions to the "normal" animals we typically think about, just to bring home just how varied and, well, weird, the natural world can be.

Long posts, short posts, informative posts — but a throwaway note on my Sunday lunch brings out more comments than any other post I write. Tells us something about human nature, perhaps. Food and sex, there's two subjects that never go wrong.

Excellent Command Line tips for anybody using a shell under Linux. Really; some of these can save you hours or days. Take a look.

Technical books tell a story, which is why they still matter even though the web is chock-full of freely available information. I don't expect the technical book to go away anytime soon.

Friday, May 18, 2012

Dave on Japanese Ph.D.

Newly-minted Ph.D. Dave (fun blog) has a post on doing a Ph.D. in Japan. As he actually went and did exactly this, his perspective is of course a good deal more authoritative then mine. Read it.

I mostly agree with what he writes, but I do have a few minor disagreements stemming from us simply being active at different institutions. While Japanese is helpful, the places I have worked with so far (ATR, NAIST and OIST) are all basically English-language institutes, with coursework and seminars in English, and the international grad students have not had any study-related language problems.

Of course, your social life may well suffer without Japanese. But then, your social life will suffer no matter where you are, if you do not know the language. You'd have the same problem fitting in in Germany, Sweden, Italy... And if you go to Britain or the US, there's a reason most, for example, Chinese students tend to socialize mostly with themselves; North European students with themselves; Japanese with themselves and so on. Even when you do sort-of know the language, lack of confidence and cultural differences mean you're still likely to opt for the comfortable and familiar.

Also, his assessment on thesis advisors are spot on — but not in any way specific to Japan. What kind of lab and what kind of advisor to choose is a huge subject, and there's countless blogs out there hashing through the pros and the cons. Most important, I think, is to have an "acting" advisor (who may or may not be your formal one) that you work with, and that you're comfortable working with.

Having a Big Name advisor that see you twice a year is no problem at all if they have the foresight to hand you off to a younger but skilled researcher to teach you the ropes in their stead. In a way that is the best of both worlds: you get frequent hands-on tutoring from someone still young enough to know what you're going through; and you get a Big Name vouching for you when you scramble for that first Post-doc once you're done.

Tuesday, May 15, 2012

There I Fixed It

(Note: for personal reasons posting may be light to non-existent for a while.)

You have a laptop. A good one, only two years old, and mostly working fine. Now, unfortunately, the laptop fan is — not broken, exactly, but sometimes it doesn't spin up when it should. Maybe the bearings are clogged, the motor may be going bad or perhaps a temperature sensor is malfunctioning.

The reason doesn't really matter — when the fails your laptop runs hot. Really hot. Even a slight extra load, such as watching a Youtube movie, is enough for it to slowly overheat and grind to a halt. It happens increasingly often, and it's becoming difficult to even use the machine by now. You need to do something.

What do you do? You could bring it to a repair center and have them fix it. But the machine is two years old and out of warranty. You're probably within a year from a new laptop anyhow, so a possibly expensive repair doesn't strike you as a great idea. And you depend on the machine every day, so you'd need to find and set up a replacement computer for a couple of weeks while it is in for repairs. Serious money. Major hassle.

You could open it up and hope to find some obvious flaw such as clogged-up dust or a loose cable. But you've already dusted the fan from the outside, these machines are difficult to open without special tools, and integrated laptop motherboards leave very little scope for home repairs. You're far more likely to break something else than to fix anything.

Or, you could take a junk-drawer cooling fan1, a left-over cellphone USB cable, a soldering iron and liberal amounts of gaffers tape:

There, I fixed it
There, I fixed it!

USB ports give you 5 volts and 100mA of power for low-power devices. The fan I found draws 0.4 watts at 5 volts, or 80mA — nicely within the low-power limit. Solder the leads red-to-red and black-to-black, then use tape or heat-shrink tubing to isolate the connections (remember to thread the tubing on the leads before you solder... I always do that).

