Saturday, December 25, 2010

White Christmas

I understand that Sweden has a spot of weather at the moment. Not to be outdone, as we left home earlier this morning we saw actual snowflakes - plural! - wafting down from the sky.

I guess this technically counts as a white Christmas for Osaka - you know, in the same way that Ozawa may be technically innocent of graft. But for weather as for election laws it's technical that counts.

Friday, December 24, 2010

Merry Christmas

Akasaka Prince Hotel
Akasaka Prince Hotel

It's Christmas Eve, and I'm taking a break from my end-of year panic together with Ritsuko. We've had a non-traditional cross-cultural Christmas dinner (meaning fried chicken, apple salad, cake, cheese and wine) and I'm mellowing out with the last of the wine while writing this post.

To the left is Akasaka Prince Hotel in Tokyo. It's a distinctive building in a pretty well-done 1970's style, and they apparently do some large-scale decorations for Christmas every year. This is the last Christmas though; it's slated to close and get torn down next year. Just to the right, beyond the edge of the picture, is restaurant Stockholm, where we had Swedish Smörgåsbord last week.

Oh, and we've had presents too, of course. Here's mine:


Otonona No Kagaku, Twin-lens reflex camera kit.

Otona No Kagaku is a great series of sciency kits for adults, with a new issue every few months. I've been eyeing this twin-lens camera kit ever since it was released early this year, and now Ritsuko gave it to me for Christmas. She knows me only too well I think.

Merry Christmas everyone!

Thursday, December 23, 2010

Quickie Time - Bic Camera Edition

It's a national holiday today - which for me mostly means I get to work from home. But I did go out over lunch, and popped in to Bic Camera in Namba.

First, they have the Sony E-reader I mentioned in my previous post. I brought a memory card with a couple of research papers in PDF format to try out. Surprisingly, it works quite well. I first tried playing with the zoom function but that was too cumbersome. Then I noticed it has several modes for PDF reading, and one mode divides each page in four, showing you one quarter at a time. That works perfectly for typical two-column PDFs. Clear and easy to read, and all illustrations and all math came out perfect as well. Perhaps I should see if I can buy one for the project next year...

Second, Bic in Namba has not been very good for film camera users the past year or two, with a small, unreliable selection of films and developing gear. I'm happy to say this has changed. They now have most black and white films I know about, including a complete selection of Ilford films and even Ilfords Kentmere brand films and some Czech Foma films (tip: Fomapan 400 is best used at iso 200).

Third, I asked about medium format film developing at Bic, and to my surprise they do both medium format negative and slide film development in an hour, the same as for 35mm. Most places - including Naniwa and Yodobashi in Umeda - take a couple of days to do it. Very convenient, and worth remembering.

Sunday, December 19, 2010

Back Home

We've just arrived home from our Tokyo weekend. I'll write a picture-post thing later, when I'm done with the images. Until then, a few random observations:

* I didn't have real internet access all weekend, and it was wonderful. Well, I did have my smartphone of course, but it doesn't invite you to random surfing for hours on end. I'm bone tired, but I feel way more relaxed than I ever do after a normal weekend.

* We passed a Sony store and I took a quick look at their new e-book reader, the Touch 650. It was, well ... amazing, really. I mean, I almost bought it right there and then, and had Ritsuko - always a voice of reason - not been along I really would have plonked down the money right in the store.

It's an e-ink based reader, like the Kindle from Amazon. Which means it really looks like paper rather than a screen. It's nicely bright and contrasty (black and white photographs look pretty good), and there's a typical "flash" when you change pages. So far, so good.

But it's light. Really light; the weight feels like a thin pocket book, and you could easily hold it for hours on end without getting tired. Could have it in a pocket or in your bag and never know it's there. And it has a touch-screen, so you can navigate by swiping your finger, you can click on icons and type notes right on screen. It even has a simple drawing program that is surprisingly useful; the e-ink screen only has to update a small bit at a time so it doesn't lag. Surprisingly (for Sony), it supports plenty of open formats, so it's easy to get texts on it. No net connection but USB and SD cards are supported. The battery is good for weeks.

I've tried the Kindle 3 too - it has the same screen - and the Sony is just plain better. It's lighter, smaller and the touch screen makes using it much more natural. For reading it handily beats tablets like the Samsung Tab and the iPad; they're heavier (much heavier for the iPad) and don't have the battery life or the paper-like screen.

Why didn't I get it then (apart from Ritsuko reminding me I don't actually need it)? Research papers. A major reason for me to get it would be to read research papers in PDF format. They are notoriously difficult to read well on-screen; I usually resort to printing them. An e-ink screen should render them much better. But I suspect the screen size (15cm - 6 inches) and the PDF reader application just aren't up to the task of showing them properly. I didn't have any example PDF-files with me, and I'm not going to buy a reader until I can test this properly.

* Most places in Japan sell a range of local specialities as travel gifts. "白い恋人" (shiroi koibito) is an extremely popular soft white chocolate cookie from Hokkaido. The name means "white sweetheart" and alludes to the white chocolate and to the wintery climate of the area. Coming back to Osaka tonight we spotted a gift store at the station selling a cookie called "面白い恋人" (omoshiroi koibito). Which means, roughly, "interesting sweetheart" or "amusing sweetheart". That, to me, sums up Osaka pretty well. I'm happy to be back.

Thursday, December 16, 2010

That Was Fast

Remember that I'd reached 77kg about a month ago? I've lost another kilo since then, without even trying. There's nothing like pervasive stress and lack of sleep to make you lose weight, I guess. Not that I lack appetite, mind you - I'm plenty hungry at dinner time - but I feel full as soon as I start eating.

Anyway, this is just a temporary problem. Tomorrow is my second vacation day of the year. Ritsuko is going to Tokyo even as I write, and after work tonight I will take the train and join her for a long weekend in the capital. We'll go see a big outdoor temple market in Asakusa, spend an afternoon in Jimbocho (home to hundreds of specialist used book sellers), have Smörgåsbord at a Swedish restaurant and probably spend Sunday in nearby Yokohama and its large, lively Chinatown.

I strongly suspect I'll gain back the weight I've lost, and then some, by the time we come back.

Sunday, December 12, 2010

Writers Block - The Definitive Study

Writers block is all too common for anybody who writes. Fortunately, science is here to help. I just stumbled on a wonderful, brief classic paper on the failure of self-treatment of writers block, published in "Journal of Applied Behavior Analysis" in 1974, and freely accessible here. Go on - it's an easy read for non-specialists.

Of course, a lot of psychological research used to be focused exclusively on northern Europeans and Americans. We know better today than to generalize results from one culture to others, so a group of researchers have replicated the original study from a cross-cultural perspective here.

I really have to find a way to cite either study in my next paper.

Wednesday, December 8, 2010

We Have a Communications Problem

Test Tubes

We all recently got a nice example of how communication can go wrong, and how the research community suffers as a result.

A few weeks ago, NASA sent out a cryptic press release about an upcoming research finding "that will impact the search for evidence of extraterrestrial life." The net explodes with speculation, some wildly unfounded, some informed and down-to-earth.

The big day arrives, and it turns out to be an entirely terrestrial bit of research: Researchers have taken a type of arsenic-tolerant bacteria that lives in an arsenic-rich lake, and coaxed them to actually incorporate the arsenic into their own body chemistry. Kind of cool, but nothing extraterrestrial, no "new life" or some different kind of life or anything. The first round of news articles did their best to play it up as a major breakthrough, while the first reaction from actual researchers was cautious and not overly enthusiastic.

Good thing they were cautious. People have now studied the paper in more detail and the results don't look nearly as good as the authors first claimed. The results are tenuous and not well supported, and the bacteria may in fact not have incorporated arsenic as a functional part of their body chemistry at all.

So, we go from immense hype and speculation, to uncritical reporting of a less-exciting result, to serious doubt that there is any positive result to report on at all. Enormous excitement to complete letdown in a few weeks. What went wrong?

First, take a look at who finally popped the whole media balloon: working researchers in the field that read and reflected on the paper, then wrote up their comments on their blogs or on news sites. Would it not have been good for everyone if they'd be able to chime in right from the start, rather than weeks after the media frenzy? Why weren't they? Why did the whole thing crash so spectacularly?

One reason is spelled "embargo". Many news outlets refuse to cover events like published research unless they can publish their articles right when it's announced. A research project may take five years, and writing and publishing the paper can take six months or a year, but if your newspaper has to wait for two days while their reporter reads the paper they refuse to mention it. Also, the impact of publication is greater for the journal if it's accompanied by a flurry of press coverage at the same time.

What high-profile research journals do is embargo interesting papers: They forbid anybody involved from speaking about the research until the publication date, and give some science journalists advance access to the paper and to the researchers. That gives them time to prepare their articles and lets them all publish at the same time, with higher public impact for everyone.

There's a few problems with that of course. Since nobody else knows about the research the journalist can't ask other researchers for a different perspective. The "journalist" is reduced to a PR-flack rewriting the press release1 in their own words. That gives us all those completely uncritical, overly positive science articles like the ones accompanying this arsenic paper.

And the people who really are well-placed to give a solid opinion on the paper - other researchers - didn't have advance access, and couldn't give their opinion right at publication. We had to wait a week for that, and by that time the damage - to the researchers, to NASA's reputation and to the science journalists - had already been done.

This was made worse in this case by a misleading and sensationalist press release by NASA well before publication. It was designed to fan the flames of media hype from the start, and it succeeded admirably. The people who could normally pour some cold water of reason on those flames could not, since the paper was embargoed and could offer no solid opinion on it.

But research is peer-reviewed; why weren't the problems caught well before publication in the first place? We can't know for sure of course, but people are speculating that the problems were caught by reviewers, but were overruled by the journal editors.

The highest-profile journals like Science and Nature are different from the normal journals most papers get published in. They aim for a wide audience and tend to go for the ground-breaking and surprising stuff - the kind of research that leads to prices and fame (they are called glamour journals for a reason).

Now, they normally publish very high-quality research, don't get me wrong, and having a paper in either of those can make a career. I'd give a body part to have a paper in either journal2. But the reality is that while the research is often very high quality, the actual papers are not. Their allowed page count is too low to give a lot of details or a good bibliography, and in the scramble to be first they can sometimes be rushed and badly edited. I rarely cite a paper in Science or Nature - it's usually better to look for a longer, more thorough paper from the same group published in a normal research journal.

Newsworthiness can trump thoroughness, and people speculate that this is what happened here. From what I understand (this is not my own field) the group would have needed to conduct another series of control experiments to rule out plausible error sources, and that would have added six months or another year to the publication time. The editors may well have felt it was more important to get it out now, rather than wait another year and get scooped by a different group and different journal.

So, here's the problems, in turn: A paper gets substandard peer review, or the journal overrides the review in the interest of speed; the paper gets embargoed - kept in the dark from anybody with the competence to evaluate it - leaving journalists to interpret the results themselves, with no input from specialists; a besieged and attention-starved research organization publishes a factually wrong, hype-inducing press release that triggers a frenzy of speculation and media attention.

The one thing that's not a problem in this mess is the paper itself. Wrong papers are published all the time; that's part of how science works. We don't have peer review to catch wrong papers. It's there to catch papers that are uninteresting, or just replicating earlier results, or that have methodological or experimental problems.

You usually don't know if a paper is wrong until later - years or decades later, sometimes - when pitted against other results and analysed by other research groups. Einsteins theory of general relativity took four years to the first tentative tests and more than fifty years to get definite confirmation. The idea of an ether was around for centuries before getting disproved, and nobody still has a clue if some version of the string theory is the right description of the subatomic universe, more than forty years after it first appeared.

Now, if we'd not had an embargo this would never have become such a big problem. The paper would be published, people chime in on the science and it would never have become such a media debacle. Most journalists would probably have refrained from covering it, once they'd realized the paper wasn't all that amazing, and quite possibly wrong. The only reason to embargo results is to fan media attention, and as we see this can backfire spectacularly. If a newspaper refuses to cover a result unless they can get advance, exclusive access then tough - don't cover it. Embargoes are a bad idea.

But if you must have an embargo, make sure that 1) Everybody respects it - no advance press releases; and 2) include a selection of other researchers, not just journalists, among the people getting advance access. That'd cut the damaging hype, and it would give journalists a better basis on which to write their articles, and perhaps to decide it's not worth covering after all.

#1 And the paper, theoretically, though you'd be surprised how many science journalists have no background in science and couldn't read a research paper if their life depended on it. Rewritten press releases is too often all that you get.

#2 Well... One that grows back.

Monday, December 6, 2010


Oh yes, the season of the Japanese Language Proficiency test is upon us once again. Yesterday was the first time I took the new, redesigned test. I no longer fail 1-kyuu; I now fail N1 instead. Same level, different name.

And different test. It's still a multiple-choice exam, and the overall questions are quite similar but there the similarity ends. The old test had three parts: vocabulary and kanji; listening; and reading and grammar. The new test puts vocabulary, kanji, reading and grammar into one section, with listening as the other one.

The test is, I believe, a fair bit shorter than before. It now starts after lunch and takes only four hours including a half-hour break. The listening section is as long as before, and possibly a bit more difficult. The picture questions are gone, instead there's a fast section with single sentences followed by possible responses. It's really more a test of knowing your expressions and reading tone than of simple comprehension. There are a few longer, more involved passages that really tax your ability to remember who is saying what (I failed miserably; I just can't keep long passages straight in my head).

The reading is as long as before, or longer. There must have been a dozen texts of various lengths, with questions both on the overall meaning and of specific expressions. The texts seemed to be "real" writing, without much editing for the test; overall a little easier than the Asahi Shinbun articles I try to read in the mornings but not by much. The last question was a page from an application form for financial grants to foreign post-graduate students, and you had to figure out which of a set of candidates would be eligible to receive the money, and what a specific candidate had to do before they could apply. I really suck at administrativia like this in any language so I'm pretty sure I messed this one up as well.

What has become shorter is grammar and vocabulary, to some extent, and especially kanji. There were none of the puzzle-like questions of the older test ("Select the answer sentence that has an underlined compound kanji word with the same pronunciation as the underlined compound word in the question sentence"), and there were overall fewer simple knowledge questions. Of course, the reading and listening parts all make heavy demand on kanji, vocabulary and grammar so it's still tested a lot, just not as much in isolation.

Overall, I think the new test is much better balanced. The focus (at least at level N1) is properly on comprehension and use of real-life Japanese, with less focus on memorizing facts for their own sake. If there is anything still missing, it would be a test of actual language production. Many language tests do have an essay-writing section or a live interview, but that would probably increase the cost too much to be realistic.

For my test, I did feel I know this a bit better than last year, but the test also seems a bit harder. The scoring system has completely changed, though, so I really have no idea how well I'll do. I did fail, but I don't know how badly. Anyway, I think it's time for me to try it for real next time around. I'll get an exam practice book and start studying for the test once my workload drops a little, then try to pass the thing next December.

Friday, December 3, 2010

New Kanji


This sort of slipped by this blog when it was first decided this spring, but Japan has increased the number of common-use kanji by almost two hundred, while removing half a dozen or so. The actual change is imminent, and prompted Asahi Shinbun to print an article on it last Wednesday, with a list of the new characters.

Common-use kanji (常用漢字) are the characters everybody learns in primary and high-school, as decided by the ministry of culture and education (and science, and technology and - for whatever reason - sports). There's around 2000 characters total - 2136 with this change - and an additional few hundred used for family and given names.

This list matters, as official documents and announcements, school materials and so on can use only characters on this list1. Private publishers can, and do, use whatever kanji they like of course, but it's generally a good idea to heed this list as your readers are guaranteed to know it.

Once upon a time the intention was to gradually abolish kanji. The common-use kanji list was a step in this direction, and newspapers and other publishers were required to stick to this list. But you can't dictate language use from above of course; just look at the futility of French governments trying to keep their language pure of Anglicisms for an example. Languages belong to its users, and it's the users that decide on use, not officials or language academies.

The education ministry no longer tries to dictate use; changes to this list are simply adapting to actual changes in real-world usage. The revision this time around is the largest increase in common-use kanji ever. The reason for the increase is of course that people are using more kanji than before (so much for abolishing them). And the reason for that, in turn, is the computer and the phone.

It's hard to remember how to write a character you rarely use. But it's much, much easier to recognize it when you see it. With a computer or phone you no longer need to remember exactly how to write them - you write the sound of each word and select the appropriate characters from a pop-up list. And there's a network effect: people start using rare characters in email and text, making them more common and encouraging other people to start using them too.