Gaffers tape works great both to hold the fan and to create a flexible, pliable enclosure to fit onto the air exhaust on the side. Gaffers tape is wonderful stuff — it ­cuts without tools, it's strong and flexible, and the glue doesn't leave any residue. A roll is pretty expensive but it lasts for years at home.

The result? My laptop idles at 75-80° without the fan, and will soon hit critical temperatures with any extra load. With this fix the machine stays between 55-60° in normal use and will remain below 80° even when I run 3-D applications or do intensive image processing. It's not completely silent, but the sound is so soft and muted — the tape dampens any vibrations — that I soon forget it's even there.

It's a hack. But when I can ill afford the time and money to repair or replace the computer, this hack solves my problem at no cost and with minimal effort.

We often underestimate the utility of the hack, the kludge, the temporary patch. It's not as good as a permanent fix, but often it doesn't need to be. If this hack keeps my machine running fine until it's time to replace it, then it's just as good as a real repair. Better, as it took less than an hour instead of many days or even weeks.

"Everything worth doing is not worth doing well", as a wise man put it. "'Perfect' is the enemy of 'good enough'", said another. Words of wisdom.

#1 Aren't you happy you saved that fan a few years ago? All that junk really does come in handy from time to time, no matter what other family members may say.

Sunday, May 13, 2012


I've finally finished "火車" ("Fire Engine" perhaps? It's a little subtle) after a whole year. That's not a snub at Miyabe Miyuki; this book was, if anything, tighter and better played than "Riyuu". Neither is it too difficult, as I could read large parts of it with only occasional support of a dictionary. Instead, work and family issues has taken up much of my time, and the book has lied unread for weeks and months at a time.

The book mirrors Riyuu in using a crime as a backdrop to highlight a societal problem — the rise of consumer credit in this case. Unlike Riyuu, though, it stays focused on the crime story, and reads much like any detective novel. It was a fun read, and it's a testament to Miyabe's skill that I was motivated to pick it up again as soon as I could after leaving it for months.

Now, what to read next? We do have another Miyabe Miyuki novel at home called "模倣犯" ("Copycat") but it's in five(!) volumes and would take me years to get through. Murakami Harumi's "海辺のカフカ" ("Kafka on the shore") is waiting on the bookshelf. His style is deceptively simple but there's a lot of subtext, and I'm afraid I'm still not good enough to read it without missing much of the point. I'll leave it for another year.

I have a bad book-buying habit, so I have plenty of less weighty novels to choose from. "死の点滴" ("Drip Of Death"), for instance, was a fun tv-drama and I doubt there is much deep subtext there for me to miss. "Kitchen" by Yoshimoto Banana seems a short, tight read. I also have several classics in Japanese translation, such as "Neuromancer" by William Gibson, "The Caves of Steel" by Asimov and "Mio my Mio" by Astrid Lindgren. As I've read them in original already they'd make for a quick, enjoyable read.

Or I could do nonfiction. A book on Euler's formula or on Penrose tiles both look like fun. I have an introduction to cuttlefish biology that seems fascinating, and one on insect neurology that I've wanted to read for years already. Two fun-looking books are "電車の運転" ("Rail operation") about how railway systems (not just the trains themselves) work; and "さおだけ屋はなぜ潰れないのか" ("Why don't laundry pole shops go bankrupt?"), a popular introduction to accounting.

I'll have a few days to decide. We'll see.

Thursday, May 10, 2012

Ph.D. in Japan

I got a question recently in a comment about doing a PhD in Japan:

Test Tubes
Hello, I found this blog while looking for OIST. I was wondering if you could give me some info on how different are japanese graduate studies if compared with America or Europe (I'm doing a master degree in Canada right now).

Also, except OIST, is there other good opportunities for non-japanese graduate students (especially in the neurosciences, pharmacology and microscopy techniques) on the main island. I'm talking about institutes with good reputations and which are friendly to English speaking foreigners and where you can do a PhD. Do you know how competitive it is to enter OIST or one of these graduate schools?
First, let me make a few things clear: I never did a Ph.D. in Japan, and I have not been directly involved in Ph.D. student training in Japan or elsewhere. I came here as a post-doc and have mostly worked at research institutes with little direct contact with graduate students. The information I have is second-hand or inferred from things I do know. I'm not an authority on this.