Is this automation bad? Nope. A decent analogy is English spelling: you no longer have to remember how to spell rodhorenron rhodorendron rhorhodenron rhonhorendron rhododendron; our spell checkers help us get it right. I wouldn't have tried to memorize that word - without a computer I would simply have written "dark green shrubbery plant", written it wrong or skipped it altogether.

There are two kinds of additions: Kanji used in place names, and kanji already in common use in newspapers, advertisements and so on.

When I looked at the list itself I was surprised, frankly. Even I know a number of them, and I'd assumed many of them were common-use already. 嵐 (arashi - storm, tempest) for instance, or 潰 (tsubusu - to crush). 串 (kushi - skewer) and 貼 (haru - to stick) are both seen in streets everywhere as part of 串カツ (kushikatsu - Osaka-style meat skewers), and 貼り紙禁止 (harigami kinshi - "posters forbidden").

虎 (tora - tiger) and 熊 (kuma - bear) finally get their characters, though we may need to put them in a 籠 (kago - cage) and lock the 鍵 (kagi - key). We can now eat 鍋 (nabe - pot or stew) and 麺 (men - noodles) without resorting to hiragana. 狙 (nerau - aim), 袖 (sode - sleeve), 誰 (dare - who?) and 虹 (niji - rainbow) are other surprises.

Among place names we have 岡 (oka) as used in Fukuoka and Chizukoa, 奈 (na) for Nara and 阪 (saka) for Osaka.

Some other characters are still rare, overall, but show up in single words that are reasonably common. 鬱病 (utsubyou - depression) has become a poster-child for people opposed to this change; "utsu" is complicated and rare - even one of the components is very rare in itself - and really only used in this single word. Of course, people will mostly need to read it, not write it, and chances are this one will see more use too, once it becomes more familiar.

Overall, the change is a non-event for most people; they already know the characters, or will easily pick them up. Newspapers will adopt some of them and skip others for now. People will use them or not as they see fit. The real significance really is the fact of the increase in itself. It's a affirmation that kanji aren't going away, and an acknowledgement that technology has a role in driving language changes.

#1 You can use other characters if you add "furigana" - tiny kana characters indicating the pronunciation - to them. Book and magazine publishers sometimes use furigana for rare characters, and childrens and young adult books use them for any kanji the readers aren't expected to know yet. This is one reason that YA literature can be good practice material for adult language learners too.

Tuesday, November 30, 2010

Japanese agriculture

Still no end in sight at work. I've spent far too much trying to track down a subtle bug that seems to appear only when I run batch - not individual - simulations on the remote cluster. So instead of wasting time here, jump over to "Twisting Flowers" who has a nice summary post about the state of Japanese agriculture.

In short, the agricultural sector is protected by far more, and far higher tariffs than elsewhere. Farming is completely dominated by elderly farmers - at or above pension age - with very few young people coming into the profession, and almost none who aren't born into a farming family already. The total number of farmers in Japan is about 2% of the population.

Not mentioned there, but I have read elsewhere that about 10% of those counting as farmers never actually farm anything; they have a plot of land (often inherited I guess) and membership in the agricultural association. Sizeable amounts of land lie fallow due to these ghost farmers, and due to a lack of people willing and able to work it.

So when you hear that Japan declines a free trade agreement that would greatly help its industrial (13% of the population) and service sectors (65% of the population) out of consideration for the farmers, realize that they are protecting 2% of the population, the majority of whom are already eligible for a pension anyhow. Also, the agricultural industry has modernized so production cost of staple foods like rice is no longer much higher than elsewhere. Open markets would not destroy farming, though it would forced to modernize and consolidate. But then, as the number of farmers keep dropping this is what's happening already.

And in case you wonder why political parties keep favouring the old and the few over the young and the many, all you need to do is look at voting power disparity. Small, rural districts have several times the voting power of large urban areas. That old farmer really is worth four or five Tokyo company workers, as far as political power is concerned. The courts have declared it illegal several times, but the parties keep ignoring it and the courts are powerless to impose any kind of sanctions.

Eventually, of course, the problem will disappear along with the farmers. As old farmers die out and rural areas depopulate they will eventually no longer wield enough voting clout to dictate terms for the rest of the country. The question is how much damage will be done before this happens.

Friday, November 26, 2010


We go to Kobe once or twice every month. We get to Kyoto at least a few times every year. But for some reason we almost never go to Nara. This despite the fact that Nara is the closest city we have here, closer than any of the others we visit (ok, Sakai and the other cities of Osaka county are even closer, but I can't really see them as separate from Osaka). I even work in Nara county and go most of the way there and back every day. And yet, I've even been to Tokyo more often - I've been to Hokkaido more often, even - than I've been to Nara right next door.

So when we went to Nara a few weeks ago1 it was the first time for us in years. It was a long weekend, and the whole town was packed with tourists. It's not a large city, Nara, nor is it very scenic. Most visitors are drawn there by its history. It was the first real capital of Japan (though for less than a century) and has a very large, very old temple area in the outskirts of town2. Nara historical museum holds a large collection of early national treasures. Our visit coincided with the yearly public exhibition, and that certainly added to the throngs of people; when we passed by the museum, the line was over two hours long.

Study Time

Nara is a normal town, not just an outdoor museum. If you live here the scenery is all part of your normal environment. Here a student has found himself a warm, sunny spot by some old temple.

The main draw of Nara is Todaiji, a large, old temple with the largest3 Buddha statue in Japan. The surrounding park is filled with free-wandering deer that are not to be hurt in any way, without exception even for a savoury red-wine stew of venison and potatoes with sauteed autumn vegetables. Harsh rule, that. There's no reciprocal rule of not hurting humans either, so parents need to keep an eye on their children lest they get mobbed by aggressive deer looking for snacks.


Wakakusa mountain, Nara.

Wakakusa mountain is actually a large, steep grassy hill; it's quite spectacular in its way. The sunny hillside is pleasantly warm even in autumn and gives you a good view of Nara. Lots of couples seem to climb up here to sit together on the grass and look at the view, and a fair number of people were sliding down the steep hill on plastic mats, or bouncing a ball up the hill, then try to catch it on the way down.

Nara is a pleasant enough day trip. The temple area is pretty cool, and there's a fair amount of beautiful walking paths among the hills nearby. But there's lots more temples and shrines in Kyoto if that's the kind of stuff you're interested in, and the Fushimi Inari shrine between Kyoto and Nara is both more spectacular than the Nara hills for walking, and less crowded too. Nice, but I doubt we'll make a habit of coming here very often.


There's plenty of green spaces where people gather for picnics or playing games. With less people it would be a great place for family outings. Here's a small, determined park visitor, and Ritsuko in the background.

#1 Yes, this post is weeks late, I know. I have posts planned that should have gone up months ago. I'm very behind with work, and it's not going to improve anytime soon.

#2 It was the sheer number of temples in Nara that cut short its time as capital: the throngs of priests were so intent on playing politics that the then emperor finally simply gave up and moved house, and forbade any of the temples from following him, on pain of, well, pain I assume. The emperor left and the temples stayed behind, to the delight of modern-day Nara.

#3 Well, it's the largest statue when you ask people in Todaiji. If you go to Kamakura southwest of Tokyo they'll tell you that their Buddha is the largest. I know better than to get into a religious dispute so let's just say they're both really, impressively big and leave it at that. The Todaiji one looks cooler, though.

Saturday, November 20, 2010

World Press Photo and Burning Trash

We've gone to the World Press Photo exhibition every year for a few years now. I couldn't make it to the exhibition in Osaka this summer - work kept me too busy - but it's a travelling exhibition so we caught it this weekend at the Ritsumeikan university exhibition hall in Kusatsu east of Kyoto.

It was good; overall I found it to be better than last year. The quality was more even, but I didn't really find any images that popped out and stood out above the rest. This was most obvious in the portrait section, which last year was much more interesting than now. It's almost as if the jury had gotten a lot of heat for its previous eclectic and none-too-flattering portrait selection and got a bit gun-shy this time around.

There were more graphic and violent images this time around - one sequence showing a stoning is pretty disturbing - but that may simply be a reflection of more truly distressing events this year than before. And none of the images strike me as exploitative or speculative; they really are well chosen as documentary images. It's been a good exhibition every year so far, and I can recommend you catch it if it comes to your area.