Graduate student from Turkey at ATR.

With that said, I would say doing a Ph.D. is pretty much the same the world over. In my experience the research world has its own culture. The working culture of your lab is more similar to research labs in other countries than to the local culture where you are. There is probably a lot more variation between universities, between research fields and between labs within a field than there is between labs in different countries.

The general process is much the same in Japan as elsewhere. It's three years with a combination of coursework and your own research. In the sciences your thesis will be your published papers — at NAIST, my current workplace, at least one paper must have appeared in an international journal — together with some sort of introduction. The thesis is presented and defended at a seminar; it's not really closed, but generally only the directly affected parties attend.

The details of your studies can vary enormously, depending on your chosen field and on your lab. You may be working alone or as part of a large team. You may have complete freedom to decide your direction or none at all. The department may be a cozy, collegial discussion club or a high-stakes, high-stress, winner-take-all pressure cooker. It depends on the university, field of study and on the particulars of the lab, and is, again, not specific to any one country.1

Patch Clamp
Patch clamp microscope, OIST.

In general, graduate schools in Japan are interested in foreign students, and many are actively looking for them. One reason is the same as everywhere of course: graduate students — whether domestic or foreign — bring funding, directly and indirectly, and they are the traditional cheap labour of the research world. But many labs are also actively seeking to become more international. They look for broader cooperation with the wider international research community, and encourage their Ph.D. students to go abroad as well.

Language is not a big problem. Universities that seek international graduate students offer their courses in English. Many labs now actively encourage the use of English in seminars and lectures even when they have no foreign students to better prepare the students for international meetings and publications. Some places, like OIST use English as their official working language in all school matters.

One issue is that the school year starts in April in Japan, rather than early autumn, though that is a problem for visiting students more than for those doing their entire Ph.D. here.

We have three or four foreign Ph.D. students — from Brazil, Indonesia and China — at the lab. We also cooperate with an institute in India so we frequently have Indian graduate students coming for shorter visits, and graduate students and post-docs visit India in turn. None of the foreign students seem to have had any serious language difficulties and I've noticed that they all seem to pick up Japanese fairly well over time too.

Papero robots. NAIST.

So, how do you find a lab? I've asked around a bit, and it seems most foreign graduate students find a place through the Japanese embassy or Japanese consulate in their home area, or through a local funding agency with a Japan program. You can also ask your own university; larger universities have their own office for this kind of thing. And there may well be that somebody at your own department already knows a researcher or two in Japan and can refer you to them directly.

One way to pick possible places is to simply look at the web sites of any likely universities. Any larger university will have a comprehensive English-language website with information for prospective students and graduate students. Here's international graduate school information for OIST, NAIST and Kyoto University Faculty of Science. A quick search will give you similar information for any university in Japan.

How difficult is it to actually get accepted? That's not completely straightforward to answer. A graduate student represents a substantial investment for the department, and nobody wants to accept somebody that is unlikely to finish. Like elsewhere, the number of positions often isn't really fixed; if you're particularly well qualified — you have some experience already and your research interests fit nicely with the lab — there will always be room for you, while labs will rather let a position go unfulfilled rather than give it to somebody not quite qualified for it.

The exact procedures for acceptance differ between universities. Some hold a general entrance examination while other schools may use interviews or other methods. One problem is that the school year starts in April in Japan while most countries start around August-September. That is mostly a problem for those that want to do just one part of their graduate studies in Japan and not so much for those doing their entire Ph.D. there. If you want to do this and you're qualified you won't have a problem finding a place.

The biggest hurdle, I think, is to decide to actually apply. You're committing years to grad school and it will change the future course of your life. Doing it in another country is all the more intimidating. Doing a doctorate is stressful, uncertain and can be intensely frustrating when things don't work. The financial rewards are uncertain and a research career is insecure and highly competitive.

But if you're up for it then grad school can be hugely rewarding; it is perhaps the only time in your life when you can give your curiosity free rein for a couple of years with no other responsibilities and no strings attached. If that sounds like your kind of fun then you should absolutely consider it.