Trash fire

What's left of the trash heap after the fire and the fire brigade was through with it. Didn't get a shot of the fire itself; they didn't let people out on the street, and I wasn't too keen of going out in that smoke anyhow.

In other, not-very-notable news, a trash dumpster caught fire on the street outside last night. The trash collection round happens after midnight here, and apparently a dumpster truck had a fire start in its cargo just as it was passing by. The driver quite sensibly dumped the entire load on the street before the truck itself caught fire. So we had a quite large, very smelly pile of burning trash and a dozen firemen blocking the entire main road outside and sending the resulting smoke up into the building ventilation system. A smoke that, remember, was caused by rotting leftovers, soggy plastic and pet poo set ablaze. Imagine a cool, fresh early dawn in a dew-sprinkled pine forest, just as the summer sun is drying up the moisture. Then imagine the polar opposite. Makes you appreciate just how much worse Osaka air could be.

Wednesday, November 17, 2010


It really, really sucks to sort-of have a cold. I mean, at least a real, proper cold or an influenza is unambiguous: you have it or you don't. If you have it you're sick and you're not going to do anything but feel sorry for yourself until you get better.

But a sort-of cold isn't a proper disease. You feel sluggish and tired, and your throat is just painful enough to be annoying. But you're not really sick; you can still go about your day, you can still get things done. Of course, just because you can do stuff it doesn't mean it gets done quickly or well.

I've been under the weather for a couple of days now, and today it's evolved into this dreaded sort-of cold. I've dragged my sorry behind around work all day with my head feeling like its filled with cotton wool. With my luck this'll probably linger on into next week, never really erupting into a proper illness, but not going away either.

Seems it's going to be one of those winters.

Wednesday, November 10, 2010

Saving Data for Posterity

Test Tubes
Research generates data. Sometimes lots of data - the LHC accellerator at CERN generates petabytes even after heavy filtering - and sometimes less. All of that data has to be processed and analysed. Analysis leads to results. Results lead to papers. And papers lead to funding which leads to money for more research as well as food, shelter and clothing for the researcher1.

But once the paper is published and the project is over the data remains. And not just the data, but also the source code for simulation models or analysis tools, hardware specifications for one-off lab equipment, customized reagents and so on. And keeping that data, source code and other material around is important. We need to keep the data so that other researchers can compare results and replicate the work. We need the data so we can resolve any discrepancies from different labs. We need the data so we can use new, better analysis tools to wring out more information when they become available in the future. Data retention can even become political as with the climate research data controversy at University of West Anglia2.

Keeping research data is hard, much harder than it may seem at first glance. Ars Technica is running a really intresting series on the issue of data retention in science; here's part 1 and part 2. But a major problem is only hinted at so far: whose responsibility is it to store data over long time frames - years and decades - and who pays for this?
I built a model in a previous project, ran it against some inputs, and ended up with a journal paper. The model, the inputs and the resulting data is about, oh, one Gb in all. If anybody wants to build on our work that code and data would be quite useful. A Gb isn't that much today; you can comfortably store it on a DVD or memory stick, or put on a webserver somewhere. But whose DVD, and whose webserver? In our current project both the model and the analysis is a lot more complicated, and the resulting data sets are larger. Where to we park this data so that it'll still be publicly available in five years? Ten years? Thirty years?

The individual researcher - me and my colleagues - can't really have sole responsibility. Your departmental web pages and file stores are only good for as long as you work there. When you leave you lose your access rights so you can no longer maintain the data. I've switched projects and workplaces often enough that I don't even bother setting up a local web page.

We bring our data and code with us when we move of course - I have a copy of my own of everything important - but that's not very reliable over the long term. I don't have the discipline or the will to pay for decades of off-site backups of multiple gigabytes of simulation data that nobody is ever likely to ask for, so I have only a local backup. One house fire or earthquake could wipe it all out. When people leave research altogether they may no longer want to keep all that old data around, and when we die our relatives are very unlikely to keep any data or personal online repositories any longer. Besides, even if researchers keep their data, actually finding them years or decades after the publication can be very difficult.

Putting responsibility on the department or lab is no better. Active researchers can keep their project data around, but web pages and data sets from old projects by long-gone people tend to disappear over time since nobody has an active interest in it. Lab-level servers are usually maintained by a busy graduate student or faculty member and are none too reliable as a result. Servers die or move, backups fail or get misplaced and when nobody feels ownership over that old data it just never gets restored or propagated properly over time. Entire departments and labs can disappear, taking any local data with it into oblivion.

Universities can (and should, perhaps) set up a central data repository. They have research libraries and often already have a publication repository so they have the know-how. But there are a number of obstacles to make a university-wide repository work.

One major problem is to make researchers actually use such a repository. Our universities already have publication repositories and other such services, and unfortunately most researchers simply don't use them. It takes time and it takes effort, and unless you have a way to compel people it'll go unused. That means making it mandatory, easy to use and be completely data agnostic, and resources (money and manpower) must be available to help, prod and force researchers to use it properly.

It also takes a good deal of money, money that needs to come from somewhere. Using some of the cut universities take from research grants3 is an obvious solution, but that money is already spoken for so you'd have some ugly fights ahead of you to make that happen. And any university with a large collection of potentially valuable research data will be sorely tempted to lock it in to exploit the money-making opportunities rather than make it open and accessible, making this a non-solution to the original problem. Also, published research happens at other places than universities so this would not solve the data retention problem in general.

The public funding agencies would be natural for keeping a data repository. They are paying for the data in the first place after all, and have the clout to specify every aspect of a project already. They typically require extensive reports and documentation at the end of a project; it would be just another small step to require a documented data and source code dump as well. Funding agencies typically don't have a direct commercial interest in the results and don't have the same incentives as universities to keep the data to themselves. Of course, not all research is funded this way, so again, it would not be a general solution.

Lastly, the journals themselves should do this. They are the ones publishing the papers based on the data after all, and have an interest in making the data available for analysis and control. Many journals already charge high fees from researchers for publishing their papers4, and they already have a content repository system for all their published papers and supplementary materials. They could add a data dump to the system, and require authors to submit relevant data sets and source code as a precondition for publication. Data and source code would be a legitimate use of supplemental material - more so than the annoying trend among some journals to have the printed paper only be an introduction, with most actual details in the supplementary online section (a topic best left for another post).

So, the journals and the funding agencies should be the primary stakeholders for research data retention. That doesn't let the rest of us off the hook though; I feel we still have a personal obligation to make data, source and papers available to others as best we can, within the legal and other limits that apply. You can't disclose raw data that would identify patients or experimental subjects for instance, and you have no obligation to send off a sample of a bacterial strain to somebody that doesn't have the facilities to make use of it. But the default assumption should be one of openness - we should keep and disclose our data unless we have specific reasons not to do so. Not the other way around.

#1 Never underestimate basic necessities and security as motivation for people. There are those who seem to think science should be a calling; a noble intellectual pursuit for truth and the betterment of humanity far removed from any grubby considerations of money. Those people either are not scientists themselves, they have tenure or they are independently wealthy. The rest of us have a perfectly sensible interest in seeing that we and our loved ones have food to eat, a home to eat it in and savings to fall back on once we're too old to get funded any longer.

#2 Just to make it crystal clear: the controversy is purely political. There was no fraud or deception, just some sloppy data retention and private emails never meant for a wide audience.

And there really is no doubt any longer that man-made climate change is very real; any scientific debate is about the magnitude, the mechanisms and the nature and distribution of effects over time. If you're opposed to climate change for political reasons then sorry - reality doesn't care about what we want to be true. Holding your ears and shouting "lalalalalala" won't make it go away.

#3 As little as 35% or as much as 50% of the awarded grant money. It goes to pay for lab and office space, secretary and admininstrative services and so on. Data storage and retention would fit right in. However, at most universities the external science research funds are an extra income; the cut they take is larger than needed to pay for the research-related costs - you pay this whether you actually use any services or not - and so research actually subsidizes education. Cutting research would, for many universities, mean losing money, not saving it.

#4 Yes, you pay the journal to publish your work. You volunteer to review submitted papers for journals, without pay. If you're a high-level researcher you may get invited to serve as editor - gratis - for an issue of the journal. Then your university library pays dearly for a yearly subscription so other people can read about the research you've done. Journal publishing is a serious moneymaker.

Monday, November 8, 2010

Seven. Seventyseven.

Seven years in Japan this month. And 77 kilos. Which is right at the upper end of normal weight for somebody my height. And it's 14 kilos less than I weighed when I first came here. I've lost 2 kilos per year since I came to Japan; faster the first couple of years but I'm still losing about 1-1.5 kilos per year. Without any kind of dieting or restrictions; without, in fact, thinking of my weight at all.


The latest picture of myself. We ran into this discarded couch in Kobe a few weeks ago, and Ritsuko took this with my Pentax 67. This scene would make a pretty good band promotion picture I think.

Why have I lost weight? I eat balanced meals - meat and fish and fatty fried stuff, but mostly vegetables, pickles and fruit. It's easier and cheaper to eat local food so I no longer eat pizza, sandwiches or kebabs, and we usually make Japanese food at home. I normally eat set meals, at set times, with no snacks in between. My photography hobby and my daily commute have me walking 10k steps or more every day.

Salmon Dinner

A typical weekday set meal for us - salmon, miso soup, a couple of vegetable side dishes and rice. The "set" bit is important, I suspect; we all tend to eat not until we're full but until we have no food left. There's more rice and stuff in the kitchen if I want it, but I rarely take more since it's not right in front of me. Had the extra food been on the table I would probably finish it all.

I was able to break with a lot of old habits and set up new ones because I moved. It's much easier to break old habits when your life is changing, and moving to a different continent where you know nobody and don't speak the language would probably qualify as change. I was able to quit Swedish chewing tobacco ("snus") - a highly addictive form of tobacco not available in Japan - with minimal pain at the same time.

77kg is nice, but ideally I'd like to drop another couple of kilos; my ideal weight is around 75kg. At this rate I'll probably get there in another couple of years. Good enough for me.

Sunday, October 31, 2010

Vivitar Mariner

The Feeling Negative site has an ongoing traveling camera project: people send a camera to each other in turn, and every recipient takes a roll of film with it before sending it on. It's a fun idea, if somewhat slow as each stop takes a few weeks at least and the participants are spread out over the world.

The camera stopped by here in Osaka last month. I opened the very light cardboard box to find this:

Vivitar Mariner

The Vivitar Mariner. Fifty grams of plasticky 35mm goodness.

The Travelling Camera is a film project so I thought it fitting to take this shot with film too. I used the Pentax 67 with 90mm lens; it doesn't focus very closely so I've had to crop this quite a lot. I really should get a set of extension tubes. The film is Ektar 100, a recent negative film from Kodak with strong colors and very fine grain; the results are akin to slide film, but with much better dynamic range.

Last year I tried a Fuji single-use camera on a day-trip to Kobe. It was simple and dingy but a lot of fun to use. I thought about having a camera just like it but reusable, so you wouldn't have to send it off for development just to change film. The Vivitar Mariner is exactly that camera. I'm not the only one who thinks it's a good idea, apparently, as prices for a used one - a used low-quality 35mm film camera, note - can reach 100 US dollars or more, though more normal prices seem to be around 15-30 Euro.

Early Bird

When I step out on my way to work the morning rush is already underway, and a fair a of office workers are bustling to reach the office early.

The resolution and contrast isn't exactly jumping off the page here. Compare to the medium-format shot above; cameras and lenses, and formats, really do matter a lot.

The complete Mariner has a water-proof enclosure - our one doesn't have it any more - but apart from that this is remarkably similar to the Fuji camera. There's no settable aperture or shutter speeds, and the cheap plastic lens is set at a fixed focus distance of a couple of meters. The body is a very lightweight plastic construction that doesn't exactly inspire confidence but is up to the task of keeping the film in and the light out.


Delivery trucks are still parked at the depot, waiting for the morning shift to get going.

The aperture and speed of the camera is about perfect for open shade like this when used with 400-speed film.

With a 400-speed film you get plenty of light for daylight shots. I would say it's even a little too bright, and if you want to use this on bright summer days you would probably want to try a 100-speed film instead. Of course, it's made for underwater use where the extra light makes sense. There's a flash built-in that takes a 1.5v pen battery, but I didn't try it so I have no idea what the results are like; my guess is that it's not much use beyond a meter or two.


Tosabori canal, Minami Senba, Osaka. On my way to work with just a tiny detour.

The lens is really wide, much wider than the viewfinder. On the positive side it's fun with a real wide-angle. Less positive is the distortion; the leftmost pillar here should really be straight, not bulging. Of course, the pillar wasn't even visible in the viewfinder. If you insist on decent image quality (and if you are, why are you using this camera?) you should probably crop to the viewfinder to avoid the worst distortions.

Using it is simple. You wind the film, open the front hatch and press the shutter. The film counter is only approximate, and the whole mechanism feels creaky and wobbly, but it works. The stated focal length is 28mm, but I wonder if that isn't a bit of a white lie. The finder may be 28mm, but the shot you get on film is a lot wider than what the finder was showing you. Really - I wouldn't be surprised if the focal length is closer to 21mm or something like that. A wider lens would make sense for underwater use of course. Forget using the viewfinder for precise composition, and you can stop worrying about not getting everything in your shot; even if you didn't even see it in the finder, chances are you still got it on film.

Sakaisuji Honmachi

Sakaisuji Honmachi station, Osaka.

This kind of light really is at or beyond the outer limit for this camera. It's mostly amazing that I got anything at all; at f/9 and 1/125 shutter speed the light here is about five to six stops too low.

With a lens this wide, and with absolutely no controls to set, you can use this camera completely unattended. Just point it vaguely in the general direction of the stuff you want to shoot, and you'll get it. Give it to a child and they'll be bound to more or less get what they wanted, and if it breaks it's cheap enough that it's no real loss.

Ishikiri Station

The train stops at Ishikiri station on the way to Kita Ikoma. This station always strikes me as a sunny, cheerful place for some reason. Should get off one day and take a look at the area.

You can see all the rest of the pictures from my morning commute in this set

Monday, October 25, 2010

When Life Hands You Test Tubes

So there I was, at the NEURO 2010 conference in Kobe last month. It's a really large conference, with thousands of attendees. Ten parallel seminar tracks over three days, and posters by the hundreds, on row after row of poster boards on two floors of the conference center. Two centers, really; the conference didn't fit in one building but was held at two adjacent locations.

NEURO 2010

One of the poster session rooms in early morning as I arrived to set up our poster. With multiple seminar tracks and many hundreds of posters, this kind of conference forces you to only look at the stuff that really interest you. Which means you miss out on all the non-relevant research. But it's the seemingly irrelevant stuff that tends to give you good, new ideas, that fire up your imagination, that make you try things you previously wouldn't have. I much prefer a smaller conference like SAB for precisely this reason.

With so many attendees from very lucrative medical and pharmaceutical fields, plenty of companies choose to sponsor the conference and exhibit their products. Mostly it's research-oriented stuff such as laboratory equipment, books, software and so on. There were several rows of companies touting various clinical and lab-oriented sciency stuff.

Now, disposable gloves or automated rat feeding stations aren't exactly going to set your heart racing, not when your attention is mostly on the seminars and presentations. So many companies had some small ploy to raise interest - they'd give away candy or pens, or they'd sponsor free coffee at the poster session or something like that.

One company, a manufacturer of PCR equipment and accessories, held a raffle with some decent prices; you gave them your business card in exchange for a chance to win an iPad, a Nintendo DS and other prices. And even if you didn't win a real price, you could still win a sample of their products, delivered after the conference. I didn't win any of the cool prices of course, but I did win a product sample. A friend of mine did too; I suspect most people at the raffle did.

The "sample" arrived last week. I got an email from the building management telling me I have a delivery and could I come down and pick it up?

Lottery Win! We Got Them Tubes

Two boxes of plastic test tubes for PCR use. Two large boxes. Three hundred 50ml tubes and three hundred 15ml ones. With caps. If this is a sample, I really wonder what a proper shipment looks like for this company. My friend got a similar shipment to his office in Tokyo, and one of our graduate students here got two boxes as well.

Test Tubes

A 50ml tube and an 15ml tube; for some reason the 15ml one is only marked up to 14ml. We gave away most of it to the bioscience department where they can make better use of the stuff, but I've kept one bag of each - 25 and 50 units - as a memento, and because, well, they seem too useful not to keep a few around.