Blimp Time
Preparing a remote sensing experiment. NAIST.
#1 When I started, my advisor dumped half a dozen books in my lap and asked me to please contact him once I figured out what kind of thing I wanted to do. It took me three years, with occasional false starts.

On the other hand, at the very same university I've seen an announcement for a Ph.D. position (in analytical chemistry I think it was) as part of an existing large-scale project where your course list, your teaching activities and your Ph.D. research was already determined down to the expected number and contents of published papers and a preliminary title for your thesis.

Don't expect too much uniformity even within one particular university in other words.

Monday, May 7, 2012


The Golden Week holidays are over, and with that, so is spring. The spring here in Osaka is beautiful but all too short — just a month ago I could finally start wearing my new spring coat even in the early morning; now it's already getting too hot to use any coat at all. We're quickly moving into summer territory now, with high heat, high humidity and hurricane season on the horizon.

So, here's a selection of pictures to remind us of a time when mornings were cool, the light was subdued and the world still smelled of spring.

Fashion Statement
A pair of young gentlemen sports the latest in spring fashion in typical subdued Osaka style.

Early morning mist at Kita Ikoma station.

Outlet! Nagahori street, Osaka.

The Owls Are Not What They Seem
If the garage is too small for your car, then so much worse for your garage.

Last of the Sakura
The last of the sakura.

Tuesday, May 1, 2012


It's the Golden Week holidays — well, I'm at work today and tomorrow — and I'm trying to catch up on things. Here's a blog post that has been cooking for a long time now. Last summer I worked in Okiawa for a few weeks, and on the way back I bought a sampler set of Awamori, Okinawan rice liquor. Around New Year I finally tried them out and took a few pictures. And for various reasons it's taken me until now to actually write about it.

Ryūkoku brand Awamori. From left, a ten-year old with 25% alcohol; an eight-year old with 35% alcohol; and a 5-year old with 43% alcohol.

Awamori is similar to mainland Japanese Shōchū: a rice-based clear alcoholic drink, but usually with more flavours and fragrances retained than in European vodka. Shōchū, by the way, is not limited to rice; potato-based variants are very popular too.

Okinawa has long been a trading point between east-Asian powers. Awamori is different from mainland Shōchū in that it uses long-grain Thai rice imported from south Asia rather than the short-grain Japonica rice. Also, good quality Awamori is often aged rather than drunken fresh, and gives it a mellower, fuller taste. Shōchū is almost always 20-25% alcohol, while Awamori can range from 20% up to 50% or more.

Awamori samples.

Perhaps the best way to drink Awamori is to cut it with hot or cold water. Hot water may sound odd for a subtropical island chain but it brings out the flavour and is very relaxing in the evening, with stars shining above and a cool breeze coming in from the Pacific.

The five-year old is a little sweet and obviously strong. The alcohol flavour dominates and it's really not much different from a middling-quality vodka. If I drink this at all it's preferably as a mixer, not just with water. The eight-year old is much better balanced. Rather thick, sweet flavour with a heady nose. It goes down a treat.

The ten year-old is far more subtle. There's less flavour all around but also less alcohol so the resulting balance is great. Hardly sweet at all, and with a very delicate fragrance. Cut this one just a little, and sip. It's delicious; by far the best of the three.

Seems to me there's a parallel between beer and spirits, in that dark, flavourful beers can support — indeed demand — higher alcohol content to achieve a good balance, while pale, light beers are best with much less alcohol. A stout or a Belgian dark beer can easily have 7-8% without feeling the least bit overpowering, while many classical light beers are best at half that.

In the same way, Whisky, Rum and flavoured vodkas work really well at around 40-50% or so. But subtle spirits such as Shōchū and Awamori are at their best well below 30%. Neat vodka has use only as a liquor base or drink mixer, of course, and doesn't really fit this classification.

It really hit me how much the alcohol content plays a part in the overall impression of these three samples. If you're looking to try some Awamori, it may be worth keeping this in mind.