So, what to do with the ones I kept? They are possibly useful for film and darkroom work I think. Could use them as fun, thematic shot glasses - any strongly colored drink would look cool. Molds for fruit jelly or home-made ice cream. Neat containers for small screws, bolts and nuts. They'd make a pretty cool spice rack, except that spices should be stored in the dark. Props, of course, whenever I want to take a sciency-looking picture. I'm open to suggestions.

Thursday, October 21, 2010

Paris Aftermath: Cameras

I used three cameras while in France. I brought the Yashica Mat and my Xperia smartphone, and Ritsuko brought her Canon Demi, which I borrowed when she wasn't using it. The idea was, I'd use the Yashica for "real" pictures and the phone for throwaway snapshots.

The Yashica Mat is a consumer-grade medium-format TLR from the early 1980's. It's compact and light - good for travel - and I have taken it on trips a number of times. This this time I wish I had brought a different camera, though. First, it was always a fairly inexpensive camera so the lens is not the greatest one out there. It's prone to flare and distortion, so you'll want to avoid any direct light sources, having anything important near a corner of the image, or open the aperture beyond f/6.7 or so.

Kansai Airport

Kansai Airport departure hall. A large, airy atrium, like a huge greenhouse. I used Ilford HP5+ at iso 800 for this trip. This film, at this speed, gives a pleasing contrast without getting too grainy. As I need to stop down this lens quite a bit the speed helps a lot, and the relatively low resolution of this film is no problem since the lens isn't very high resolution either. Anyway, with this film and camera I get 20mp or so, more than enough for me.


Charles de Gaulle departure hall. Illustrates the design difference to Kansai airport quite nicely. CdG is all curvy tunnels, like an enormous digestive system ingesting passengers in one end and emitting airplanes out the other after extracting as much money as possible along the way. It's cool but I like Kansai better.

Also, the build quality of the Mat is not the greatest. One reason the camera is so light is because parts of the mechanism is made of plastic rather than metal. The film advance started to lock up intermittently last winter, and it's getting more frequent. During the Paris trip, it locked up about once every other roll. So far it's always unjammed when I jiggle and rattle the crank, then fire the shutter with the lens covered, but sooner or later it is going to seize up permanently. The frame spacing on the roll is also getting more and more erratic, with some frames almost bumping into each other. It seems the entire film winder mechanism is starting to wear out, and rebuilding it will probably be more expensive than the camera is worth.

This time I also wish I had brought a real tripod on the trip; I've lost several potential low-light images simply due to camera shake. Perhaps I should have brought the Pentax 67. Sure, it's a pain to carry in a backpack all day, but the chance of photographing in the museum would have been worth it alone. Ideally I should have some camera with the image quality of the Pentax, but fixed lens and easy to bring on trips.

This may sound like I'm trying to excuse a future camera purchase, and you may well be completely correct. I'm idly evaluating possible cameras right now, and may get a replacement travel camera next year or so.

Quartier Latin

Quartier Latin. Fuji PN400N color film. And yes, the film does make a difference. The color rendering, the grain, the amount of detail you capture all change quite a lot with the film you use. PN400 is comparatively expensive, but really - I only shoot enough film in a month to pay for a lunch and a beer at the most. I'd rather get better images than save a couple hundred yen on film.

The second camera is my Xperia X10. It's an Android smartphone by Sony Ericsson, and noted for having a not-horrible camera; that's one of the reasons I chose it. It's nominally 8mp, but as with any camera this size you can pretty much ignore the stated resolution. Just treat is as having around 2mp - you're not recording any more detail than that. The dynamic range is pretty low so you'll tend to have parts blown out or blocked up. Unfortunately the noise reduction is too heavy-handed and not adjustable, so everything takes on a too-smooth plastic appearance. Images from this camera actually improve when you add a bit of noise afterwards. If there's any one thing I wish for it's being able to set the level of noise removal myself.

But the images really are useful. For this kind of blog posts they're sufficient, if not exactly great. Small prints will look decent. In low light or scaled up the images start falling apart but that's asking a lot of such a tiny camera unit. I don't expect it to perform as well as a dedicated camera, and it does well enough in many cases.


Lunch at the Clos Luce. You can see how all detail is sort of smeared out, giving it a watercolor appearance. If S-E would only allow us to reduce the amount of noise removal this image could improve a lot. But it still looks much better than my earlier cellphone camera, and I would say it's close enough to be usable for a blog like this.

Manga Cafe

Manga cafe in Paris. When it gets dark, image quality suffers of course. But if my aim was simply to show that yes, there are manga cafes in Paris, then this shot would be more than enough.

The Canon Demi is a half-frame 35mm film camera. "Half-frame" means it records two vertical half-sized images in the same area normally used for one horizontal 35mm film frame. These cameras were popular in the 1960's and 70's, when color film became wide-spread. It was expensive to buy and develop color film at the time, so cramming two images in place of one was a way to economize. They may have been born from a sense of thrift, but some of them are still high quality cameras. The Olympus Pen F, for instance, had a lens mount instead of a fixed lens, and there were a number of high-quality lenses available for it. That one is still fairly popular, and used bodies and lenses can sell for quite respectable amounts of money.

We've been sort of led to believe that digital is leaps and bounds ahead of film, and in many ways it is true. Higher-end digital cameras sport high resolution, high-quality lenses and low-light sensitivity beyond anything normal film is capable of. But of course those are fairly big, expensive cameras, and most people use small compacts with tiny sensors and much less performance. The Canon Demi - a compact camera with a small film format - is better compared to them rather than a DSLR. And it does quite well in comparison. It's automatic, so it meters and sets shutter speed. You only need to control focus - it's scale focusing so you just guess the distance - and optionally the aperture. The meter is pretty accurate and the lens is decent, so the results are surprisingly good.

Clos Luce, restaurant

Lunchtime for the conference at the restaurant in the park of Clos Luce. Pretty good. It's film so there's plenty of dynamic range - I've increased contrast quite a bit from the original scan. Here's a larger version, and here's the size as scanned. There's a fair amount of detail in the image, and while it doesn't come anywhere near a serious camera it does about as well as a budget digital camera.

So, for travel I'd avoid the phone. It's really convenient for snapshots and it's always with me, but it's not acceptable as a single camera. It is a phone, not a camera, and it's just doesn't handle like a real one. You spend too much of your time staring at the screen controls rather than at your subject. The Yashica and the Canon are designed to be cameras from the ground up, with physical controls rather than menu items, laid out so they're easy to use without taking your eyes off the scene. The resulting image quality of the Canon Demi is also clearly better than the phone.

The Demi is fun, and it could work for travel if you're fine with lower-resolution, gritty street-life style images. You get 72 shots per roll, so you can snap away with abandon - treat it like a digital camera, really - without worrying about cost. But the lack of manual controls means you can't really use it at night, and the low resolution can make scenic images a bit disappointing.

Image quality-wise, the Yashica wins hands down. It's very pleasant to use; the controls are well laid out and I love the top-down view of the waist-level finder. It is a bit slow though, as you need to measure the light, set the shutter and aperture, use the loupe to focus, then frame the shot. It's the opposite of the Demi (or the Rollei 35) - great for contemplative shots, but too slow for fast-moving events. Still, it's the travel camera of choice for me.

Monday, October 18, 2010

Summer Is Winding Down

Forget about work for a day. Have a slow, lazy Sunday barbecue, and enjoy the last of the summer sunshine.


Life at its best.

Monday, October 11, 2010

Fake Evidence for Fun and Profit

In spring a year ago I wrote about a case where companies had abused the reduced postal rates intended for handicap-support organizations. They'd set up a fake disability support group to send out their advertisements, and welfare ministry officials gave them the needed certification knowing the group was fraudulent. A DPJ (then opposition) lawmaker seemed to be involved as well.

The police arrested the officials, as well as their head Atsuko Muraki, director general in the welfare ministry, last summer. Prosecutors and police claimed she was behind issuing the fake postal certificate. Testimony from her arrested subordinates supported this. So, high-level administrator abuses power to line own pockets. A nice and juicy story, and with political implications too. Of course, as MTC pointed out at the time, you do not arrest a high-ranking official unless you're really sure of your case. If you're wrong, the backlash would be absolutely fierce.

You know what's coming next, don't you: The case against Muraki came up in court, and in court the junior officials retracted their testimony. They denied that their boss had been involved in any way. During the interrogations (which, in Japan, is often not recorded and without a lawyer1) they first claimed she'd had nothing to do with it, but the prosecutors lied to them, saying the others had fingered her, and that unless their testimony agreed they'd get a much harsher sentence than the others. This kind of pressure is, needless to say, not legal. When this came to light the judge immediately discarded all suspicious testimony as evidence. Without it the case fell apart, and she was found innocent of any charges last month.

But wait - it gets better! Her acquittal not only made the Osaka Special Prosecutor unit look bad, it kicked up exactly the kind of anthill that MTC predicted last year. And amid the scurrying, one defence lawyer took a second look at a certain floppy disk with the certificate that the prosecutors had seized. This eagle-eyed lawyer realized that the date of last change of that file had been altered by the prosecutors. The date on the disk seemed to corroborate the prosecutors claims, but the original date (which had been noted in the initial documents) contradicted it; and the original date was in fact evidence of her innocence.

At this point, the excrement hit the fan. Pachyderm-scale excrement and an industrial fan, with lots of spreading power. Star prosecutor Tsunehiko Maeda admitted he had changed the date on the disk but claimed he'd done it by mistake. Later on - as the investigation proceeded - he admitted he'd done it deliberately, both to destroy unfavourable evidence that she was innocent and to create a better case for her guilt.

So, a prosecutor deliberately destroyed evidence of the accuseds innocence and faked evidence against. He even talks about this with his colleagues at one point, and four of them go to their bosses, unit chief Otsubo and his deputy Saga, in February and tell them about Maedas fake evidence. Appalled, Otsubo and Saga immediately order an internal investigation to get to the bottom of it -

Hahaha!! This is the Osaka prosecutors office - of course they didn't! What Otsubo and Saga did was order the four prosecutors to keep their mouths shut, and ordered Maeda to make up a good excuse and write an internal report, in case the tampering came to light. He had to rewrite the report a number of times, in fact, until Otsubo was satisfied the excuse was good enough. Cover up the whole thing in other words, and continue with the case pretending the evidence tampering hadn't happened and ignoring that their main suspect was innocent.

So here we have not just one rogue prosecutor, but seven, in a special investigative unit - supposedly the best of the best, handling the difficult, sensitive cases - all covering up illegal tampering with evidence. All knowing the testimonies are untrue. All of them realizing their suspect is in fact innocent, but still dead set on bringing her to trial and send her to prison for a crime she never did. All of them believing that their own careers and saving face of the Osaka prosecutor's office is worth imprisoning and destroying the life of an innocent person.

Would you believe that this is a single, isolated incident? No, me neither. And defendants in earlier cases with the same unit are already showing up, claiming they got railroaded in the same way, with witnesses pressured to change their stories to fit the prosecutors case. This piece of morbid entertainment may well go on all through next year or longer.

And neither should you expect this to be limited to Osaka. Prosecutors have a rotating system where they change workplace every few years, and the same people - and the same corrupt culture - moves between Osaka, Tokyo and the other large cities (rural districts aren't good enough for these people so the culture may well be different there). If there are no recent cases of prosecutors altering testimony and covering up evidence in Tokyo then it's probably because nobody has looked for it.

A final question is why they arrested her in the first case. It seems they never had any evidence on her, but went on a fishing expedition that came up empty. They had real suspects already, that really are guilty of the crime. They didn't need another suspect to solve the case. Again, you don't arrest people with power, money and friends in high places unless you're pretty sure of yourself; and yet, they did2.

My completely unfounded guess is that it's election related. Remember, at the time it seemed there was a connection to Muraki and to a DPJ diet member - an opposition party member - and this fraud was uncovered just as the national election campaign was heating up. An embattled LPD could really have used a juicy scandal to hang on the opposition. My guess is that some LDP member leaned on the prosecutors office - called in a few favours perhaps - to be aggressive and move very fast with this case, so that any connection to that DPJ member would be uncovered before the election. As it turned out there was no connection to find, the LDP lost the election, and the prosecutors found themselves stuck with an innocent high-level administrator they never should have arrested in the first place.

This is a disaster for the already tarnished image of the Japanese judicial system. It's worth noting that the witness tampering didn't really raise many eyebrows; that kind of misbehavior is pretty much expected already. People are already wary of reporting things or coming forward as witnesses on the fear of becoming accused of something. But the falsified evidence brings it to a different level. A trustworthy legal system - like reliable social security, defence, disaster management and medical systems - is fundamental for a stable society, and if it frays badly then everybody loses out.

#1 The heavy reliance on testimony and confessions over other forms of evidence seems to be a serious weakness of the Japanese judicial system, when you consider just how unreliable and malleable our memories are. Given enough time and pressure - and prosecutors have plenty, with suspects in jail for months at a time - you can make people believe they saw or did almost anything. This is nothing new; the conviction rate of over 99% is, let's say, improbable at best, and the unreliability of testimony is probably a major cause of that. There's a drive for mandatory recording of all interrogations in order to detect undue pressure and attempts to change statements to fit the case. The police and prosecutors are dead set against such recordings, presumably for the very same reason.

#2 Equality in the eyes of the law is an important principle and an admirable ideal. The reality - in Japan and everywhere else - is of course that we're not equal. A homeless, barely literate day labourer will not have the same treatment by the law as a high-level government official. Money buys you better lawyers and resources to do your own investigations; your web of contacts gives you access to all kinds of other resources and information (references to high-powered lawyers and other professionals for instance); and your education and professional life gives you knowledge of your rights, of the resources you can draw on, and - importantly - the social confidence to make use of all of this in the face of scolding officials. And officials, knowing all this, will be much gentler and more careful when the suspect is from the top of society rather than the bottom.

Thursday, October 7, 2010

Not So Social Scientists

Blogging is usually a welcome change of pace from work for me. But sometimes I need to do a lot of writing for work, and when I do, writing for fun will interfere. It becomes a distraction rather than a diversion. Don't expect a large volume of posts here for the next few weeks at least.

But there was a post recently about socially inept scientists that's pricked my interest. It's basically a good practical post about attending conferences if you're introverted or socially awkward. But one thing leapt out at me (and others commenting on this post):

A final point is to realize that scientists as a group tend to be more socially inept than other groups.

I don't think this is true, actually.

There are plenty of socially inept scientists out there of course. Insensitive bullies that trample everyone else in the pursuit of their career; desperately tongue-tied introverts that hide behind their desk in the far corner of the lab lest anyone actually approach them; oblivious monomaniacs that will drive people insane with their obsessions. People that look and act like their mom dressed them for their first day of middle school and haven't changed their style since. There are people that amaze you by being able to go through an entire workday without the guidance of an assistant or support person.

But the reason we remember these characters we meet in our labs is because they're not actually that common. They are the exception, not the rule. Most doctoral students and researchers you meet are normal, social people with a deep interest in their work. Don't confuse passion for your work with social ineptitude, by the way; it's two separate things. Inability to clearly explain your work is no sign of social clumsiness either. Explaining complex things for the non-expert is hard; that's why we need an entire separate profession - science writers and journalists - to do it well.

And consider of some other professions for a moment. Accountants. Industrial laundry workers. Payroll clerks. Chemical process engineers. Lawyers. Systems analysts. Vehicle pool maintenance personnel. Computer programmers. You will find withdrawn, introverted, awkward, rude and oblivious people in all of these jobs, and in many, many more. There's no reason to think that scientists have more people like that than any other group.

So where does this notion come from? There are a number of reasons, no doubt, but I think one reason is that science is a very social career. You collaborate with others - the lone scientist is a rare exception - and you interact with your collaborators more or less constantly. You may be teaching and mentoring students and PhD candidates, lead a team of researchers in a common project, or serve on committees and adminstrative posts. You change your workplace and coworkers often, and getting to know people and getting along with them is critical for finding people to work with and labs to work in.

And you are always, always presenting your results and yourself - in the form of journal papers, true, but also in conference presentations, seminars, workshops, meetings and informal discussions. Whenever you visit a lab, if only to meet one of their members, you're often expected to give a talk about your research. I've even heard of people mentioning where they're going on vacation, only to be roped in for a quick, informal three-hour seminar at a nearby university while they're in the neighbourhood.

Science is very social, so the scientists who aren't will tend to stick out. When you show some researcher on TV, you're asking them to take on the job of TV personality, and not everybody is up to the task. Every oddly dressed post-doc that stutters through an interview will reinforce the idea of the socially inept scientist. Accountants or meat packers are, on the other hand, very rarely asked to do any kind of public appearance. If they are introverted or socially clumsy nobody will notice. It's not that socially inept scientists are more common, but simply that they're more visible.

None of which matters of course. The image of the weird scientist will live on, together with the white coat, test tubes with multicolored liquids and all the other clichés of this profession. Oh well, it could be worse. At least I'm not an accountant:

Sunday, October 3, 2010

Grunting Helps

You know how, in tennis, many players grunt or shout loudly as they hit the ball? People believe it gives the player an advantage. A couple of researchers have tested this and found that yes, it does give an advantage to the player.

Autumn Baseball

OK, so it's baseball, not tennis. I was just lucky to have any ball-hitting related picture at all.

They made a set of videos of a tennis player hitting a ball towards either side of the court. They showed them to research subjects, and asked them to decide as quickly as possible which direction the ball would go. Sometimes they played a brief noise just as the ball was hit on video, sometimes not. The results are clear: the subjects were slower to react and were wrong more often when the noise was played than when it was not. The difference was not large, but in professional sports very small advantages can make a real difference to the game.

Why would the noise make a difference? A common belief is that the noise blocks the sound of the racket hitting the ball. The racket sound would otherwise help the opposing player determine when and where the ball would arrive. Of course, most grunts really aren't loud enough to completely mask the ball-hitting sound, so a related idea is that the grunt diverts attention from the racket sound at the crucial moment.

They also tested the idea that the sound is actually diverting visual attention from the racket and ball. The grunt comes from a different place after all, and sound can certainly grab visual attention (pop a balloon behind somebody to see for yourself). They measured the eye movements of the subjects to see if the noise made any difference. But the eye movements didn't change, with or without the noise, so the sound wasn't grabbing visual attention away from the ball.

Grunts do seem to help tennis players, then, by distracting the opponent. Of course, it's possible grunting could also help the player directly, to help them focus and time their shot. People tend to grunt or scream in many sports, and we don't know if or how that helps them in those cases. The effectiveness of grunting during bathroom visits likewise remains an open question.

Friday, October 1, 2010

Paris III: The Conference

The point of this trip was the SAB conference. As I was mostly working, there wasn't much time for sightseeing. The conference was a total of five days, workshop included, from early morning until night. It was fun, certainly - it's perhaps my favourite conference - but conference rooms are not normally noted for their touristy appeal. But this conference was held at the Museum of Natural History, perhaps the coolest conference venue I've ever had the pleasure to visit. And we got free passes to all the main exhibits.

The Paris Museum of Natural History

This museum seems to explicitly allow cameras. My regret is that I didn't bring the Pentax 67 and a real tripod. Carrying it around for a week would have been a small price to pay for a better chance at scenes like this.

The SAB conference itself was good; it usually is. I attended the active sensing workshop which had a really good talk (and a related talk in the main conference) about how insects use visual flow not just for short-term navigation but also for elevation control. If insects try to keep the ground below moving at a constant speed they can regulate their speed, and start and land simply by changing the flying height, and they will automatically land if the wind grows too strong to fly in. Another good talk was about how weakly electric fish actually decide the location of obstacles based on potential changes along the electrical sense organs (here's their conference paper).

The Mosque Cafe

The coffee breaks were not at the museum, but at the Paris Mosque right next door at a restaurant and cafe. Again, it's a far cry from the usual table set up outside the conference rooms, and apparently cheaper as well.

My favourite talk at the conference was about a slime-mold inspired robot by Andrew Russell (he doesn't seem to have the robot on his website yet). It used active smell - send out a puff of alcohol, then sense the concentration around the robot - to find obstacles, and it also had a simple but ingenious way to create omnidirectional movement without having to deal with complex, expensive omnidirectional wheels. Exactly the kind of creative and slightly oddball research I hope to find at this conference.

There were a couple of fun papers on rat whiskers, how rats use them to sense their environment and how we could use them for robotics. The whiskers are not passive touch sensors; the rat constantly sweeps them about to feel not just the position and range of obstacles but also texture and other features of its environment. And the groups are of course building whisker-equipped robots to test their models in the real world. Makes me want to do the same.

The title Insectomorphic Robot Maneuvering on a Movable Ball says it all, really. If you have an insect-like robot, how can it climb onto a large ball, move about by rotating the ball with its legs, and then get off again? My reaction was, in order: "Heh. Fun." Followed by "Why on earth would you want to do this?" immediately silenced by "I would love to have a robot insect balancing on a ball! An entire robot circus! With steam-powered mechanical elephants!" But yes, there's a serious angle to this: Robots need to adapt to a dynamic world where their actions affect the world in turn, and getting onto and balancing on a large moveable ball is a neat, well-defined test problem. Still: I want my Arachnoid Acrobat Automatons!

My own talk, about our model of the early saccade generation system, was just a little abstract for this conference. We don't use a robot or any kind of real-life input yet, and the model itself is too computationally intensive to be immediately useful in robotics so we got a bit of criticism for that. Our aim is to understand the original biological system at this stage, rather than create an effective synthetic one. We were far from the only abstract paper of course, but it's the papers with tangible results that people really like in this conference. The papers I mention above are all practical in nature.

Here's the whole proceedings if you have institutional access (springer is pretty uptight about access rights). If not, there's plenty of other ways to find the papers of course.

Zamansky Tower

The workshops and the poster sessions were not at the museum, but at the Zamansky Tower in Marie Curie University. At the top floor. The view is quite breathtaking; you can see a shot from there in the first post from Paris.

Every conference gives you stuff. Not just the proceedings, but anything from notebooks to bags to pens to coffee mugs to keyrings... They come from the conference itself, from sponsors and from who-knows-where. We got the usual conference bag with a notebook, a flipbook and bookmark with all conference poster designs (most of them made by Jean Solé and really cool - see previous ones here), proceedings and data on a CD - and The Pen.


It's a pen. It's a laser pointer. It's a 2Gb USB memory. Almost everything a presenter needs.

The Pen is almost everything you need for a conference. There's never a laser pointer around when you need one, or if there is the batteries have just run out. And in case disaster strikes and you lose your laptop - could be dropped, get stolen, taken in customs, have coffee spilled all over it an so on - you need backups of your presentation1 and all your important travel information. With your data on a memory stick you can at least borrow somebody's laptop and give your talk.


The buffet at the poster sessions. Between the food and the view a lot of people had trouble focusing on the posters, and that included some of the poster presenters.

Museum of Natural History


Museum of Natural History

Whale skeleton. I think.

Clos Luce

Clos Luce, Amboise.

The last day of the conference was not in Paris but in Amboise a couple of hours away. Clos Luce is where Leonardo da Vinci spent the last few years of his life, invited by some king or other. Today it's a museum and conference place. Very pleasant. We had a final session and the panel discussion at the mansion, followed by lunch.


Replica helicopter design by da Vinci. Not likely to fly anytime soon. As someone pointed out at the conference, if you want to become known as an inventor it certainly helps to be a world-famous artist first.

Les Caves Duhard

Les Caves Duhard.

We left the mansion in the afternoon for a wine cellar tour and wine tasting event at the nearby Les Caves Duhard. They're a wine wholesaler with a set of limestone tunnels to store wine. The tour is fun, and the wine tasting and dinner/snack was great. Various kinds of wines and plenty of cheeses, sausage, fruits and other stuff to enjoy with it.

Les Caves Duhard

Limestone wine cellars.

#1 A tip: save your Powerpoint or Openoffice file if you want, but also export the presentation as a PDF file. PDF viewers have a "presentation mode" that lets you show the PDF as a presentation. And since you have all graphics and all non-standard fonts and everything embedded in the file itself it is sure to work no matter what kind of computer you end up showing your presentation from. It's no fun to have half your text missing because you used a locale, font or character encoding that's not installed in the particular computer you use.

And if you have a poster, also print it out as a set of A3 or A4-sized tiles and stick in an envelope in your bag. If something happens to your poster you can still tile these on the poster board with thumb tacks. Not as neat as a real poster but much better than showing up empty-handed.